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Zooplankton carcasses are ubiquitous in marine and freshwater systems, implicating the importance of non-predatory mortality, but both are often overlooked in ecological studies compared with predatory mortality. The development of several microscopic methods allows the distinction between live and dead zooplankton in field samples, and the reported percentages of dead zooplankton average 11.6 (minimum) to 59.8 (maximum) in marine environments, and 7.4 (minimum) to 47.6 (maximum) in fresh and inland waters. Common causes of non-predatory mortality among zooplankton include senescence, temperature change, physical and chemical stresses, parasitism and food-related factors. Carcasses resulting from non-predatory mortality may undergo decomposition leading to an increase in microbial production and a shift in microbial composition in the water column. Alternatively, sinking carcasses may contribute significantly to vertical carbon flux especially outside the phytoplankton growth seasons, and become a food source for the benthos. Global climate change is already altering freshwater ecosystems on multiple levels, and likely will have significant positive or negative effects on zooplankton non-predatory mortality. Better spatial and temporal studies of zooplankton carcasses and non-predatory mortality rates will improve our understanding of this important but under-appreciated topic.
Recent reports of increasing iron (Fe) concentrations in freshwaters are of concern, given the fundamental role of Fe in biogeochemical processes. Still, little is known about the frequency and geographical distribution of Fe trends or about the underlying drivers. We analyzed temporal trends of Fe concentrations across 340 water bodies distributed over 10 countries in northern Europe and North America in order to gain a clearer understanding of where, to what extent, and why Fe concentrations are on the rise. We found that Fe concentrations have significantly increased in 28% of sites, and decreased in 4%, with most positive trends located in northern Europe. Regions with rising Fe concentrations tend to coincide with those with organic carbon (OC) increases. Fe and OC increases may not be directly mechanistically linked, but may nevertheless be responding to common regional-scale drivers such as declining sulfur deposition or hydrological changes. A role of hydrological factors was supported by covarying trends in Fe and dissolved silica, as these elements tend to stem from similar soil depths. A positive relationship between Fe increases and conifer cover suggests that changing land use and expanded forestry could have contributed to enhanced Fe export, although increases were also observed in nonforested areas. We conclude that the phenomenon of increasing Fe concentrations is widespread, especially in northern Europe, with potentially significant implications for wider ecosystem biogeochemistry, and for the current browning of freshwaters.
Ecosystems are generally linked via fluxes of nutrients and energy across their boundaries. For example, freshwater ecosystems in temperate regions may receive significant inputs of terrestrially derived carbon via autumnal leaf litter. This terrestrial particulate organic carbon (POC) is hypothesized to subsidize animal production in lakes, but direct evidence is still lacking. We divided two small eutrophic lakes each into two sections and added isotopically distinct maize litter to the treatment sections to simulate increased terrestrial POC inputs via leaf litter in autumn. We quantified the reliance of aquatic consumers on terrestrial resources (allochthony) in the year subsequent to POC additions by applying mixing models of stable isotopes. We also estimated lake-wide carbon (C) balances to calculate the C flow to the production of the major aquatic consumer groups: benthic macroinvertebrates, crustacean zooplankton, and fish. The sum of secondary production of crustaceans and benthic macroinvertebrates supported by terrestrial POC was higher in the treatment sections of both lakes. In contrast, total secondary and tertiary production (supported by both autochthonous and allochthonous C) was higher in the reference than in the treatment sections of both lakes. Average aquatic consumer allochthony per lake section was 27-40%, although terrestrial POC contributed less than about 10% to total organic C supply to the lakes. The production of aquatic consumers incorporated less than 5% of the total organic C supply in both lakes, indicating a low ecological efficiency. We suggest that the consumption of terrestrial POC by aquatic consumers facilitates a strong coupling with the terrestrial environment. However, the high autochthonous production and the large pool of autochthonous detritus in these nutrient-rich lakes make terrestrial POC quantitatively unimportant for the C flows within food webs.
The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 x 10(9) bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.
The ecological relevance of fungi in freshwater ecosystems is becoming increasingly evident, particularly in processing the extensive amounts of polymeric organic carbon such as cellulose, chitin, and humic substances (HS). We isolated several fungal strains from oligo-mesotrophic Lake Stechlin, Brandenburg, Germany, and analyzed their ability to degrade polymeric-like substrates. Using liquid chromatography-organic carbon detection, we determined the byproducts of HS transformation by the freshwater fungus Cladosporium sp. KR14. We demonstrate the ability of this fungus to degrade and simultaneously synthesize HS, and that transformation processes were intensified when iron, as indicator of the occurrence of Fenton reactions, was present in the medium. Furthermore, we showed that structural complexity of the HS produced changed with the availability of other polymeric substances in the medium. Our study highlights the contribution of freshwater Ascomycetes to the transformation of complex organic compounds. As such, it has important implications for understanding the ecological contribution of fungi to aquatic food webs and related biogeochemical cycles.
In ecology, biodiversity-ecosystem functioning (BEE) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEE of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEE using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEE studies are often inadequate to unravel BEE relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEE relationships and thus generating systematic principles in microbial ecology and more generally ecology.
Sediment resuspension represents a key process in all natural aquatic systems, owing to its role in nutrient cycling and transport of potential contaminants. Although suspended solids are generally accepted as an important quality parameter, current monitoring programs cover quantitative aspects only. Established methodologies do not provide information on origin, fate, and risks associated with uncontrolled inputs of solids in waters. Here we discuss the analytical approaches to assess the occurrence and ecological relevance of resuspended particulate matter in freshwaters, with a focus on the dynamics of associated contaminants and microorganisms. Triggered by the identification of specific physical-chemical traits and community structure of particle-associated microorganisms, recent findings suggest that a quantitative determination of microorganisms can be reasonably used to trace the origin of particulate matter by means of nucleic acid-based assays in different aquatic systems.
Algal tests have developed into routine tools for testing toxicity of pollutants in aquatic environments. Meanwhile, in addition to algal growth rates, an increasing number of fluorescence based methods are used for rapid and sensitive toxicity measures. The present study stresses the suitability of delayed fluorescence (DF) as a promising parameter for biotests. DF is based on the recombination fluorescence at the reaction centre of photosystem II, which is emitted only by photosynthetically active cells. We analyzed the effects of three chemicals (3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), 3,5 Dichlorophenol (3,5 DCP) and copper) on the shape of the DF decay kinetics for potential use in phytoplankton toxicity tests. The short incubation tests were done with four phytoplankton species, with special emphasis on the cyanobacterium Microcystis aeruginosa. All species exhibited a high sensitivity to DCMU, but cyanobacteria were more affected by copper and less by 3,5 DCP than the tested green algae. Analyses of changes in the DF decay curve in response to the added chemicals indicated the feasibility of the DF decay approach as a rapid and sensitive testing tool.
Global change has complex eco-evolutionary consequences for organisms and ecosystems, but related concepts (e.g., novel ecosystems) do not cover their full range. Here we propose an umbrella concept of "ecological novelty" comprising (1) a site-specific and (2) an organism-centered, eco-evolutionary perspective. Under this umbrella, complementary options for studying and communicating effects of global change on organisms, ecosystems, and landscapes can be included in a toolbox. This allows researchers to address ecological novelty from different perspectives, e.g., by defining it based on (a) categorical or continuous measures, (b) reference conditions related to sites or organisms, and (c) types of human activities. We suggest striving for a descriptive, non-normative usage of the term "ecological novelty" in science. Normative evaluations and decisions about conservation policies or management are important, but require additional societal processes and engagement with multiple stakeholders.
Extreme weather events can pervasively influence ecosystems. Observations in lakes indicate that severe storms in particular can have pronounced ecosystem-scale consequences, but the underlying mechanisms have not been rigorously assessed in experiments. One major effect of storms on lakes is the redistribution of mineral resources and plankton communities as a result of abrupt thermocline deepening. We aimed at elucidating the importance of this effect by mimicking in replicated large enclosures (each 9 m in diameter, ca. 20 m deep, ca. 1300 m 3 in volume) a mixing event caused by a severe natural storm that was previously observed in a deep clear-water lake. Metabolic rates were derived from diel changes in vertical profiles of dissolved oxygen concentrations using a Bayesian modelling approach, based on high-frequency measurements. Experimental thermocline deepening stimulated daily gross primary production (GPP) in surface waters by an average of 63% for > 4 weeks even though thermal stratification re-established within 5 days. Ecosystem respiration (ER) was tightly coupled to GPP, exceeding that in control enclosures by 53% over the same period. As GPP responded more strongly than ER, net ecosystem productivity (NEP) of the entire water column was also increased. These protracted increases in ecosystem metabolism and autotrophy were driven by a proliferation of inedible filamentous cyanobacteria released from light and nutrient limitation after they were entrained from below the thermocline into the surface water. Thus, thermocline deepening by a single severe storm can induce prolonged responses of lake ecosystem metabolism independent of other storm-induced effects, such as inputs of terrestrial materials by increased catchment run-off. This highlights that future shifts in frequency, severity or timing of storms are an important component of climate change, whose impacts on lake thermal structure will superimpose upon climate trends to influence algal dynamics and organic matter cycling in clear-water lakes. Keywords: climate variability, ecosystem productivity, extreme events, gross primary production, mesocosm, respiration stratified lakes
Winter is an important season for many limnological processes, which can range from biogeochemical transformations to ecological interactions. Interest in the structure and function of lake ecosystems under ice is on the rise. Although limnologists working at polar latitudes have a long history of winter work, the required knowledge to successfully sample under winter conditions is not widely available and relatively few limnologists receive formal training. In particular, the deployment and operation of equipment in below 0 degrees C temperatures pose considerable logistical and methodological challenges, as do the safety risks of sampling during the ice-covered period. Here, we consolidate information on winter lake sampling and describe effective methods to measure physical, chemical, and biological variables in and under ice. We describe variation in snow and ice conditions and discuss implications for sampling logistics and safety. We outline commonly encountered methodological challenges and make recommendations for best practices to maximize safety and efficiency when sampling through ice or deploying instruments in ice-covered lakes. Application of such practices over a broad range of ice-covered lakes will contribute to a better understanding of the factors that regulate lakes during winter and how winter conditions affect the subsequent ice-free period.
Compared to the well-studied open water of the "growing" season, under-ice conditions in lakes are characterized by low and rather constant temperature, slow water movements, limited light availability, and reduced exchange with the surrounding landscape. These conditions interact with ice-cover duration to shape microbial processes in temperate lakes and ultimately influence the phenology of community and ecosystem processes. We review the current knowledge on microorganisms in seasonally frozen lakes. Specifically, we highlight how under-ice conditions alter lake physics and the ways that this can affect the distribution and metabolism of auto-and heterotrophic microorganisms. We identify functional traits that we hypothesize are important for understanding under-ice dynamics and discuss how these traits influence species interactions. As ice coverage duration has already been seen to reduce as air temperatures have warmed, the dynamics of the under-ice microbiome are important for understanding and predicting the dynamics and functioning of seasonally frozen lakes in the near future.
The use of high-frequency sensors on profiling buoys to investigate physical, chemical, and biological processes in lakes is
increasing rapidly. Profiling buoys with automated winches and sensors that collect high-frequency chlorophyll fluorescence
(ChlF) profiles in 11 lakes in the Global Lake Ecological Observatory Network (GLEON) allowed the study of the vertical
and temporal distribution of ChlF, including the formation of subsurface chlorophyll maxima (SSCM). The effectiveness of 3
methods for sampling phytoplankton distributions in lakes, including (1) manual profiles, (2) single-depth buoys, and (3)
profiling buoys were assessed. High-frequency ChlF surface data and profiles were compared to predictions from the
Plankton Ecology Group (PEG) model. The depth-integrated ChlF dynamics measured by the profiling buoy data revealed a
greater complexity that neither conventional sampling nor the generalized PEG model captured. Conventional sampling
techniques would have missed SSCM in 7 of 11 study lakes. Although surface-only ChlF data underestimated average water
column ChlF, at times by nearly 2-fold in 4 of the lakes, overall there was a remarkable similarity between surface and mean
water column data. Contrary to the PEG model’s proposed negligible role for physical control of phytoplankton during the
growing season, thermal structure and light availability were closely associated with ChlF seasonal depth distribution. Thus,
an extension of the PEG model is proposed, with a new conceptual framework that explicitly includes physical metrics to
better predict SSCM formation in lakes and highlight when profiling buoys are especially informative.
Antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. However, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic-resistant strains. While it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic resistance is also observed in natural bacteria of remote places unlikely to be impacted by human intervention. Both antibiotic biosynthetic genes and resistance-conferring genes have been known to evolve billions of years ago, long before clinical use of antibiotics. Hence it appears that antibiotics and antibiotics resistance determinants have some other roles in nature, which often elude our attention because of overemphasis on the therapeutic importance of antibiotics and the crisis imposed by the antibiotic resistance in pathogens. In the natural milieu, antibiotics are often found to be present in sub-inhibitory concentrations acting as signaling molecules supporting the process of quorum sensing and biofilm formation. They also play an important role in the production of virulence factors and influence host-parasite interactions (e.g., phagocytosis, adherence to the target cell, and so on). The evolutionary and ecological aspects of antibiotics and antibiotic resistance in the naturally occurring microbial community are little understood. Therefore, the actual role of antibiotics in nature warrants in-depth investigations. Studies on such an intriguing behavior of the microorganisms promise insight into the intricacies of the microbial physiology and are likely to provide some lead in controlling the emergence and subsequent dissemination of antibiotic resistance. This article highlights some of the recent findings on the role of antibiotics and the genes that confer resistance to antibiotics in nature.
Landscapes can be viewed as spatially heterogeneous areas encompassing terrestrial and aquatic domains. To date, most landscape carbon (C) fluxes have been estimated by accounting for terrestrial ecosystems, while aquatic ecosystems have been largely neglected. However, a robust assessment of C fluxes on the landscape scale requires the estimation of fluxes within and between both landscape components. Here, we compiled data from the literature on C fluxes across the air–water interface from various landscape components. We simulated C emissions and uptake for five different scenarios which represent a gradient of increasing spatial heterogeneity within a temperate young moraine landscape: (I) a homogeneous landscape with only cropland and large lakes; (II) separation of the terrestrial domain into cropland and forest; (III) further separation into cropland, forest, and grassland; (IV) additional division of the aquatic area into large lakes and peatlands; and (V) further separation of the aquatic area into large lakes, peatlands, running waters, and small water bodies These simulations suggest that C fluxes at the landscape scale might depend on spatial heterogeneity and landscape diversity, among other factors. When we consider spatial heterogeneity and diversity alone, small inland waters appear to play a pivotal and previously underestimated role in landscape greenhouse gas emissions that may be regarded as C hot spots. Approaches focusing on the landscape scale will also enable improved projections of ecosystems’ responses to perturbations, e.g., due to global change and anthropogenic activities, and evaluations of the specific role individual landscape components play in regional C fluxes. WIREs Water 2016, 3:601–617. doi: 10.1002/wat2.1147
Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280 degrees longitudinal and 90 degrees latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.
Microplastics (MP) constitute a widespread contaminant all over the globe. Rivers and wastewater treatment plants (WWTP) transport annually several million tons of MP into freshwaters, estuaries and oceans, where they provide increasing artificial surfaces for microbial colonization. As knowledge on MP-attached communities is insufficient for brackish ecosystems, we conducted exposure experiments in the coastal Baltic Sea, an in-flowing river and a WWTP within the drainage basin. While reporting on prokaryotic and fungal communities from the same set-up previously, we focus here on the entire eukaryotic communities. Using high-throughput 18S rRNA gene sequencing, we analyzed the eukaryotes colonizing on two types of MP, polyethylene and polystyrene, and compared them to the ones in the surrounding water and on a natural surface (wood). More than 500 different taxa across almost all kingdoms of the eukaryotic tree of life were identified on MP, dominated by Alveolata, Metazoa, and Chloroplastida. The eukaryotic community composition on MP was significantly distinct from wood and the surrounding water, with overall lower diversity and the potentially harmful dinoflagellate Pfiesteria being enriched on MP. Co-occurrence networks, which include prokaryotic and eukaryotic taxa, hint at possibilities for dynamic microbial interactions on MP. This first report on total eukaryotic communities on MP in brackish environments highlights the complexity of MP-associated biofilms, potentially leading to altered microbial activities and hence changes in ecosystem functions.
Microplastics (MP) constitute a widespread contaminant all over the globe. Rivers and wastewater treatment plants (WWTP) transport annually several million tons of MP into freshwaters, estuaries and oceans, where they provide increasing artificial surfaces for microbial colonization. As knowledge on MP-attached communities is insufficient for brackish ecosystems, we conducted exposure experiments in the coastal Baltic Sea, an in-flowing river and a WWTP within the drainage basin. While reporting on prokaryotic and fungal communities from the same set-up previously, we focus here on the entire eukaryotic communities. Using high-throughput 18S rRNA gene sequencing, we analyzed the eukaryotes colonizing on two types of MP, polyethylene and polystyrene, and compared them to the ones in the surrounding water and on a natural surface (wood). More than 500 different taxa across almost all kingdoms of the eukaryotic tree of life were identified on MP, dominated by Alveolata, Metazoa, and Chloroplastida. The eukaryotic community composition on MP was significantly distinct from wood and the surrounding water, with overall lower diversity and the potentially harmful dinoflagellate Pfiesteria being enriched on MP. Co-occurrence networks, which include prokaryotic and eukaryotic taxa, hint at possibilities for dynamic microbial interactions on MP. This first report on total eukaryotic communities on MP in brackish environments highlights the complexity of MP-associated biofilms, potentially leading to altered microbial activities and hence changes in ecosystem functions.
Studies on the ecological role of fungi and, to a lesser extent, oomycetes, are receiving increasing attention, mainly due to their participation in the cycling of organic matter in aquatic ecosystems. To unravel their importance in humification processes, we isolated several strains of fungi and oomycetes from Anzali lagoon, Iran. We then performed taxonomic characterization by morphological and molecular methods, analyzed the ability to degrade several polymeric substrates, performed metabolic fingerprinting with Ecoplates, and determined the degradation of humic substances (HS) using liquid chromatography-organic carbon detection. Our analyses highlighted the capacity of aquatic fungi to better degrade a plethora of organic molecules, including complex polymers. Specifically, we were able to demonstrate not only the utilization of these complex polymers, but also the role of fungi in the production of HS. In contrast, oomycetes, despite some morphological and physiological similarities with aquatic fungi, exhibited a propensity toward opportunism, quickly benefitting from the availability of small organic molecules, while exhibiting sensitivity toward more complex polymers. Despite their contrasting roles, our study highlights the importance of both oomycetes and fungi in aquatic organic matter transformation and cycling with potential implications for the global carbon cycle.
Hypolimnetic oxygen demand in lakes is often assumed to be driven mainly by sediment microbial processes, while the role of Chaoborus larvae, which are prevalent in eutrophic lakes with hypoxic to anoxic bottoms, has been overlooked. We experimentally measured the respiration rates of C flavicans at different temperatures yielding a Q(10) of 1.44-1.71 and a respiratory quotient of 0.84-0.98. Applying the experimental data in a system analytical approach, we showed that migrating Chaoborus larvae can significantly add to the water column and sediment oxygen demand, and contribute to the observed linear relationship between water column respiration and depth. The estimated phosphorus excretion by Chaoborus in sediment is comparable in magnitude to the required phosphorus loading for eutrophication. Migrating Chaoborus larvae thereby essentially trap nutrients between the water column and the sediment, and this continuous internal loading of nutrients would delay lake remediation even when external inputs are stopped. (C) 2017 Elsevier Ltd. All rights reserved.
Marine sponges host highly diverse but specific bacterial communities that provide essential functions for the sponge holobiont, including antimicrobial defense. Here, we characterized the bacterial microbiome of the marine sponge Haliclona cnidata that has been in culture in an artificial marine aquarium system. We tested the hypotheses (1) that the long-term aquarium cultured sponge H. cnidata is tightly associated with a typical sponge bacterial microbiota and (2) that the symbiotic Bacteria sustain bioactivity under harmful environmental conditions to facilitate holobiont survival by preventing pathogen invasion. Microscopic and phylogenetic analyses of the bacterial microbiota revealed that H. cnidata represents a high microbial abundance (HMA) sponge with a temporally stable bacterial community that significantly shifts with changing aquarium conditions. A 4-week incubation experiment was performed in small closed aquarium systems with antibiotic and/or light exclusion treatments to reduce the total bacterial and photosynthetically active sponge-associated microbiota to a treatment-specific resilient community. While the holobiont was severely affected by the experimental treatment (i.e., bleaching of the sponge, reduced bacterial abundance, shifted bacterial community composition), the biological defense and bacterial community interactions (i.e., quorum sensing activity) remained intact. 16S rRNA gene amplicon sequencing revealed a resilient community of 105 bacterial taxa, which remained in the treated sponges. These 105 taxa accounted for a relative abundance of 72-83% of the bacterial sponge microbiota of non-treated sponge fragments that have been cultured under the same conditions. We conclude that a sponge-specific resilient community stays biologically active under harmful environmental conditions, facilitating the resilience of the holobiont. In H. cnidata, bacteria are located in bacteriocytes, which may have contributed to the observed phenomenon.
1. Global pressures on freshwater ecosystems are high and rising. Viewed primarily as a resource for humans, current practices of water use have led to catastrophic declines in freshwater species and the degradation of freshwater ecosystems, including their genetic and functional diversity. Approximately three-quarters of the world's inland wetlands have been lost, one-third of the 28 000 freshwater species assessed for the International Union for Conservation of Nature (IUCN) Red List are threatened with extinction, and freshwater vertebrate populations are undergoing declines that are more rapid than those of terrestrial and marine species. This global loss continues unchecked, despite the importance of freshwater ecosystems as a source of clean water, food, livelihoods, recreation, and inspiration.
2. The causes of these declines include hydrological alterations, habitat degradation and loss, overexploitation, invasive species, pollution, and the multiple impacts of climate change. Although there are policy initiatives that aim to protect freshwater life, these are rarely implemented with sufficient conviction and enforcement. Policies that focus on the development and management of fresh waters as a resource for people almost universally neglect the biodiversity that they contain.
3. Here we introduce the Alliance for Freshwater Life, a global initiative, uniting specialists in research, data synthesis, conservation, education and outreach, and policymaking. This expert network aims to provide the critical mass required for the effective representation of freshwater biodiversity at policy meetings, to develop solutions balancing the needs of development and conservation, and to better convey the important role freshwater ecosystems play in human well-being. Through this united effort we hope to reverse this tide of loss and decline in freshwater biodiversity. We introduce several short- and medium-term actions as examples for making positive change, and invite individuals, organizations, authorities, and governments to join the Alliance for Freshwater Life.
Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.
Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.
Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.
Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.
Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for >50% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acIActinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed.
Zooplankton support distinct bacterial communities in high concentrations relative to the surrounding water, but little is known about how the compositions and functionalities of these bacterial communities change through time in relation to environmental conditions. We conducted a year-long field study of bacterial communities associated with common zooplankton groups as well as free-living bacterial communities in the York River, a tributary of Chesapeake Bay. Bacterial community genetic fingerprints and their carbon substrate usage were examined by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA and by Biolog EcoPlates, respectively. Zooplankton-associated communities were genetically distinct from free-living bacterial communities but utilized a similar array of carbon substrates. On average, bacteria associated with different zooplankton groups were genetically more similar to each other within each month (65.4% similarity) than to bacterial communities of the same zooplankton group from different months (28 to 30% similarity), which suggests the importance of ambient environmental conditions in shaping resident zooplankton-associated bacterial communities. Monthly changes in carbon substrate utilization were less variable for zooplankton-associated bacteria than for free-living bacteria, suggesting that the zooplankton microhabitat is more stable than the surrounding water and supports specific bacterial groups in the otherwise unfavorable conditions in the water column.
We investigated changes in quality and quantity of extracellular and biomass-derived organic matter (OM) from three axenic algae (genera Rhodomonas, Chlamydomonas, Coelastrum) during growth of Limnohabitans parvus, Limnohabitans planktonicus and Polynucleobacter acidiphobus representing important clusters of freshwater planktonic Betaproteobacteria. Total extracellular and biomass-derived OM concentrations from each alga were approximately 20 mg l(-1) and 1 mg l(-1) respectively, from which up to 9% could be identified as free carbohydrates, polyamines, or free and combined amino acids. Carbohydrates represented 54%-61% of identified compounds of the extracellular OM from each alga. In biomass-derived OM of Rhodomonas and Chlamydomonas 71%-77% were amino acids and polyamines, while in that of Coelastrum 85% were carbohydrates. All bacteria grew on alga-derived OM of Coelastrum, whereas only Limnohabitans strains grew on OM from Rhodomonas and Chlamydomonas. Bacteria consumed 24%-76% and 38%-82% of all identified extracellular and biomass-derived OM compounds respectively, and their consumption was proportional to the concentration of each OM compound in the different treatments. The bacterial biomass yield was higher than the total identifiable OM consumption indicating that bacteria also utilized other unidentified alga-derived OM compounds. Bacteria, however, also produced specific OM compounds suggesting enzymatic polymer degradation or de novo exudation.
Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico-to the microscale (0.2 to 200 lm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso-and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size-fractions, distinct prokaryotic communities were detected in each size-fraction, and whereas bacteria were more diverse in the larger size-fractions, archaea were more diverse in the smaller size-fractions. Comparison of prokaryotic community composition among particle size-fractions showed that most, but not all, taxonomic groups have a preference for a certain size-fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size-fraction preferences, may explain why this trend is not conserved in all taxa.
Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.
Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment
(2017)
Background
Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments.
Methods
We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1–4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota.
Results
Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5–14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions.
Conclusions
By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper “replacement horizon” is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower “depauperate horizon” is characterized by low taxonomic richness, more stable “low-energy” conditions, and a dominance of enigmatic Archaea.
Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment
(2017)
Background: Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. Methods: We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to Cs-137 dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Results: Community beta-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. Conclusions: By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.
Plans are currently being drafted for the next decade of action on biodiversity-both the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD) and Biodiversity Strategy of the European Union (EU). Freshwater biodiversity is disproportionately threatened and underprioritized relative to the marine and terrestrial biota, despite supporting a richness of species and ecosystems with their own intrinsic value and providing multiple essential ecosystem services. Future policies and strategies must have a greater focus on the unique ecology of freshwater life and its multiple threats, and now is a critical time to reflect on how this may be achieved. We identify priority topics including environmental flows, water quality, invasive species, integrated water resources management, strategic conservation planning, and emerging technologies for freshwater ecosystem monitoring. We synthesize these topics with decades of first-hand experience and recent literature into 14 special recommendations for global freshwater biodiversity conservation based on the successes and setbacks of European policy, management, and research. Applying and following these recommendations will inform and enhance the ability of global and European post-2020 biodiversity agreements to halt and reverse the rapid global decline of freshwater biodiversity.
Retrieval of water constituents from hyperspectral in-situ measurements under variable cloud cover
(2018)
Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring.
Retrieval of water constituents from hyperspectral in-situ measurements under variable cloud cover
(2018)
Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring.
Heterocystous cyanobacteria of the genus Nodularia form extensive blooms in the Baltic Sea and contribute substantially to the total annual primary production. Moreover, they dispense a large fraction of new nitrogen to the ecosystem when inorganic nitrogen concentration in summer is low. Thus, it is of ecological importance to know how Nodularia will react to future environmental changes, in particular to increasing carbon dioxide (CO2) concentrations and what consequences there might arise for cycling of organic matter in the Baltic Sea. Here, we determined carbon (C) and dinitrogen (N-2) fixation rates, growth, elemental stoichiometry of particulate organic matter and nitrogen turnover in batch cultures of the heterocystous cyanobacterium Nodularia spumigena under low (median 315 mu atm), mid (median 353 mu atm), and high (median 548 mu atm) CO2 concentrations. Our results demonstrate an overall stimulating effect of rising pCO(2) on C and N-2 fixation, as well as on cell growth. An increase in pCO(2) during incubation days 0 to 9 resulted in an elevation in growth rate by 84 +/- 38% (low vs. high pCO(2)) and 40 +/- 25% (mid vs. high pCO(2)), as well as in N-2 fixation by 93 +/- 35% and 38 +/- 1%, respectively. C uptake rates showed high standard deviations within treatments and in between sampling days. Nevertheless, C fixation in the high pCO(2) treatment was elevated compared to the other two treatments by 97% (high vs. low) and 44% (high vs. mid) at day 0 and day 3, but this effect diminished afterwards. Additionally, elevation in carbon to nitrogen and nitrogen to phosphorus ratios of the particulate biomass formed (POC : POP and PON : POP) was observed at high pCO(2). Our findings suggest that rising pCO(2) stimulates the growth of heterocystous diazotrophic cyanobacteria, in a similar way as reported for the non-heterocystous diazotroph Trichodesmium. Implications for biogeochemical cycling and food web dynamics, as well as ecological and socio-economical aspects in the Baltic Sea are discussed.
Reduction-oxidation cycles of organic matter increase bacterial activity in the pelagic oxycline
(2017)
Dissolved organic matter (DOM) in aquatic ecosystems contains redox-active moieties, which are prone to oxidation and reduction reactions. Oxidized moieties feature reduction potentials E-h, so that the moieties may be used as terminal electron acceptors (TEAs) in microbial respiration with a thermodynamic energy yield between nitrate and sulfate reduction. Here, we study the response of pelagic freshwater bacteria to exposure to native DOM with varying availabilities of oxidized moieties and hence redox state. Our results show that the prevalence of oxidized DOM favors microbial production and growth in anoxic waters. Reduced DOM in stratified lakes may be oxidized when fluctuations of the oxycline expose DOM in previously anoxic water to epilimnetic oxygen. The resulting oxidized DOM may be rapidly used as TEAs in microbial respiration during subsequent periods of anoxia. We further investigate if the prevalence of these organic electron sinks in anaerobic incubations can induce changes in the microbial community. Our results reveal that DOM traversing transient redox interfaces selects for species that profit from such spatially confined and cyclically restored TEA reservoirs.
Influenza A viruses (IAV) are zoonotic pathogens relevant to human, domestic animal and wildlife health. Many avian IAVs are transmitted among waterfowl via a faecal-oral-route. Therefore, environmental water where waterfowl congregate may play an important role in the ecology and epidemiology of avian IAV. Water and sediment may sustain and transmit virus among individuals or species. It is unclear at what concentrations waterborne viruses are infectious or remain detectable. To address this, we performed lake water and sediment dilution experiments with varying concentrations or infectious doses of four IAV strains from seal, turkey, duck and gull. To test for infectivity of the IAV strains in a concentration dependent manner, we applied cultivation to specific pathogen free (SPF) embryonated chicken eggs and Madin-Darby Canine Kidney (MDCK) cells. IAV recovery was more effective from embryonated chicken eggs than MDCK cells for freshwater lake dilutions, whereas, MDCK cells were more effective for viral recovery from sediment samples. Low infectious dose (1 PFU/200 mu L) was sufficient in most cases to detect and recover IAV from lake water dilutions. Sediment required higher initial infectious doses (>= 100 PFU/200 mu L).
Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics
(2018)
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics
(2018)
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.
Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.
Latest data on the hydrophysical and biological state of the residual basins of the Aral Sea are presented and compared. Direct, quasi-simultaneous observations were carried out in the central part of the Western Large Aral Sea, the northern extremity of the Large Aral known as Chernyshev Bay, Lake Tshchebas, and the Small Aral Sea in October 2014. The Large Aral Sea and Lake Tshchebas transformed into hyperhaline water bodies with highly special taxocene structure. The Small Aral Sea was a relatively diverse brackish ecosystem, which was rather similar to the pre-desiccation environment. The Small Aral Sea and Lake Tshchebas exhibited a fully-mixed vertical structure, whereas the Western Large Aral Sea was strongly stratified. Our data show that during desiccation, different parts of the Aral Sea experienced different environmental conditions, resulting in qualitative and quantitative differences in the physical and biological regimes among the different residual basins.
Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems.
Diurnally-migrating Chaoborus spp. reach populations of up to 130,000 individuals m−2 in lakes up to 70 meters deep on all continents except Antarctica. Linked to eutrophication, migrating Chaoborus spp. dwell in the anoxic sediment during daytime and feed in the oxic surface layer at night. Our experiments show that by burrowing into the sediment, Chaoborus spp. utilize the high dissolved gas partial pressure of sediment methane to inflate their tracheal sacs. This mechanism provides a significant energetic advantage that allows the larvae to migrate via passive buoyancy rather than more energy-costly swimming. The Chaoborus spp. larvae, in addition to potentially releasing sediment methane bubbles twice a day by entering and leaving the sediment, also transport porewater methane within their gas vesicles into the water column, resulting in a flux of 0.01–2 mol m−2 yr−1 depending on population density and water depth. Chaoborus spp. emerging annually as flies also result in 0.1–6 mol m−2 yr−1 of carbon export from the system. Finding the tipping point in lake eutrophication enabling this methane-powered migration mechanism is crucial for ultimately reconstructing the geographical expansion of Chaoborus spp., and the corresponding shifts in the lake’s biogeochemistry, carbon cycling and food web structure.
Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean.
In aquatic systems, natural organic matter (NOM) and in particular humic substances effectively absorb the ultraviolet (UV)/visible light spectrum of solar radiation and act as a photoprotective filter for organisms. Simultaneously, UV contributes to the generation of potentially harmful reactive oxygen species (ROS). Dose-response experiments were conducted on cyanobacteria and green algae with hydrogen peroxide (H2O2) as a long-lived representative of ROS. Delayed fluorescence (DF) decay kinetics was used as a non-invasive tool to follow changes of phytoplankton activity in real time. In order to investigate phototoxicity and photoprotection by NOM on phytoplankton, we exposed algae to UV-pre-irradiated NOM and direct UV excitation. Cyanobacteria responded to H2O2 concentrations as low as 10(-7) M, while green algae were 2 orders of magnitude less sensitive. UV irradiation of medium with NOM generated H2O2 concentrations of 1.5 x 10(-7) to 3.6 x 10(-7) M. When exposed to these concentrations, only the DF of cyanobacteria led to a measurable effect while that of green algae did not change. The addition of NOM protected all phytoplankton from direct UV irradiation, but cyanobacteria benefitted less. From this we conclude that UV-irradiated water enriched with NOM can adversely affect the physiology of cyanobacteria, but not of green algae, which might control phytoplankton composition and species-specific activities.
The vertical distribution of chlorophyll in stratified lakes and reservoirs frequently exhibits a maximum peak deep in the water column, referred to as the deep chlorophyll maximum (DCM). DCMs are ecologically important hot spots of primary production and nutrient cycling, and their location can determine vertical habitat gradients for primary consumers. Consequently, the drivers of DCM structure regulate many characteristics of aquatic food webs and biogeochemistry. Previous studies have identified light and thermal stratification as important drivers of summer DCM depth, but their relative importance across a broad range of lakes is not well resolved. We analyzed profiles of chlorophyll fluorescence, temperature, and light during summer stratification from 100 lakes in the Global Lake Ecological Observatory Network (GLEON) and quantified two characteristics of DCM structure: depth and thickness. While DCMs do form in oligotrophic lakes, we found that they can also form in eutrophic to dystrophic lakes. Using a random forest algorithm, we assessed the relative importance of variables associated with light attenuation vs. thermal stratification for predicting DCM structure in lakes that spanned broad gradients of morphometry and transparency. Our analyses revealed that light attenuation was a more important predictor of DCM depth than thermal stratification and that DCMs deepen with increasing lake clarity. DCM thickness was best predicted by lake size with larger lakes having thicker DCMs. Additionally, our analysis demonstrates that the relative importance of light and thermal stratification on DCM structure is not uniform across a diversity of lake types.
Many studies on bacterial community composition (BCC) do not distinguish between particle associated (PA) and free-living (FL) bacteria or neglect the PA fraction by pre-filtration removing most particles. Although temporal and spatial gradients in environmental variables are known to shape BCC, it remains unclear how and to what extent PA and FL bacterial diversity responds to such environmental changes. To elucidate the BCC of both bacterial fractions related to different environmental settings, we studied surface samples of three Baltic Sea stations (marine, mesohaline, and oligohaline) in two different seasons (summer and fall/winter). Amplicon sequencing of the 16S rRNA gene revealed significant differences in BCC of both bacterial fractions among stations and seasons, with a particularly high number of PA operational taxonomic units (OTUs at genus-level) at the marine station in both seasons. "Shannon and Simpson indices" showed a higher diversity of PA than FL bacteria at the marine station in both seasons and at the oligohaline station in fall/winter. In general, a high fraction of bacterial OTUs was found exclusively in the PA fraction (52% of total OTUs). These findings indicate that PA bacteria significantly contribute to overall bacterial richness and that they differ from FL bacteria. Therefore, to gain a deeper understanding on diversity and dynamics of aquatic bacteria, PA and FL bacteria should be generally studied independently.
Many studies on bacterial community composition (BCC) do not distinguish between particle associated (PA) and free-living (FL) bacteria or neglect the PA fraction by pre-filtration removing most particles. Although temporal and spatial gradients in environmental variables are known to shape BCC, it remains unclear how and to what extent PA and FL bacterial diversity responds to such environmental changes. To elucidate the BCC of both bacterial fractions related to different environmental settings, we studied surface samples of three Baltic Sea stations (marine, mesohaline, and oligohaline) in two different seasons (summer and fall/winter). Amplicon sequencing of the 16S rRNA gene revealed significant differences in BCC of both bacterial fractions among stations and seasons, with a particularly high number of PA operational taxonomic units (OTUs at genus-level) at the marine station in both seasons. "Shannon and Simpson indices" showed a higher diversity of PA than FL bacteria at the marine station in both seasons and at the oligohaline station in fall/winter. In general, a high fraction of bacterial OTUs was found exclusively in the PA fraction (52% of total OTUs). These findings indicate that PA bacteria significantly contribute to overall bacterial richness and that they differ from FL bacteria. Therefore, to gain a deeper understanding on diversity and dynamics of aquatic bacteria, PA and FL bacteria should be generally studied independently.
The widely reported paradox of methane oversaturation in oxygenated water challenges the prevailing paradigm that microbial methanogenesis only occurs under anoxic conditions. Using a combination of field sampling, incubation experiments, and modeling, we show that the recurring mid-water methane peak in Lake Stechlin, northeast Germany, was not dependent on methane input from the littoral zone or bottom sediment or on the presence of known micro-anoxic zones. The methane peak repeatedly overlapped with oxygen oversaturation in the seasonal thermocline. Incubation experiments and isotope analysis indicated active methane production, which was likely linked to photosynthesis and/or nitrogen fixation within the oxygenated water, whereas lessening of methane oxidation by light allowed accumulation of methane in the oxygen-rich upper layer. Estimated methane efflux from the surface water was up to 5 mmol m(-2) d(-1). Mid-water methane oversaturation was also observed in nine other lakes that collectively showed a strongly negative gradient of methane concentration within 0-20% dissolved oxygen (DO) in the bottom water, and a positive gradient within >= 20% DO in the upper water column. Further investigation into the responsible organisms and biochemical pathways will help improve our understanding of the global methane cycle.
Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.
Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.
The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3–4 particles of identical source and age and further evaluated the consequences of averaging 10–1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as “the bottle-effect.” In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn’t change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems.
Benthic microbial communities (BMCs) play important roles in the carbon cycle of lakes, and benthic littoral zones in particular have been previously highlighted as biogeochemical hotspots. Dissolved organic matter (DOM) presents the major carbon pool in lakes, and although the effect of DOM composition on the pelagic microbial community composition is widely accepted, little is known about its effect on BMCs, particularly aquatic fungi. Therefore, we investigated the composition of benthic littoral microbial communities in twenty highly diverse lakes in northeast Germany. DOM quality was analyzed via size exclusion chromatography (SEC), fluorescence parallel factor analyses (PRAFACs) and UV-Vis spectroscopy. We determined the BMC composition and biomass using phospholipid-derived fatty acids (PLFA) and extended the interpretation to the analysis of fungi by applying a Bayesian mixed model. We present evidence that the quality of DOM structures the BMCs, which are dominated by heterotrophic bacteria and show low fungal biomass. The fungal biomass increases when the DOM pool is processed by microorganisms of allochthonous origin, whereas the opposite is true for bacteria.
The oceans absorb about a quarter of the annually produced anthropogenic atmospheric carbon dioxide (CO2), resulting in a decrease in surface water pH, a process termed ocean acidification (OA). Surprisingly little is known about how OA affects the physiology of heterotrophic bacteria or the coupling of heterotrophic bacteria to phytoplankton when nutrients are limited. Previous experiments were, for the most part, undertaken during productive phases or following nutrient additions designed to stimulate algal blooms. Therefore, we performed an in situ large-volume mesocosm (similar to 55 m(3)) experiment in the Baltic Sea by simulating different fugacities of CO2 (fCO(2)) extending from present to future conditions. The study was conducted in July-August after the nominal spring bloom, in order to maintain low-nutrient conditions throughout the experiment. This resulted in phytoplankton communities dominated by small-sized functional groups (picophytoplankton). There was no consistent fCO(2)-induced effect on bacterial protein production (BPP), cell-specific BPP (csBPP) or biovolumes (BVs) of either free-living (FL) or particle-associated (PA) heterotrophic bacteria, when considered as individual components (univariate analyses). Permutational Multivariate Analysis of Variance (PERMANOVA) revealed a significant effect of the fCO(2) treatment on entire assemblages of dissolved and particulate nutrients, metabolic parameters and the bacteria-phytoplankton community. However, distance-based linear modelling only identified fCO(2) as a factor explaining the variability observed amongst the microbial community composition, but not for explaining variability within the metabolic parameters. This suggests that fCO(2) impacts on microbial metabolic parameters occurred indirectly through varying physicochemical parameters and microbial species composition. Cluster analyses examining the co-occurrence of different functional groups of bacteria and phytoplankton further revealed a separation of the four fCO(2)-treated mesocosms from both control mesocosms, indicating that complex trophic interactions might be altered in a future acidified ocean. Possible consequences for nutrient cycling and carbon export are still largely unknown, in particular in a nutrient-limited ocean.
The oceans absorb about a quarter of the annually produced anthropogenic atmospheric carbon dioxide (CO2), resulting in a decrease in surface water pH, a process termed ocean acidification (OA). Surprisingly little is known about how OA affects the physiology of heterotrophic bacteria or the coupling of heterotrophic bacteria to phytoplankton when nutrients are limited. Previous experiments were, for the most part, undertaken during productive phases or following nutrient additions designed to stimulate algal blooms. Therefore, we performed an in situ large-volume mesocosm (similar to 55 m(3)) experiment in the Baltic Sea by simulating different fugacities of CO2 (fCO(2)) extending from present to future conditions. The study was conducted in July-August after the nominal spring bloom, in order to maintain low-nutrient conditions throughout the experiment. This resulted in phytoplankton communities dominated by small-sized functional groups (picophytoplankton). There was no consistent fCO(2)-induced effect on bacterial protein production (BPP), cell-specific BPP (csBPP) or biovolumes (BVs) of either free-living (FL) or particle-associated (PA) heterotrophic bacteria, when considered as individual components (univariate analyses). Permutational Multivariate Analysis of Variance (PERMANOVA) revealed a significant effect of the fCO(2) treatment on entire assemblages of dissolved and particulate nutrients, metabolic parameters and the bacteria-phytoplankton community. However, distance-based linear modelling only identified fCO(2) as a factor explaining the variability observed amongst the microbial community composition, but not for explaining variability within the metabolic parameters. This suggests that fCO(2) impacts on microbial metabolic parameters occurred indirectly through varying physicochemical parameters and microbial species composition. Cluster analyses examining the co-occurrence of different functional groups of bacteria and phytoplankton further revealed a separation of the four fCO(2)-treated mesocosms from both control mesocosms, indicating that complex trophic interactions might be altered in a future acidified ocean. Possible consequences for nutrient cycling and carbon export are still largely unknown, in particular in a nutrient-limited ocean.
Novosphingobium fuchskuhlense sp nov., isolated from the north-east basin of Lake Grosse Fuchskuhle
(2013)
A yellow pigmented, Gram-negative, rod-shaped bacterium designated FNE08-7(T) was isolated from subsurface water of the north-east basin of the bog lake Grosse Fuchskuhle (Brandenburg, Germany). A first analysis of the nearly full-length 16S rRNA gene sequence analysis including environmental 16S rRNA gene sequences derived from freshwater ecosystems showed that strain FNE08-7(T) is the first cultured representative, to our knowledge, of the freshwater tribe Novo-A2. Further analysis indicates highest 16S rRNA gene sequence similarities to the type strains of Novosphingobium stygium (98.0%) and Novosphingobium taihuense (97.4%) and between 94.0% and 96.9% sequence similarity to other members of the genus Novosphingobium. Reconstruction of phylogenetic trees showed that strain FNE08-7(T) formed a distinct cluster with the type strains of N. stygium and N. taihuense supported by high bootstrap values. DNA DNA hybridization of strain FNE08-7(T) with N. stygium SMCC B0712(T) and N. taihuense DSM 17507(T) revealed low similarity values of 18.4% (reciprocal: 11.4%) and 23.1% (reciprocal: 54.2%), respectively. The predominant fatty acid of the isolate is C-18:1 omega 7c (56.4%) and two characteristic 2-hydroxy fatty acids, C-14:0 2-OH (16.5%) and C-15:0 2-OH (3.3%) occur. Ubiquinone Q-10 is the major respiratory quinone. The predominant polar lipids are phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine and minor amounts of diphosphatidylglycerol. Spermidine is the predominant polyamine. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicate that strain FNE08-7(T) represents a novel species of the genus Novosphingobium within the Alphaproteobacteria. Therefore, we propose the species Novosphingobium fuchskuhlense sp. nov., with FNE08-7(T) (=DSM 25065(T)=CCM 7978(T)=CCUG 61508(T)) as the type strain.
Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems.
New Methods, New Concepts
(2020)
Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the “Black Queen Hypothesis”) derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.
New Methods, New Concepts
(2020)
Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the “Black Queen Hypothesis”) derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.
Using the carcass sinking rate and density determined in laboratory for several freshwater zooplankton species, we developed a model of zooplankton carcass sinking as affected by turbulence and stratification. The model was subsequently used to estimate the residence time of zooplankton carcasses in the water column of Lake Stechlin, a typical temperate dimictic lake in northeastern Germany. The residence time varied among the different species and was strongly affected by thermal stratification. At the peak of summer stratification, the carcasses stayed up to 5 d in the 70 m-deep water column before reaching the lake bottom. Residence time was long enough that zooplankton carcasses could serve as an important matter and energy source for bacteria in the lake's pelagic zone and hence have the potential to significantly affect aquatic carbon and nutrient cycling. The proposed model of sinking rates, based on physically sound relationships, can be easily applied to other passively sinking particles, and be integrated into large ecosystem models.
Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.
Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.
Within the wealth of molecules constituting marine dissolved organic matter, carbohydrates make up the largest coherent and quantifiable fraction. Their main sources are from primary producers, which release large amounts of photosynthetic products – mainly polysaccharides – directly into the surrounding water via passive and active exudation. The organic carbon and other nutrients derived from these photosynthates enrich the ‘phycosphere’ and attract heterotrophic bacteria. The rapid uptake and remineralization of dissolved free monosaccharides by heterotrophic bacteria account for the barely detectable levels of these compounds. By contrast, dissolved combined polysaccharides can reach high concentrations, especially during phytoplankton blooms. Polysaccharides are too large to be taken up directly by heterotrophic bacteria, instead requiring hydrolytic cleavage to smaller oligo- or monomers by bacteria with a suitable set of exoenzymes. The release of diverse polysaccharides by various phytoplankton taxa is generally interpreted as the deposition of excess organic material. However, these molecules likely also fulfil distinct, yet not fully understood functions, as inferred from their active modulation in terms of quality and quantity when phytoplankton becomes nutrient limited or is exposed to heterotrophic bacteria. This minireview summarizes current knowledge regarding the exudation and composition of phytoplankton-derived exopolysaccharides and acquisition of these compounds by heterotrophic bacteria.
Heterotrophic microbes with the capability to process considerable amounts of organic matter can colonize microplastic particles (MP) in aquatic ecosystems. Weather colonization of microorganisms on MP will alter ecological niche and functioning of microbial communities remains still unanswered. Therefore, we compared the functional diversity of biofilms on microplastics when incubated in three lakes in northeastern Germany differing in trophy and limnological features. For all lakes, we compared heterotrophic activities of MP biofilms with those of microorganisms in the surrounding water by using Biolog (R) EcoPlates and assessed their oxygen consumption in microcosm assays with and without MP. The present study found that the total biofilm biomass was higher in the oligo-mesotrophic and dystrophic lakes than in the eutrophic lake. In all lakes, functional diversity profiles of MP biofilms consistently differed from those in the surrounding water. However, solely in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. These results demonstrate that the functionality and hence the ecological role of MP-associated microbial communities are context-dependent, i.e. different environments lead to substantial changes in biomass build up and heterotrophic activities of MP biofilms. We propose that MP surfaces act as new niches for aquatic microorganisms and that the constantly increasing MP pollution has the potential to globally impact carbon dynamics of pelagic environments by altering heterotrophic activities. (C) 2018 Elsevier B.V. All rights reserved.
Plastic pollution is a major global concern with several million microplastic particles entering every day freshwater ecosystems via wastewater discharge. Microplastic particles stimulate biofilm formation (plastisphere) throughout the water column and have the potential to affect microbial community structure if they accumulate in pelagic waters, especially enhancing the proliferation of biohazardous bacteria. To test this scenario, we simulated the inflow of treated wastewater into a temperate lake using a continuous culture system with a gradient of concentration of microplastic particles. We followed the effect of microplastics on the microbial community structure and on the occurrence of integrase 1 (intl), a marker associated with mobile genetic elements known as a proxy for anthropogenic effects on the spread of antimicrobial resistance genes. The abundance of intl increased in the plastisphere with increasing microplastic particle concentration, but not in the water surrounding the microplastic particles. Likewise, the microbial community on microplastic was more similar to the original wastewater community with increasing microplastic concentrations. Our results show that microplastic particles indeed promote persistence of typical indicators of microbial anthropogenic pollution in natural waters, and substantiate that their removal from treated wastewater should be prioritised. (C) 2017 Elsevier Ltd. All rights reserved.
Despite increasing concerns about microplastic (MP) pollution in aquatic ecosystems, there is insufficient knowledge on how MP affect fungal communities. In this study, we explored the diversity and community composition of fungi attached to polyethylene (PE) and polystyrene (PS) particles incubated in different aquatic systems in north-east Germany: the Baltic Sea, the River Warnow and a wastewater treatment plant. Based on next generation 18S rRNA gene sequencing, 347 different operational taxonomic units assigned to 81 fungal taxa were identified on PE and PS. The MP-associated communities were distinct from fungal communities in the surrounding water and on the natural substrate wood. They also differed significantly among sampling locations, pointing towards a substrate and location specific fungal colonization. Members of Chytridiomycota, Cryptomycota and Ascomycota dominated the fungal assemblages, suggesting that both parasitic and saprophytic fungi thrive in MP biofilms. Thus, considering the worldwide increasing accumulation of plastic particles as well as the substantial vector potential of MP, especially these fungal taxa might benefit from MP pollution in the aquatic environment with yet unknown impacts on their worldwide distribution, as well as biodiversity and food web dynamics at large.
Pollution by microplastics in aquatic ecosystems is accumulating at an unprecedented scale, emerging as a new surface for biofilm formation and gene exchange. In this study, we determined the permissiveness of aquatic bacteria towards a model antibiotic resistance plasmid, comparing communities that form biofilms on microplastics vs. those that are free-living. We used an exogenous and red-fluorescent E. coli donor strain to introduce the green-fluorescent broad-host-range plasmid pKJKS which encodes for trimethoprim resistance. We demonstrate an increased frequency of plasmid transfer in bacteria associated with microplastics compared to bacteria that are free-living or in natural aggregates. Moreover, comparison of communities grown on polycarbonate filters showed that increased gene exchange occurs in a broad range of phylogenetically-diverse bacteria. Our results indicate horizontal gene transfer in this habitat could distinctly affect the ecology of aquatic microbial communities on a global scale. The spread of antibiotic resistance through microplastics could also have profound consequences for the evolution of aquatic bacteria and poses a neglected hazard for human health.
Microcystins do not necessarily lower the sensitivity of Microcystis aeruginosa to tannic acid
(2016)
Different phytoplankton strains have been shown to possess varying sensitivities towards macrophyte allelochemicals, yet the reasons for this are largely unknown. To test whether microcystin (MC) is responsible for strain-specific sensitivities of Microcystis aeruginosa to macrophyte allelochemicals, we compared the sensitivity of 12 MC- and non-MC-producing M. aeruginosa strains, including an MC-deficient mutant and its wild type, to the polyphenolic allelochemical tannic acid (TA). Non-MC-producing strains showed a significantly higher sensitivity to TA than MC-producing strains, both in Chlorophyll a concentrations and quantum yields of photosystem II. In contrast, an MC-deficient mutant displayed a higher fitness against TA compared to its wild type. These results suggest that the resistance of M. aeruginosa to polyphenolic allelochemicals is not primarily related to MCs per se, but to other yet unknown protective mechanisms related to MCs.
Microbial response to experimentally controlled redox transitions at the sediment water interface
(2015)
The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface.
Microbial response to experimentally controlled redox transitions at the sediment water interface
(2015)
The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface.
The prevailing paradigm in aquatic science is that microbial methanogenesis happens primarily in anoxic environments. Here, we used multiple complementary approaches to show that microbial methane production could and did occur in the well-oxygenated water column of an oligotrophic lake (Lake Stechlin, Germany). Oversaturation of methane was repeatedly recorded in the well-oxygenated upper 10 m of the water column, and the methane maxima coincided with oxygen oversaturation at 6 m. Laboratory incubations of unamended epilimnetic lake water and inoculations of photoautotrophs with a lake-enrichment culture both led to methane production even in the presence of oxygen, and the production was not affected by the addition of inorganic phosphate or methylated compounds. Methane production was also detected by in-lake incubations of lake water, and the highest production rate was 1.8-2.4 nM.h(-1) at 6 m, which could explain 33-44% of the observed ambient methane accumulation in the same month. Temporal and spatial uncoupling between methanogenesis and methanotrophy was supported by field and laboratory measurements, which also helped explain the oversaturation of methane in the upper water column. Potentially methanogenic Archaea were detected in situ in the oxygenated, methane-rich epilimnion, and their attachment to photoautotrophs might allow for anaerobic growth and direct transfer of substrates for methane production. Specific PCR on mRNA of the methyl coenzyme M reductase A gene revealed active methanogenesis. Microbial methane production in oxygenated water represents a hitherto overlooked source of methane and can be important for carbon cycling in the aquatic environments and water to air methane flux.
Associated heterotrophic bacteria alter the microenvironment of cyanobacteria and potentially influence cyanobacterial development. Therefore, we studied interactions of the unicellular freshwater cyanobacterium Microcystis aeruginosa with heterotrophic bacteria. The associated bacterial community was greatly driven by temperature as seen by DNA fingerprinting. However, the associated microbes also closely interacted with the cyanobacteria indicating changing ecological consequence of the associated bacterial community with temperature. Whereas concentration of dissolved organic carbon in cyanobacterial cultures changed in a temperature-dependent manner, its quality greatly varied under the same environmental conditions, but with different associated bacterial communities. Furthermore, temperature affected quantity and quality of cell-bound microcystins, whereby interactions between M. aeruginosa and their associated community often masked this temperature effect. Both macro- and microenvironment of active cyanobacterial strains were characterized by high pH and oxygen values creating a unique habitat that potentially affects microbial diversity and function. For example, archaea including 'anaerobic' methanogens contributed to the associated microbial community. This implies so far uncharacterized interactions between Microcystis aeruginosa and its associated prokaryotic community, which has unknown ecological consequences in a climatically changing world.
Cyanobacterial mass developments impact the community composition of heterotrophic microorganisms with far-reaching consequences for biogeochemical and energy cycles of freshwater ecosystems including reservoirs. Here we sought to evaluate the temporal stability of methanogenic archaea in the water column and further scrutinize their associations with cyanobacteria. Monthly samples were collected from October 2009 to December 2010 in hypereutrophic Pampulha reservoir with permanently blooming cyanobacteria, and from January to December 2011 in oligotrophic Volta Grande reservoir with only sporadic cyanobacteria incidence. The presence of archaea in cyanobacterial cultures was investigated by screening numerous strains of Microcystis spp. from these reservoirs as well as from lakes in Europe, Asia, and North-America. We consistently determined the occurrence of archaea, in particular methanogenic archaea, in both reservoirs throughout the year. However, archaea were only associated with two strains (Microcystis sp. UFMG 165 and UFMG 175) recently isolated from these reservoirs. These findings do not implicate archaea in the occurrence of methane in the epilimnion of inland waters, but rather serve to highlight the potential of microhabitats associated with particles, including phytoplankton, to shelter unique microbial communities.
Active methane production in oxygenated lake waters challenges the long-standing paradigm that microbial methane production occurs only under anoxic conditions and forces us to rethink the ecology and environmental dynamics of this powerful greenhouse gas. Methane production in the upper oxic water layers places the methane source closer to the air water interface, where convective mixing and microbubble detrainment can lead to a methane efflux higher than that previously assumed. Microorganisms may produce methane in oxic environments by being equipped with enzymes to counteract the effects of molecular oxygen during methanogenesis or using alternative pathways that do not involve oxygen-sensitive enzymes. As this process appears to be influenced by thermal stratification, water transparency, and primary production, changes in lake ecology due to climate change will alter methane formation in oxic water layers, with far-reaching consequences for methane flux and climate feedback.
In this pilot study, we describe a high-pressure incubation system allowing multiple subsampling of a pressurized culture without decompression. The system was tested using one piezophilic (Photobacterium profundum), one piezotolerant (Colwellia maris) bacterial strain and a decompressed sample from the Mediterranean deep sea (3044 m) determining bacterial community composition, protein production (BPP) and cell multiplication rates (BCM) up to 27 MPa. The results showed elevation of BPP at high pressure was by a factor of 1.5 +/- 1.4 and 3.9 +/- 2.3 for P. profundum and C. maris, respectively, compared to ambient-pressure treatments and by a factor of 6.9 +/- 3.8 fold in the field samples. In P. profundum and C. maris, BCM at high pressure was elevated (3.1 +/- 1.5 and 2.9 +/- 1.7 fold, respectively) compared to the ambient-pressure treatments. After 3 days of incubation at 27 MPa, the natural bacterial deep-sea community was dominated by one phylum of the genus Exiguobacterium, indicating the rapid selection of piezotolerant bacteria. In future studies, our novel incubation system could be part of an isopiestic pressure chain, allowing more accurate measurement of bacterial activity rates which is important both for modeling and for predicting the efficiency of the oceanic carbon pump.
In winter 2009/10, a sudden under-ice bloom of heterotrophic bacteria occurred in the seasonally ice-covered, temperate, deep, oligotrophic Lake Stechlin (Germany). Extraordinarily high bacterial abundance and biomass were fueled by the breakdown of a massive bloom of Aphanizomenon flos-aquae after ice formation. A reduction in light resulting from snow coverage exerted a pronounced physiological stress on the cyanobacteria. Consequently, these were rapidly colonized, leading to a sudden proliferation of attached and subsequently of free-living heterotrophic bacteria. Total bacterial protein production reached 201 mg C L-1 d(-1), ca. five times higher than spring-peak values that year. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis at high temporal resolution showed pronounced changes in bacterial community structure coinciding with changes in the physiology of the cyanobacteria. Pyrosequencing of 16S rRNA genes revealed that during breakdown of the cyanobacterial population, the diversity of attached and free-living bacterial communities were reduced to a few dominant families. Some of these were not detectable during the early stages of the cyanobacterial bloom indicating that only specific, well adapted bacterial communities can colonize senescent cyanobacteria. Our study suggests that in winter, unlike commonly postulated, carbon rather than temperature is the limiting factor for bacterial growth. Frequent phytoplankton blooms in ice-covered systems highlight the need for year-round studies of aquatic ecosystems including the winter season to correctly understand element and energy cycling through aquatic food webs, particularly the microbial loop. On a global scale, such knowledge is required to determine climate change induced alterations in carbon budgets in polar and temperate aquatic systems.
Seasonal changes in environmental conditions have a strong impact on microbial community structure and dynamics in aquatic habitats. To better elucidate the response of bacterial communities to environmental changes, we have measured a large variety of limnetic variables and investigated bacterial community composition (BCC) and dynamics over seven consecutive years between 2003 and 2009 in mesotrophic Lake Tiefwaren (NE Germany). We separated between free-living (FL, > 0.2, < 5.0 mu m) and particle-associated (PA, > 5.0 mu m) bacteria to account for different bacterial lifestyles and to obtain a higher resolution of the microbial diversity. Changes in BCC were studied by DGGE based on PCR-amplified 16S rRNA gene fragments. Sequencing of DGGE bands revealed that ca. 70 % of all FL bacteria belonged to the Actinobacteria, whereas PA bacteria were dominated by Cyanobacteria (43 %). FL communities were generally less diverse and rather stable over time compared to their PA counterpart. Annual changes in reoccurring seasonal patterns of dominant freshwater bacteria were supported by statistical analyses, which revealed several significant correlations between DGGE profiles and various environmental variables, e.g. temperature and nutrients. Overall, FL bacteria were generally less affected by environmental changes than members of the PA fraction. Close association of PA bacteria with phytoplankton and zooplankton suggests a tight coupling of PA bacteria to organisms of higher trophic levels. Our results indicate substantial differences in bacterial lifestyle of pelagic freshwater bacteria, which are reflected by contrasting seasonal dynamics and relationships to a number of environmental variables.
There is now increasing evidence for the importance of microbial regulation of biogeochemical cycling in streams. Resource availability shapes microbial community structure, but less is known about how landscape-mediated availability of nutrients and carbon can control microbial functions in streams. Using comparative metagenomics, we examined the relationship between microbial functional genes and composition of dissolved organic matter (DOM), nutrients, and suspended microbial communities in 11 streams, divided into three groups based on the predominant land cover category (agriculture, forested, or wetland). Using weighted gene co-occurrence network analysis, we identified clusters of functions related to DOM composition, agricultural land use, and/or wetland and forest land cover. Wetland-dominated streams were characterized by functions related to nitrogen metabolism and processing of aromatic carbon compounds, with strong positive correlations with dissolved organic carbon concentration and DOM aromaticity. Forested streams were characterized by metabolic functions related to monomer uptake and carbohydrates, such as mannose and fructose metabolism. In agricultural streams, microbial functions were correlated with more labile, protein-like DOM, PO4, and NO3, likely reflecting functional adaptation to labile DOM and higher nutrient concentrations. Distinct changes in the functional composition and loss of functional diversity of microorganisms became evident when comparing natural to agricultural catchments. Although all streams showed signs of functional redundancy, loss of species richness per function in agricultural catchments suggests that microbial functions in natural catchments may be more resilient to disturbance. Our results provide new insight into microbial community functions involved in nutrient and carbon biogeochemical cycles and their dependence on specific environmental settings.
Microbial communities are essential components of aquatic ecosystems through their contribution to food web dynamics and biogeochemical processes. Aquatic microbial diversity is immense and a general challenge is to understand how metabolism and interactions of single organisms shape microbial community dynamics and ecosystem-scale biogeochemical transformations. Metagenomic approaches have developed rapidly, and proven to be powerful in linking microbial community dynamics to biogeochemical processes. In this review, we provide an overview of metagenomic approaches, followed by a discussion on some recent insights they have provided, including those in this special issue. These include the discovery of new taxa and metabolisms in aquatic microbiomes, insights into community assembly and functional ecology as well as evolutionary processes shaping microbial genomes and microbiomes, and the influence of human activities on aquatic microbiomes. Given that metagenomics can now be considered a mature technology where data generation and descriptive analyses are relatively routine and informative, we then discuss metagenomic-enabled research avenues to further link microbial dynamics to biogeochemical processes. These include the integration of metagenomics into well-designed ecological experiments, the use of metagenomics to inform and validate metabolic and biogeochemical models, and the pressing need for ecologically relevant model organisms and simple microbial systems to better interpret the taxonomic and functional information integrated in metagenomes. These research avenues will contribute to a more mechanistic and predictive understanding of links between microbial dynamics and biogeochemical cycles. Owing to rapid climate change and human impacts on aquatic ecosystems, the urgency of such an understanding has never been greater.
The importance of ciliates as herbivores and in biogeochemical cycles is increasingly recognized. An opportunity to observe the potential consequences of zooplankton dominated by ciliates arose when winter fish kills resulted in strong suppression of crustaceans by young planktivorous fish in two shallow lakes. On an annual average, ciliates made up 38-76% of the total zooplankton biomass in both lakes during two subsequent years. Consequently, ciliate biomass and their estimated grazing potential were extremely high compared with other lakes of various trophic states and depths. Grazing estimates based on abundance and size suggest that ciliates should have cleared the water column of small (<5 mu m) and intermediate (5-50 mu m) sized phytoplankton more than once a day. Especially, small feeders within the ciliates were important, likely exerting a strong top-down control on small phytoplankton. Particle-attached bacteria were presumably strongly suppressed by intermediate-sized ciliate feeders. In contrast to other lakes, large phytoplankton was proportionately very abundant. The phytoplankton community had a high evenness, which may be attributed to the feeding by numerous fast growing and selective ciliate species. Our study highlights ciliates as an important trophic link and adds to the growing awareness of the role of winter processes for plankton dynamics.
Complex biopolymers (BPs) such as chitin and cellulose provide the majority of organic carbon in aquatic ecosystems, but the mechanisms by which communities of bacteria in natural systems exploit them are unclear. Previous degradation experiments in artificial systems predominantly used microcosms containing a single bacterial species, neglecting effects of interspecific interactions. By constructing simplified aquatic microbial communities, we tested how the addition of other bacterial species, of a nanoflagellate protist capable of consuming bacteria, or of both, affect utilization of BPs. Surprisingly, total abundance of resident bacteria in mixed communities increased upon addition of the protist. Concomitantly, bacteria shifted from free-living to aggregated morphotypes that seemed to promote utilization of BPs. In our model system, these interactions significantly increased productivity in terms of overall bacterial numbers and carbon transfer efficiency. This indicates that interactions on microbial aggregates may be crucial for chitin and cellulose degradation. We therefore suggest that interspecific microbial interactions must be considered when attempting to model the turnover of the vast pool of complex biopolymers in aquatic ecosystems.
Internal waves (seiches) are well-studied physical processes in stratified lakes, but their effects on sediment porewater chemistry and microbiology are still largely unexplored. Due to pycnocline oscillations, sediments are exposed to recurrent changes between epilimnetic and hypolimnetic water. This results in strong differences of environmental conditions, which should be reflected in the responses of redox-sensitive biogeochemical processes at both, the sediment-water interface and deeper sediment layers. We tested in a series of mesocosm experiments the influence of seiche-induced redox changes on porewater chemistry and bacterial activity in the sediments under well controlled conditions. Thereby, we excluded effects of changes in current and temperature regimes. For a period of 10 days, intact sediment cores from oligotrophic Lake Stechlin were incubated under constant (either oxic or anoxic) or alternating redox conditions. Solute concentrations were measured as porewater profiles in the sediment, while microbial activity was determined in the upper 0.5 cm of sediment. Oxic and alternating redox conditions resulted in similar ammonium, phosphate, and methane porewater concentrations, while concentrations of each analyte were considerably higher in anoxic cores. Microbial activity was clearly lower in the anoxic cores than in the oxic and the alternating cores. In conclusion, cores with intermittent anoxic phases of up to 24 hours do not differ in biogeochemistry and microbial activities from static oxic sediments. However, due to various physical processes seiches cause oxygen to penetrate deeper into sediment layers, which affects sediment redox gradients and increase microbial activity in seiche-influenced sediments.
Intermittent riverine resuspension effects on phosphorus transformations and heterotrophic bacteria
(2013)
Intermittent riverine resuspension (IRR), a common phenomenon, was applied to investigate its effects on sedimentary resources availability and bacteria in the water column. This lab experiment used organic-rich lowland river sediment in a newly designed erosion chamber, the Benthic Water Column Simulator, generating well-defined ratios of shear velocity u* to turbulence intensity. Eight consecutive resuspension events, 1-8, were initiated at u* = 1.1 cm s(-1). Sedimentary and phosphorus entrainment decreased from 20.4 g m(-2) h(-1) and 111.6 mg m(-2) h(-1) at event 1 to 1.31 g m(-2) h(-1) and 18.7 mg m(-2) h(-1) at event 8, suggesting an exhaustion of particulate and dissolved sediment constituents. Entrainment of particle-associated (PA) bacteria (132.7 x 10(9)-251.1 x 10(9) cells m(-2) h(-1)) was strongly correlated to that of particles. Free-living (FL) bacteria (-27.6 x 10(9)-36.4 x 10(9) cells m(-2) h(-1)) were fractionally entrained. Numbers of PA bacteria remained low after each event, whereas those of FL bacteria strongly increased 5-15 h after an event because of growth due to increased availability of dissolved organic carbon and inorganic nutrients following each event. FL bacteria community structure also changed during IRR. The systematic changes over consecutive IRR cycles show a strong effect in all considered parameters that elude the typical single-event, steady-state experiments. IRR should thus be considered in two respects: experimental protocols on riverine water quality should be revised. In ecosystem modeling, IRR should be considered to better predict extent and effect of resuspension. Only IRR adequately reflects the natural interplay between hydrodynamics and organisms in rivers.
Chytridiomycota, often referred to as chytrids, can be virulent parasites with the potential to inflict mass mortalities on hosts, causing e.g. changes in phytoplankton size distributions and succession, and the delay or suppression of bloom events. Molecular environmental surveys have revealed an unexpectedly large diversity of chytrids across a wide range of aquatic ecosystems worldwide. As a result, scientific interest towards fungal parasites of phytoplankton has been gaining momentum in the past few years. Yet, we still know little about the ecology of chytrids, their life cycles, phylogeny, host specificity and range. Information on the contribution of chytrids to trophic interactions, as well as co-evolutionary feedbacks of fungal parasitism on host populations is also limited. This paper synthesizes ideas stressing the multifaceted biological relevance of phytoplankton chytridiomycosis, resulting from discussions among an international team of chytrid researchers. It presents our view on the most pressing research needs for promoting the integration of chytrid fungi into aquatic ecology.
Across a landscape, aquatic-terrestrial interfaces within and between ecosystems are hotspots of organic matter (OM) mineralization. These interfaces are characterized by sharp spatio-temporal changes in environmental conditions, which affect OM properties and thus control OM mineralization and other transformation processes. Consequently, the extent of OM movement at and across aquatic-terrestrial interfaces is crucial in determining OM turnover and carbon (C) cycling at the landscape scale. Here, we propose expanding current concepts in aquatic and terrestrial ecosystem sciences to comprehensively evaluate OM turnover at the landscape scale. We focus on three main concepts toward explaining OM turnover at the landscape scale: the landscape spatiotemporal context, OM turnover described by priming and ecological stoichiometry, and anthropogenic effects as a disruptor of natural OM transfer magnitudes and pathways. A conceptual framework is introduced that allows for discussing the disparities in spatial and temporal scales of OM transfer, changes in environmental conditions, ecosystem connectivity, and microbial-substrate interactions. The potential relevance of priming effects in both terrestrial and aquatic systems is addressed. For terrestrial systems, we hypothesize that the interplay between the influx of OM, its corresponding elemental composition, and the elemental demand of the microbial communities may alleviate spatial and metabolic thresholds. In comparison, substrate level OM dynamics may be substantially different in aquatic systems due to matrix effects that accentuate the role of abiotic conditions, substrate quality, and microbial community dynamics. We highlight the disproportionate impact anthropogenic activities can have on OM cycling across the landscape. This includes reversing natural OM flows through the landscape, disrupting ecosystem connectivity, and nutrient additions that cascade across the landscape. This knowledge is crucial for a better understanding of OM cycling in a landscape context, in particular since terrestrial and aquatic compartments may respond differently to the ongoing changes in climate, land use, and other anthropogenic interferences.
Fungi and bacteria are the major organic matter (OM) decomposers in aquatic ecosystems. While bacteria are regarded as primary mineralizers in the pelagic zone of lakes and oceans, fungi dominate OM decomposition in streams and wetlands. Recent findings indicate that fungal communities are also active in lakes, but little is known about their diversity and interactions with bacteria. Therefore, the decomposer niche overlap of saprotrophic fungi and bacteria was studied on pollen (as a seasonally recurring source of fine particulate OM) by performing microcosm experiments with three different lake types. Special emphasis was placed on analysis of fungal community composition and diversity. We hypothesized that (I) pollen select for small saprotrophic fungi and at the same time for typical particle-associated bacteria; (II) fungal communities form specific free-living and attached sub-communities in each lake type; (III) the ratio between fungi or bacteria on pollen is controlled by the lake's chemistry. Bacteria-to-fungi ratios were determined by quantitative PCR (qPCR), and bacterial and fungal diversity were studied by clone libraries and denaturing gradient gel electrophoresis (DGGE) fingerprints. A protease assay was used to identify functional differences between treatments. For generalization, systematic differences in bacteria-to-fungi ratios were analyzed with a dataset from the nearby Baltic Sea rivers. High abundances of Chytridiomycota as well as occurrences of Cryptomycota and yeast-like fungi confirm the decomposer niche overlap of saprotrophic fungi and bacteria on pollen. As hypothesized, microbial communities consistently differed between the lake types and exhibited functional differences. Bacteria-to-fungi ratios correlated well with parameters such as organic carbon and pH. The importance of dissolved organic carbon and nitrogen for bacteria-to-fungi ratios was supported by the Baltic Sea river dataset. Our findings highlight the fact that carbon-to-nitrogen ratios may also control fungal contributions to OM decomposition in aquatic ecosystems.
Impacts of extreme weather events on bacterial community composition of a temperate humic lake
(2020)
Extreme weather events are projected to increase in frequency and intensity as climate change continues. Heterotrophic bacteria play a critical role in lake ecosystems, yet little research has been done to determine how they are affected by such extremes. The purpose of this study was to use high-throughput sequencing to explore the bacterial community composition of a humic oligotrophic lake on the North Atlantic Irish coast and to assess the impacts on composition dynamics related to extreme weather events. Samples for sequencing were collected from Lough Feeagh on a fortnightly basis from April to November 2018. Filtration was used to separate free-living and particle-associated bacterial communities and amplicon sequencing was performed for the 16S rRNA V4 region. Two named storms, six high discharge events, and one drought period occurred during the sampling period. These events had variable, context-dependent effects on bacterial communities in Lough Feeagh. The particle-associated community was found to be more likely to respond to physical changes, such as mixing, while the free-living population responded to changes in nutrient and carbon concentrations. Generally, however, the high stability of the bacterial community observed in Lough Feeagh suggests that the bacterial community is relatively resilient to extreme weather events.
A mesocosm experiment was conducted to investigate the impact of rising fCO(2) on the build-up and decline of organic matter during coastal phytoplankton blooms. Five mesocosms (similar to 38 mA(3) each) were deployed in the Baltic Sea during spring (2009) and enriched with CO2 to yield a gradient of 355-862 A mu atm. Mesocosms were nutrient fertilized initially to induce phytoplankton bloom development. Changes in particulate and dissolved organic matter concentrations, including dissolved high-molecular weight (> 1 kDa) combined carbohydrates, dissolved free and combined amino acids as well as transparent exopolymer particles (TEP), were monitored over 21 days together with bacterial abundance, and hydrolytic extracellular enzyme activities. Overall, organic matter followed well-known bloom dynamics in all CO2 treatments alike. At high fCO(2,) higher Delta POC:Delta PON during bloom rise, and higher TEP concentrations during bloom peak, suggested preferential accumulation of carbon-rich components. TEP concentration at bloom peak was significantly related to subsequent sedimentation of particulate organic matter. Bacterial abundance increased during the bloom and was highest at high fCO(2). We conclude that increasing fCO(2) supports production and exudation of carbon-rich components, enhancing particle aggregation and settling, but also providing substrate and attachment sites for bacteria. More labile organic carbon and higher bacterial abundance can increase rates of oxygen consumption and may intensify the already high risk of oxygen depletion in coastal seas in the future.
Fungi are an important component of microbial communities and are well known for their ability to decompose refractory, highly polymeric organic matter. In soils and aquatic systems, fungi play an important role in carbon processing, however, their diversity, community structure and function as well as ecological role, particularly in groundwater, are poorly studied. The aim of this study was to examine the fungal community composition, diversity and function in groundwater from 16 boreholes located in the vicinity of two lakes in NE Germany that are characterized by contrasting trophic status. The analysis of 28S rRNA gene sequences amplified from the groundwater revealed high fungal diversity arid clear differences in community structure between the aquifers. Most sequences were assigned to Ascomycota and Basidiomycota, but members of Chytridiomycota, Cryptomycota, Zygomycota, Blastocladiomycota, Glomeromycota and Neocallimastigomycota were also detected. In addition, 27 species of fungi were successfully isolated from the groundwater samples and tested for their ability to decompose complex organic polymers - the predominant carbon source in the groundwater. Most isolates showed positive activities for at least one of the tested polymer types, with three strains, belonging to the genera Gibberella, Isaria and Cadophora, able to decompose all tested substrates. Our results highlight the high diversity of fungi in groundwater, and point to their important ecological role in breaking down highly polymeric organic matter in these isolated microbial habitats. (C) 2019 Elsevier Ltd and British Mycological Society. All rights reserved.
Aerobic Anoxygenic Phototrophic (AAP) bacteria are bacteriochlorophyll (BChl) a -containing organisms which use light energy to supplement their predominantly heterotrophic metabolism. Here, we investigated mortality and growth rates of AAP bacteria in three different freshwater lakes in Central Europe: the mountain lake Plesne, the oligo-mesotrophic Lake Stechlin and the forest pond Huntov. The mortality of AAP bacteria was estimated from diel changes of BChl a fluorescence. Net and gross growth rates were calculated from the increases in AAP cell numbers. The gross growth rates of AAP bacteria ranged from 0.38 to 5.6 d(-1), with the highest values observed during summer months. Simultaneously, the rapidly growing AAP cells have to cope with an intense grazing pressure by both zooplankton and protists. The presented results document that during the day, gross growth usually surpased mortality. Our results indicate that AAP bacteria utilize light energy under natural conditions to maintain rapid growth rates, which are balanced by a generally intense grazing pressure.
Freshwater fungi are a poorly studied ecological group that includes a high taxonomic diversity. Most studies on aquatic fungal diversity have focused on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in the meso-oligotrophic, temperate Lake Stechlin in North-East Germany. These included the pelagic and littoral water column, sediments, and biotic substrates. We performed high throughput sequencing using the Roche 454 platform, employing a universal eukaryotic marker region within the large ribosomal subunit (LSU) to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1027 fungal OTUs (97% sequence similarity). Richness estimates were highest in the sediment, biofilms, and benthic samples (189-231 OTUs), intermediate in water samples (42-85 OTUs), and lowest in plankton samples (8 OTUs). NMDS grouped the eight studied habitats into six clusters, indicating that community composition was strongly influenced by turnover among habitats. Fungal communities exhibited changes at the phylum and order levels along three different substrate categories from littoral to pelagic habitats. The large majority of OTUs (> 75%) could not be classified below the order level due to the lack of aquatic fungal entries in public sequence databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition. Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body.
River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth’s biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented “next-generation biomonitoring” by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.
We investigated inflow of a wastewater treatment plant and sediment of an urban lake for the presence of Clostridioides difficile by cultivation and PCR. Among seven colonies we sequenced the complete genomes of three: two non-toxigenic isolates from wastewater and one toxigenic isolate from the urban lake. For all obtained isolates, a close genomic relationship with human-derived isolates was observed. (C) 2019 Elsevier Ltd. All rights reserved.
Fungi in aquatic ecosystems
(2019)
Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.