Refine
Year of publication
Language
- English (157)
Is part of the Bibliography
- yes (157)
Keywords
- salinity gradient (6)
- Baltic Sea (5)
- freshwater (5)
- Chytridiomycota (4)
- PLFA (4)
- aquatic fungi (4)
- bacteria (4)
- biodiversity (4)
- carbon cycling (4)
- community (4)
- microbial interactions (4)
- phytoplankton (4)
- temperature (4)
- Microplastics (3)
- Sediment (3)
- bacterial production (3)
- elevated CO2 (3)
- interactions (3)
- metagenomics (3)
- microbial communities (3)
- microbial diversity (3)
- microbial ecology (3)
- sediment (3)
- stable isotopes (3)
- 454-pyrosequencing (2)
- Achlya (2)
- Achlyaceae (2)
- Antarctica (2)
- Aquatic ecosystems (2)
- Aquatic fungi (2)
- Archaea (2)
- Bacteria (2)
- Biofilm (2)
- Biofilms (2)
- Black Queen Hypothesis (2)
- Carlini Station (2)
- Costa Rica (2)
- DNA extraction (2)
- DNA metabarcoding (2)
- DNA modification (2)
- Eukaryota (2)
- European Multi Lake Survey (2)
- Illumina amplicon sequencing (2)
- Lake Stechlin (2)
- Metschnikowia (2)
- NRPS (2)
- OMICs tools (2)
- PCR (2)
- PKS (2)
- Saprolegnia (2)
- Saprolegniaceae (2)
- UV radiation (2)
- algae (2)
- anatoxin (2)
- aquatic ecosystems (2)
- baltic sea (2)
- batch effect (2)
- bias (2)
- bio-optical modeling (2)
- brackish waters (2)
- calcite (2)
- calcium carbonate inclusions (2)
- cellulose polymeric organic matter (2)
- chytridiomycota (2)
- cloud (2)
- crustacean zooplankton (2)
- cryptomycota (2)
- cylindrospermopsin (2)
- deep-sea (2)
- direct effects (2)
- diversity profiles (2)
- endophytes (2)
- environmental DNA (2)
- environmental genomics (2)
- extra-cytoplasmic pockets (2)
- extracellular enzymes (2)
- free-living (2)
- freshwater heterotrophic bacteria (2)
- fungal diversity (2)
- fungi (2)
- gene expression (2)
- heterotrophic bacteria (2)
- hyperspectral measurements (2)
- in-situ (2)
- indirect effects (2)
- inland water (2)
- inversion (2)
- kelp (2)
- laboratory practice (2)
- lake community (2)
- lake periphyton (2)
- light (2)
- mesocosm (2)
- metabarcoding (2)
- metagenomics 2.0 (2)
- microcystin (2)
- microeukaryotes (2)
- mixed cultures (2)
- network analysis (2)
- next-generation sequencing (2)
- nondemonic intrusions (2)
- particle-associated and free-living bacteria (2)
- phytoplankton host (2)
- plastic-associated biofilms (2)
- polyethylene (2)
- polymer degradation (2)
- polystyrene (2)
- promiscuous (2)
- purifying selection (2)
- quorum sensing (2)
- remote sensing (2)
- seasons (2)
- seawater (2)
- spatial distribution (2)
- streambed structure (2)
- sulfur-bacteria (2)
- surface reflection (2)
- terrestrial carbon (2)
- 13C stable isotopes (1)
- 16S rRNA Illumina amplicon sequencing (1)
- 16S rRNA gene sequencing (1)
- AAP bacteria (1)
- Aggregation (1)
- Anthropocene (1)
- Anthropogenic pollution (1)
- Antibiotic resistance (1)
- Aquifers (1)
- Atlantic-ocean (1)
- Bacteria-phytoplankton coupling (1)
- Bacterial communities (1)
- Bacterial community composition (1)
- Bacterial community composition (BCC) (1)
- Bacterial growth efficiency (1)
- Bacterial production (1)
- Beta-diversity (1)
- Biolog EcoPlates (1)
- Bray Curtis dissimilarity (1)
- C-13 stable isotopes (1)
- CDOM (1)
- CO2 emissions (1)
- Carbon (1)
- Carbon cycle (1)
- Carbon cycling (1)
- Carbon decomposition (1)
- Carbon substrates (1)
- Carbon turnover (1)
- Chaoborus (1)
- Chytrids (1)
- Climate-change ecology (1)
- Clostridioides difficile (1)
- Community (1)
- Continuous cultures (1)
- Core incubation experiments (1)
- Cutinase (1)
- Cyanobacteria (1)
- DNRA (1)
- DOC (1)
- DOC quality (1)
- Dangeardia mamillata (1)
- Denitrifiers (1)
- Desiccation (1)
- Eastern Gotland basin (1)
- Ecological interactions (1)
- Endocoenobium eudorinae (1)
- Epistylis (1)
- Eutrophication (1)
- FASTAR (1)
- FISH (1)
- Fatty acid degradation (1)
- Flagellate grazing (1)
- Flow-cytometry (1)
- Free-living and particle-associated bacteria (1)
- Freshwater (1)
- Freshwater microbial communities (1)
- Functional diversity (1)
- Genomes (1)
- Germany (1)
- Groundwater (1)
- Growth efficiency (1)
- HGT (1)
- HMA sponge (1)
- Health risk assessment (1)
- Heterotrophic activity (1)
- Horizontal gene transfer (1)
- HsbA (1)
- Humic acids (1)
- Impranil PU degradation (1)
- Integrase 1 (1)
- Internal waves (1)
- LC-OCD (1)
- Lake (1)
- Leaf litter (1)
- Limnology (1)
- Lipase (1)
- Mars (1)
- Methanogenic archaea (1)
- Microbial activities (1)
- Microbial carbon transfer (1)
- Microbial ecology (1)
- Microcystis aeruginosa (1)
- Microcystis sp (1)
- Microorganisms (1)
- Microplastics (MP) (1)
- Mineralisation (1)
- Multi-functionality index (1)
- N-acetyl-glucosamine (NAG) (1)
- Natural-waters (1)
- Nitrogen (1)
- Nitrospirae (1)
- Nutrient (1)
- Nyquist-shannon sampling theorem (1)
- Ocean acidification (1)
- Organic matter degradation (1)
- Organic matter mineralization (1)
- Oxygen (1)
- PARAFAC (1)
- PCO(2) levels (1)
- Particle-associated microorganisms (1)
- Pathogens (1)
- Peece-III (1)
- Photolysis (1)
- Pollen (1)
- Polymer degradation (1)
- Ponds (1)
- Porewater exchange (1)
- Porewater profiles (1)
- Redox conditions (1)
- Remediation (1)
- Respiration (1)
- Resuspended particulate (1)
- Rozellomycota (1)
- SOC (1)
- Sargasso Sea (1)
- Schulzensee (1)
- Sediment traps (1)
- Sediment-water interface (1)
- Shallow Lake (1)
- Size exclusion chromatography (SEC) (1)
- Spring bloom (1)
- Stable isotopes (1)
- Staurastromyces oculus (1)
- Staurastrum sp. (1)
- Submarine groundwater discharge (1)
- System ecology (1)
- TEP (1)
- Tidal pumping (1)
- Total biomass (1)
- Total suspended solids (1)
- Treated wastewater (1)
- Tropical reservoir (1)
- Turbidity (1)
- Turnover (1)
- Wastewater (1)
- Water resources (1)
- York River (1)
- Zooplankton (1)
- actively growing bacteria (AGB) (1)
- allelopathy (1)
- alluvial soil (1)
- alpha diversity (1)
- anaerobic methane oxidation (1)
- aniline blue (1)
- antagonism (1)
- anthropogenic interferences (1)
- antibiotic paradox (1)
- antibiotic resistance (1)
- antibiotics (1)
- antimicrobial defense (1)
- aquatic-terrestrial interfaces (1)
- aridity (1)
- attached (1)
- bacteriaalgae associations (1)
- bacterial community composition (1)
- bacterial symbionts (1)
- bacteriocytes (1)
- bacterioplankton (1)
- bacterivory (1)
- basal fungi (1)
- benthic food chain (1)
- benthic food web (1)
- beta-diversity (1)
- biogeography (1)
- biological carbon pump (1)
- biomarker (1)
- bromodeoxyuridine (BrdU) immunocytochemistry (1)
- buried horizon (1)
- calcite precipitation (1)
- carbon (1)
- carbon budget (1)
- carbon flows (1)
- carbon flux (1)
- carbon sinking flux (1)
- carbon turnover (1)
- carcasses (1)
- ciliate epibionts (1)
- climate change (1)
- climate variability (1)
- coastal sediments (1)
- communities (1)
- community respiration (1)
- conservation (1)
- conservation evaluation (1)
- copepod carcasses (1)
- cultures (1)
- dead sorting (1)
- deep-sea bacterial community (1)
- delayed fluorescence (1)
- development goals (1)
- drought (1)
- eco-evolutionary experience (1)
- ecological efficiency (1)
- ecological stoichiometry (1)
- ecological theory (1)
- ecosystem function (1)
- ecosystem productivity (1)
- ecosystem services (1)
- endangered species (1)
- epibiont motility (1)
- epilimnic methane peak (1)
- extreme events (1)
- extreme weather event (1)
- filamentous cyanobacteria (1)
- fish (1)
- flow cytometry (1)
- fluorescence (1)
- fluorescence-activated cell sorting (FACS) (1)
- food web (1)
- fresh-water (1)
- freshwater lakes (1)
- functional traits (1)
- fungal parasites (1)
- gene sequencing (1)
- global carbon cycle (1)
- global change (1)
- green algae (1)
- gross primary production (1)
- growth (1)
- habitat (1)
- high CO2 ocean (1)
- holobiont (1)
- humic lake (1)
- hydrostatic pressure (1)
- inland waters (1)
- inorganic nutrients (1)
- inter- and intra-species interactions (1)
- invertebrates (1)
- isotopic methods (1)
- lake (1)
- lake monitoring (1)
- lakes (1)
- landscape connectivity (1)
- latitudinal gradients (1)
- leaf litter (1)
- life cycle (1)
- live (1)
- macrophytes (1)
- marine snow (1)
- marine viruses (1)
- membrane fatty acids (1)
- mesocosm experiment (1)
- metabolism (1)
- methanogens (1)
- methods (1)
- microbial activity (1)
- microscopy (1)
- multi-lake snapshot surveys (1)
- nitrogen-fixation (1)
- nodularia spumigena (1)
- non-predatory mortality (1)
- nonconsumptive mortality (1)
- nonpredatory mortality (1)
- northern Baltic Sea (1)
- novel ecosystems (1)
- ocean acidification (1)
- oligotrophic lake Stechlin (1)
- organic matter (1)
- organic matter mineralization (1)
- organic-carbon (1)
- organic-matter (1)
- parasite (1)
- parasites (1)
- particle-associated (1)
- particle-associated bacteria (1)
- particulate matter (1)
- pelagic food chain (1)
- pelagic food web (1)
- phage (1)
- phagotrophy (1)
- phospholipid-derived fatty acid (1)
- photoheterotrophy (1)
- phycocyanin (1)
- phylotypes (1)
- phytoplankton ecology (1)
- piezophilic bacteria (1)
- populations (1)
- pressure chamber (1)
- priming effects (1)
- prokaryotes (1)
- prokaryotic community (1)
- pufM gene (1)
- quantitative food webs (1)
- reactive oxygen species (1)
- regime shift (1)
- respiration stratified lakes (1)
- ribosomal RNA (1)
- rivers (1)
- salinity (1)
- sea plankton community (1)
- seasonal dynamics (1)
- sedimentation (1)
- sediments (1)
- shallow lakes (1)
- shifting baselines (1)
- siberian reservoir (1)
- sinking speed (1)
- soil bacterial diversity (1)
- space-for-time substitution (1)
- spatial variability (1)
- species-specific (1)
- storm (1)
- stress response (1)
- study designs (1)
- sub-inhibitory concentration (1)
- submerged macrophytes (1)
- subtropical convergence zone (1)
- sulfate reduction (1)
- sustainable (1)
- tecdissolved organic nitrogen (1)
- technical note (1)
- temperate zone (1)
- terrestrial subsidies (1)
- terrestrial subsidy (1)
- transcriptome (1)
- trophic status (1)
- trophic transfer efficiency (1)
- turnover (1)
- vertical-distribution (1)
- virulence (1)
- water resources (1)
- wetlands (1)
- zooplankton (1)
- zooplankton carcasses (1)
Institute
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.
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.
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.
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.