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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.
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.
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.
Non-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh C-13-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms, that is, artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, that is, humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but does not interfere with the bacterial turnover of more refractory humic matter.
Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.
Recent discovery of oxic methane production in sea and lake waters, as well as wetlands, demands re-thinking of the global methane cycle and re-assessment of the contribution of oxic waters to atmospheric methane emission. Here we analysed system-wide sources and sinks of surface-water methane in a temperate lake. Using a mass balance analysis, we show that internal methane production in well-oxygenated surface water is an important source for surface-water methane during the stratified period. Combining our results and literature reports, oxic methane contribution to emission follows a predictive function of littoral sediment area and surface mixed layer volume. The contribution of oxic methane source(s) is predicted to increase with lake size, accounting for the majority (>50%) of surface methane emission for lakes with surface areas >1 km(2).
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.
We studied bacterial abundance and community structure of five soil cores using high-throughput sequencing of the 16S rRNA gene. Shifts in the soil bacterial composition were more pronounced within a vertical profile than across the landscape. Soil organic carbon (SOC) and nitrogen (N) concentrations decreased exponentially with soil depth and revealed a buried carbon-rich horizon between 0.8 and 1.3 m across all soil cores. This buried horizon was phylogenetically similar to its surrounding subsoils supporting the idea that the type of carbon, not necessarily the amount of carbon was driving the apparent similarities. In contrast to other studies, Nitrospirae was one of our major phyla with relatively high abundances throughout the soil profile except for the surface soil. Although depth is the major driver shaping soil bacterial community structure, positive correlations with SOC and N concentrations, however, were revealed with the bacterial abundance of Acidobacteria, one of the major, and Gemmatimonadetes, one of the minor phyla in our study. Our study showed that bacterial diversity in soils below 2.0 m can be still as high if not higher than in the above laying subsurface soil suggesting that various bacteria throughout the soil profile influence major biogeochemical processes in floodplain soils.
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.
Marine snow aggregates represent heterogeneous agglomerates of dead and living organic matter. Composition is decisive for their sinking rates, and thereby for carbon flux to the deep sea. For oligotrophic oceans, information on aggregate composition is particularly sparse. To address this, the taxonomic composition of aggregates collected from the subtropical and oligotrophic Sargasso Sea (Atlantic Ocean) was characterized by 16S and 18S rRNA gene sequencing. Taxonomy assignment was aided by a collection of the contemporary plankton community consisting of 75 morphologically and genetically identified plankton specimens. The diverse rRNA gene reads of marine snow aggregates, not considering Trichodesmium puffs, were dominated by copepods (52%), cnidarians (21%), radiolarians (11%), and alveolates (8%), with sporadic contributions by cyanobacteria, suggesting a different aggregate composition than in eutrophic regions. Composition linked significantly with sampling location but not to any measured environmental parameters or plankton biomass composition. Nevertheless, indicator and network analyses identified key roles of a few rare taxa. This points to complex regulation of aggregate composition, conceivably affected by the environment and plankton characteristics. The extent to which this has implications for particle densities, and consequently for sinking rates and carbon sequestration in oligotrophic waters, needs further interrogation.