Microbial diversity–productivity relationships in aquatic ecosystems

Key role of plankton species and nutrients on biomagnification of PAHs in the micro-food chain: A case study in plateau reservoirs of Guizhou, China

There is considerable inconsistency in results pertaining to the biomagnification of PAHs in aquatic systems. Zooplankton specifically play an important role controlling the fate and distribution of organic contaminants up the food chain, particularly in large plateau reservoirs. However, it remains largely unknown how secondary factors affect the magnification of organic compounds in zooplankton. The present study assessed plankton species and nutrients affecting the trophic transfer of PAHs through the micro-food chain in plateau reservoirs, Guizhou Province China. Results show soluble ∑PAHs range from 99.9 - 147.3 ng L-1, and concentrations of ∑PAHs in zooplankton range from 1003.2 - 22441.3, with a mean of 4460.7 ng g-1 dw. Trophic magnification factors (TMFs) > 1 show biomagnifications of PAHs from phytoplankton to zooplankton. The main mechanisms for trophic magnification > 1 are 1) small Copepoda, Cladocera and Rotifera are prey for larger N. schmackeri and P. tunguidus, and 2) the δ15N and TLs of zooplankton are increasing with the increasing nutrients TN, NO3- and CODMn. As a result, log PAHs concentrations in zooplankton are positively correlated with the trophic levels (TLs) of zooplankton, and log BAFs of the PAHs in zooplankton are increasing with increasing TLs and log Kow. Temperature further enhances TMFs and biomagnifications of PAHs as noted by temperature related reductions in δ15N. There are also available soluble PAHs in the water column which are assimilated with increasing phytoplankton biomass within the taxa groups, diatoms, dinoflagellates and chlorophytes. Notable TMFs of PAHs in zooplankton in Guizhou plateau reservoirs are not significantly affected by phytoplankton and zooplankton biomass dilutions. The present study demonstrates the important roles of species selection, nutrients and temperature in the environmental fate of PAHs in freshwaters.

A circumpolar study of surface zooplankton biodiversity of the Southern Ocean based on eDNA metabarcoding

Under pressure from climate change and fishing, the Southern Ocean ecosystems have been changing. Zooplankton plays a vital role in the food web of the Southern Ocean and is crucial for maintaining ecosystem stability. Investigating the circumpolar-scale species composition and biodiversity of zooplankton is crucial for ensuring ecosystem-based conservation and management of the Southern Ocean in a changing climate. Here, we utilized eDNA metabarcoding to assess the biodiversity of zooplankton in the surface seawater surrounding the Antarctica based on samples collected during two expeditions spanning from 2021 to 2022. The main purpose of this paper is to provide more baseline information about circumpolar zooplankton biodiversity based on the emerging eDNA metabarcoding tool. This comprehensive approach led to the identification of over 300 distinct zooplankton species, forming a diverse community dominated by Jellyfish, Mollusca and Polychaete. Surprisingly, common dominant taxonomic groups such as krill and copepods in the Southern Ocean did not show high relative abundance (reads) in surface seawater. The results of redundancy analysis (RDA) and correlation analysis highlighted that water temperature and chlorophyll a had the most significant impact on the reads and diversity of zooplankton. Notably, the influence of water temperature on zooplankton seemed to be primarily indirect, potentially mediated by its effects on primary productivity. Increasing in primary production might lead to lower zooplankton biodiversity in the Southern Ocean in future. This research underscores the effectiveness of eDNA metabarcoding as a valuable tool for monitoring zooplankton diversity in open seas. Given the ongoing changes in temperature, sea ice extent and their impact on primary production, our findings lay a crucial foundation for using eDNA techniques to establish long-term biodiversity monitoring programs across extensive marine ecosystems in the future.

Environmental forcing of phytoplankton carbon-to-diversity ratio and carbon-to-chlorophyll ratio: A case study in Jiaozhou Bay, the Yellow Sea

The relationships between phytoplankton carbon (C) biomass and diversity (i.e., C-to-H' ratio) and chlorophyll a (i.e., C-to-Chl a ratio) are good indicators of marine ecosystem functioning and stability. Here we conducted four cruises spanning 2 years in Jiaozhou Bay to explore the dynamics of C-to-H' and C-to-Chl a ratios. The results showed that the phytoplankton C biomass and diversity were dominated by diatoms, followed by dinoflagellates. The average C-to-H' ratio ranged from 84.10 to 912.17, with high values occurring in the northern region of the bay. In contrast, the average C-to-Chl a ratio ranged between 15.55 and 89.47, and high values primarily appeared in the northern or northeastern part of the bay. In addition, the redundancy analysis showed that temperature and phosphate (DIP) were significantly correlated with both ratios in most cases, indicating that temperature and DIP may be key factors affecting the dynamics of C-to-H' and C-to-Chl a ratios.

Towards a mechanistic understanding of variation in aquatic food chain length

Ecologists have long sought to understand variation in food chain length (FCL) among natural ecosystems. Various drivers of FCL, including ecosystem size, resource productivity and disturbance, have been hypothesised. However, when results are aggregated across existing empirical studies from aquatic ecosystems, we observe mixed FCL responses to these drivers. To understand this variability, we develop a unified competition-colonisation framework for complex food webs incorporating all of these drivers. With competition-colonisation tradeoffs among basal species, our model predicts that increasing ecosystem size generally results in a monotonic increase in FCL, while FCL displays non-linear, oscillatory responses to resource productivity or disturbance in large ecosystems featuring little disturbance or high productivity. Interestingly, such complex responses mirror patterns in empirical data. Therefore, this study offers a novel mechanistic explanation for observed variations in aquatic FCL driven by multiple environmental factors.

Resource availability governs polyhydroxyalkanoate (PHA) accumulation and diversity of methanotrophic enrichments from wetlands

Aquatic environments account for half of global CH4 emissions, with freshwater wetlands being the most significant contributors. These CH4 fluxes can be partially offset by aerobic CH4 oxidation driven by methanotrophs. Additionally, some methanotrophs can convert CH4 into polyhydroxyalkanoate (PHA), an energy storage molecule as well as a promising bioplastic polymer. In this study, we investigate how PHA-accumulating methanotrophic communities enriched from wetlands were shaped by varying resource availability (i.e., C and N concentrations) at a fixed C/N ratio. Cell yields, PHA accumulation, and community composition were evaluated in high (20% CH4 and 10 mM NH4 +) and low resource (0.2% CH4 and 0.1 mM NH4 +) conditions simulating engineered and environmental settings, respectively. High resource availability decreased C-based cell yields, while N-based cell yields remained stable, suggesting nutrient exchange patterns differed between methanotrophic communities at different resource concentrations. PHA accumulation was only observed in high resource enrichments, producing approximately 12.6% ± 2.4% (m/m) PHA, while PHA in low resource enrichments remained below detection. High resource enrichments were dominated by Methylocystis methanotrophs, while low resource enrichments remained significantly more diverse and contained only a minor population of methanotrophs. This study demonstrates that resource concentration shapes PHA-accumulating methanotrophic communities. Together, this provides useful information to leverage such communities in engineering settings as well as to begin understanding their role in the environment.

Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat

Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.

From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor

Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

BACKGROUND

Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention.

RESULTS

Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality.

CONCLUSIONS

This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition

Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.

Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs

The factors that influence biodiversity and productivity of hydrothermal ecosystems are not well understood. Here we investigate the relationship between fluid mixing, biodiversity, and chemosynthetic primary productivity in three co-localized hot springs (RSW, RSN, and RSE) in Yellowstone National Park that have different geochemistry. All three springs are sourced by reduced hydrothermal fluid, but RSE and RSN receive input of vapour phase gas and oxidized groundwaters, with input of both being substantially higher in RSN. Metagenomic sequencing revealed that communities in RSN were more biodiverse than those of RSE and RSW in all dimensions evaluated. Microcosm activity assays indicate that rates of dissolved inorganic carbon (DIC) uptake were also higher in RSN than in RSE and RSW. Together, these results suggest that increased mixing of reduced volcanic fluid with oxidized fluids generates additional niche space capable of supporting increasingly biodiverse communities that are more productive. These results provide insight into the factors that generate and maintain chemosynthetic biodiversity in hydrothermal systems and that influence the distribution, abundance, and diversity of microbial life in communities supported by chemosynthesis. These factors may also extend to other ecosystems not supported by photosynthesis, including the vast subterranean biosphere and biospheres beneath ice sheets and glaciers.

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer

Mucus-associated bacterial communities are critical for determining disease pathology and promoting colonization resistance. Yet the key ecological properties of mucus resident communities remain poorly defined. Using an approach that combines in situ hybridization, laser microdissection and 16s rRNA sequencing of spatially distinct regions of the mouse gut lumen, we discovered that a dense microbial community resembling a biofilm is embedded in the mucus layer. The mucus-associated biofilm-like community excluded bacteria belonging to phylum Proteobacteria. Additionally, it was significantly more diverse and consisted of bacterial species that were unique to it. By employing germ-free mice deficient in T and B lymphocytes we found that formation of biofilm-like structure was independent of adaptive immunity. Instead the integrity of biofilm-like community depended on Gram-positive commensals such as Clostridia. Additionally, biofilm-like community in the mucus lost fewer Clostridia and showed smaller bloom of Proteobacteria compared to the lumen upon antibiotic treatment. When subjected to time-restricted feeding biofilm-like structure significantly enhanced in size and showed enrichment of Clostridia. Taken together our work discloses that mucus-associated biofilm-like community represents a specialized community that is structurally and compositionally distinct that excludes aerobic bacteria while enriching for anaerobic bacteria such as Clostridia, exhibits enhanced stability to antibiotic treatment and that can be modulated by dietary changes.

Would that it were so simple: Interactions between multiple traits undermine classical single-trait-based predictions of microbial community function and evolution

Understanding how microbial traits affect the evolution and functioning of microbial communities is fundamental for improving the management of harmful microorganisms, while promoting those that are beneficial. Decades of evolutionary ecology research has focused on examining microbial cooperation, diversity, productivity and virulence but with one crucial limitation. The traits under consideration, such as public good production and resistance to antibiotics or predation, are often assumed to act in isolation. Yet, in reality, multiple traits frequently interact, which can lead to unexpected and undesired outcomes for the health of macroorganisms and ecosystem functioning. This is because many predictions generated in a single-trait context aimed at promoting diversity, reducing virulence or controlling antibiotic resistance can fail for systems where multiple traits interact. Here, we provide a much needed discussion and synthesis of the most recent research to reveal the widespread and diverse nature of multi-trait interactions and their consequences for predicting and controlling microbial community dynamics. Importantly, we argue that synthetic microbial communities and multi-trait mathematical models are powerful tools for managing the beneficial and detrimental impacts of microbial communities, such that past mistakes, like those made regarding the stewardship of antimicrobials, are not repeated.

Bacterial communities at a groundwater-surface water ecotone: gradual change or abrupt transition points along a contamination gradient?

Microbial communities contribute greatly to groundwater quality, but the impacts of land-use practices on bacteria in groundwaters and groundwater-dependent ecosystems remain poorly known. With 16S rRNA gene amplicon sequencing, we assessed bacterial community composition at the groundwater-surface water ecotone of boreal springs impacted by urbanization and agriculture, using spring water nitrate-N as a surrogate of contamination. We also measured the rate of a key ecosystem process, organic matter decomposition. We documented a recurrent pattern across all major bacterial phyla where diversity started to decrease at unexpectedly low nitrate-N concentrations (100-300 μg L^-1 ). At 400 NO₃ ^- -N μg L^-1 , 25 bacterial exact sequence variants showed a negative response, resulting in a distinct threshold in bacterial community composition. Chthonomonas, Acetobacterales and Hyphomicrobium were the most sensitive taxa, while only three taxa (Duganella, Undibacterium and Thermoanaerobaculaceae) were enriched due to increased contamination. Decomposition rate responded unimodally to increasing nitrate-N concentration, with a peak rate at ~400 NO₃ ^- -N μg L^-1 , parallelly with a major shift in bacterial community composition. Our results emphasize the utility of bacterial communities in the assessment of groundwater-dependent ecosystems. They also call for a careful reconsideration of threshold nitrate values for defining groundwater ecosystem health and protecting their microbial biodiversity.

Linking soil bacterial diversity to satellite-derived vegetation productivity: a case study in arid and semi-arid desert areas

Increasing studies have begun to focus on biodiversity-productivity relationships for soil microorganisms through molecular ecology methods. However, most of these studies involve controlled experiments, and whether the relationship remains at large spatial scales is still largely unknown. To unravel this issue, archived desert soils from long-term experiments were analysed using high-throughput sequencing, and satellite-derived vegetation datasets were acquired to quantify productivity. Most of the abundant genera were significantly different between low- and high-productivity conditions, and soil bacterial communities were strongly impacted by productivity. Soil bacterial biodiversity, including observed operational taxonomic units and the Chao1, Shannon, and Faith's PD indexes, increased rapidly with productivity at low levels and then reached a relatively stable state, and similar phenomena were observed at multiple taxonomic ranks and for most of the dominant groups. Furthermore, we discovered that the mechanisms resulting in the observed relationship might be ecosystem resource availability in large-scale regions and species competition in local regions. Collectively, these results enhance our understanding of the linkage between belowground microorganisms and aboveground vegetation in arid and semi-arid areas and confirm the potential value of satellite-derived datasets in research on soil microbial diversity at large spatial scales.

Multiple stressors shape invertebrate assemblages and reduce their trophic niche: A case study in a regulated stream

Few studies have addressed how the diversity of basal resources change with stream regulation and the potential consequences on river biota. We sampled invertebrates above and below a series of dams, over two years, at both downwelling and upwelling zones. In each zone, we recorded the daily temperature and flow variations, estimated the algal development, measured the available resources, and analysed carbon and nitrogen stable isotope compositions of the invertebrate community. The number of hydrological pulses were typically higher below the dams than above the dams especially during high-flow periods whereas the groundwater outlets had minor effects on invertebrate assemblages. Invertebrate abundance, richness and diversity tended to decrease below the dams. Co-inertia analysis showed that flow and temperature variations, and eutrophication explained most of the variance in the invertebrate assemblages, which comprised a higher number of resilient taxa below than above the dams. The proportions of pesticide-sensitive invertebrates were lower below the dams and ovoviviparous and more generalist taxa were prominent. We did not observe the expected CPOM decrease and FPOM increase downstream. Accordingly, the proportions of each functional feeding group were remarkably similar above and below the dams despite the long distance between the sectors (>100 kms). The diversity of basal resources used within assemblages progressively increased downstream above dams. In contrast, the diversity of resources used by organisms below the dams decreased from upstream to downstream suggesting a significant influence of flow regulation on aquatic food webs. Finally, the shorter trophic chains for the invertebrate assemblages below the dams suggests that the effects of stream regulation and eutrophication induced a simplification of food webs. To our knowledge, this study is the first to connect taxonomic and functional trait changes in response to multiple stressors with the associated modifications in isotopic niches within aquatic invertebrate assemblages.

CONTEXT

Understanding how stream regulation and associated anthropogenic pressures act on aquatic assemblages and trophic niches is necessary to guide management actions.

GOAL

We aimed to investigate the functional responses (traits and trophic niches) of aquatic invertebrate assemblages to stream regulation and eutrophication.

METHODS

We used univariate and multivariate analyses to compare the invertebrate assemblages above and below the dams and to assess the contributions of hydrology (including groundwater supplies to the river), temperature and eutrophication to the variability in the composition of invertebrate assemblages. We also considered the relative utilization of a selected set of traits describing invertebrate resilience, resistance and specialization to address the potential functional effects of stream regulation on invertebrate assemblages. Finally, carbon and nitrogen isotope analyses allowed us to characterize the length and width of invertebrate assemblage food webs as related to the availability and diversity of basal resources.

RESULTS

Invertebrate abundance and richness generally decreased below the dams, with the highest impacts on insect taxa. Co-inertia analysis showed that stream regulation and eutrophication were main drivers of the aquatic invertebrate assemblages. The analysis separated the sites above and below the dams according to flow and temperature variation, whereas eutrophication appeared as a secondary stressor that separated the sites within each sector. Furthermore, the series of dams resulted in (i) a higher proportion of resilient (e.g., multivoltine) and resistant (ovoviviparous) taxa and a majority of generalists in assemblages below dams, (ii) an impact on the classical dynamics of CPOM (decrease) and FPOM (increase) sources from upstream to downstream, and (iii) a reduction in the diversity of resource use and in the trophic chain length of invertebrate assemblages below dams. The cooler and less oxygenated upwelling zones had lower invertebrate abundance; however, contrary to our expectation, the variation in the groundwater supply did not affect the composition of epigean invertebrate assemblages.

CONCLUSION

This study provides insights about the impacts of flow regime alteration and eutrophication on food webs that may have been caused by regulation of permanent streams. To our knowledge, this is the first to connect taxonomic and functional trait changes in response to multiple stressors with the associated modifications in energy fluxes in aquatic invertebrate assemblages. This study suggests that bed stability, which is associated with a reduction in channel mobility below the dams and with moderate eutrophication, may provide the shelter and resources that can locally favour invertebrate assemblage dynamics and lessen the effects of flow regulation. In addition, the study suggests that the biological trait-based approach and isotope analysis are complementary approaches for addressing ecosystem functioning. The relative utilization of traits indicates the functional potential of aquatic invertebrate assemblages to face multiple stressors whereas isotope analysis is an expression of the actual effect of the stressors on the trophic structure of aquatic invertebrate assemblages.

Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa

The bioavailability of organic matter (OM) to marine heterotrophic bacterioplankton is determined by both the chemical composition of OM and the microbial community composition. In the current study, changes in OM bioavailability were identified at Ocean Station Papa as part of the 2018 Export Processes in the Ocean from Remote Sensing (EXPORTS) field study. Removal rates of carbon (C) in controlled experiments were significantly correlated with the initial composition of total hydrolyzable amino acids, and C removal rates were high when the amino acid degradation index suggested a more labile composition. Carbon remineralization rates averaged 0.19 ± 0.08 μmol C L-1 d-1 over 6-10 days while bacterial growth efficiencies averaged 31 ± 7%. Amino acid composition and tandem mass spectrometry analysis of compound classes also revealed transformations to a more degraded OM composition during experiments. There was a log2-fold increase in the relative abundances of 16S rDNA-resolved bacterioplankton taxa in most experiments by members of the Methylophilaceae family (OM43 genus) and KI89A order. Additionally, when OM was more bioavailable, relative abundances increased by at least threefold for the classes Bacteroidetes (Flavobacteriaceae NS2b genus), Alphaproteobacteria (Rhodobacteraceae Sulfitobacter genus), and Gammaproteobacteria (Alteromonadales and Ectothiorhodospiraceae orders). Our data suggest that a diverse group of bacterioplankton was responsible for removing organic carbon and altering the OM composition to a more degraded state. Elevated community diversity, as inferred from the Shannon-Wiener H index, may have contributed to relatively high growth efficiencies by the bacterioplankton. The data presented here shed light on the interconnections between OM bioavailability and key bacterioplankton taxa for the degradation of marine OM.

Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic

Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N₂) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N₂ fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N₂ fixation and net community production (NCP). Maximum N₂ fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N₂ fixation coastal sites.

Taxonomic Diversity of Pico-/Nanoeukaryotes Is Related to Dissolved Oxygen and Productivity, but Functional Composition Is Shaped by Limiting Nutrients in Eutrophic Coastal Oceans

Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small-sized fractions can be distinguished from microplankton by certain functional and ecological traits. Nevertheless, little information is available regarding patterns of their taxonomic and functional diversity and community composition along environmental gradients in coastal marine ecosystems. In this study, we applied high-throughput sequencing of 18S rRNA gene to assess the taxonomic species richness and community composition of P/NEs in surface waters of Bohai Sea and North Yellow Sea, northern China spanning a 600-km distance during summer and winter of 2011. The richness of operational taxonomic units (OTUs) formed a U-shaped relationship with concentration of chlorophyll a (Chl-a, a proxy of primary productivity), but a stronger, negative relationship with concentration of dissolved oxygen (DO). These two factors also significantly co-varied with the OTU-based community composition of P/NEs. The effect of geographic distance on community composition of P/NEs was negligible. Among the three functional groups defined by trophic traits, heterotrophs had the highest OTU richness, which exhibited a U-shaped relationship with both DO and Chl-a. The community of P/NEs was dominated by heterotrophs and mixotrophs in terms of read numbers, which showed a trade-off along the gradient of phosphate, but no significant changes along DO and Chl-a gradients, indicating functional redundancy. Similarly, the proportion of phototrophs was significantly and positively correlated with the concentration of silicate. Our results indicate that taxonomic and functional composition of P/NEs are decoupled on a regional scale, and limiting nutrients are important factors in modulating functional composition of these microorganisms in the studied area. These findings contribute toward gaining a better understanding of how diversity of small eukaryotes and their functions are structured in coastal oceans and the effect of environmental changes on the structuring process.

Linkage Between Dissolved Organic Matter Transformation, Bacterial Carbon Production, and Diversity in a Shallow Oligotrophic Aquifer: Results From Flow-Through Sediment Microcosm Experiments

Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L⁻¹_sed d⁻¹, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L⁻¹_sed d⁻¹]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L⁻¹_sed d⁻¹ and 14.3(±3.5) μgC L⁻¹_sed d⁻¹, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.

Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

Microbial communities feature an immense diversity of species and this diversity is linked to outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple resource-competition models don't allow for coexistence of a large number of species, it was recently shown that metabolic trade-offs can allow unlimited diversity. Does this diversity persist with more realistic, intermittent nutrient supply? Here, we demonstrate theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity. When a small amount of nutrient is supplied to each batch, the serial dilution dynamics mimic a chemostat-like steady state. If more nutrient is supplied, community diversity shifts due to an 'early-bird' effect. The interplay of this effect with different environmental factors and diversity-supporting mechanisms leads to a variety of relationships between nutrient supply and diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship.

Global Trends in Marine Plankton Diversity across Kingdoms of Life

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21^st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation.

Video Abstract

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Most epipelagic planktonic groups exhibit a poleward decline of diversity

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No latitudinal diversity gradient was observed below the photic zone

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Temperature emerges as the best predictor of epipelagic plankton diversity

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Global warming may increase plankton diversity, particularly at high latitudes

Community biofilm-formation, stratification and productivity in serially-transferred microcosms

The establishment of O2 gradients in liquid columns by bacterial metabolic activity produces a spatially-structured environment. This produces a high-O2 region at the top that represents an un-occupied niche which could be colonised by biofilm-competent strains. We have used this to develop an experimental model system using soil-wash inocula and a serial-transfer approach to investigate changes in community-based biofilm-formation and productivity. This involved 10 transfers of mixed-community or biofilm-only samples over a total of 10-60 days incubation. In all final-transfer communities the ability to form biofilms was retained, though in longer incubations the build-up of toxic metabolites limited productivity. Measurements of microcosm productivity, biofilm-strength and attachment levels were used to assess community-aggregated traits which showed changes at both the community and individual-strain levels. Final-transfer communities were stratified with strains demonstrating a plastic phenotype when migrating between the high and low-O2 regions. The majority of community productivity came from the O2-depleted region rather than the top of the liquid column. This model system illustrates the complexity we expect to see in natural biofilm-forming communities. The connection between biofilms and the liquid column seen here has important implications for how these structures form and respond to selective pressure.

Ecological assessment of groundwater ecosystems disturbed by recharge systems using organic matter quality, biofilm characteristics, and bacterial diversity

Recharge of aquifers by urban stormwater may trigger significant ecological changes that can be detrimental to the biodiversity and functioning of groundwater ecosystems. Here, the effects of aquifer recharge (AR) on three levels of parameters were investigated: dissolved organic carbon (DOC) quantity and quality, global biofilm characteristics, and diversity changes of bacterial communities. As DOC enrichment by AR can be mitigated by vadose zone (VZ) thickness, three AR sites with thin VZ (< 3 m) and three sites with thick VZ (> 10 m) were selected. For each AR site, clay beads were incubated over a 10-day-long rainy period through wells in recharged and non-recharged groundwaters. Total proteins, dehydrogenase, and hydrolytic activities were monitored from clay beads to assess biofilm development. Bacterial richness on beads was estimated by 16S rRNA-based metabarcoding. AR was found to significantly increase DOC and biodegradable DOC (BDOC) concentrations, biofilm development, and bacterial richness especially in sites with thin VZ. VZ thickness was inversely related to microbial growth indicators and bacterial richness in groundwater, through a control of DOC availability. The proportion of Bacteroidetes 16S rRNA gene reads was higher in recharged groundwater than in non-recharged groundwater, suggesting that this phylum could be used as an indicator of DOC enrichment associated with AR. Quantitative PCR assays for Bacteroides DNA confirmed these trends and showed an enrichment of this bacterial group in DOC-rich aquifer waters. The positive linear relationships between BDOC concentrations and biofilm variables highlighted a strong C-limitation of groundwater impacting bacterial species sorting and activity.

Resource heterogeneity structures aquatic bacterial communities

Microorganisms are strongly influenced by the bottom-up effects of resource supply. While many species respond to fluctuations in the concentration of resources, microbial diversity may also be affected by the heterogeneity of the resource pool, which often reflects a mixture of distinct molecules. To test this hypothesis, we examined resource-diversity relationships for bacterioplankton in a set of north temperate lakes that varied in their concentration and composition of dissolved organic matter (DOM), which is an important resource for heterotrophic bacteria. Using 16S rRNA transcript sequencing and ecosystem metabolomics, we documented strong relationships between bacterial alpha-diversity (richness and evenness) and the bulk concentration and the number of molecules in the DOM pool. Similarly, bacterial community beta-diversity was related to both DOM concentration and composition. However, in some lakes the relative abundance of resource generalists, which was inversely related to the DOM concentration, may have reduced the effect of DOM heterogeneity on community composition. Together, our results demonstrate the potential metabolic interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.

Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota

Nutrient supply to ecosystems has major effects on ecological diversity, but it is unclear to what degree the shape of this relationship is general versus dependent on the specific environment or community. Although the diet composition in terms of the source or proportions of different nutrient types is known to affect gut microbiota composition, the relationship between the quantity of nutrients supplied and the abundance and diversity of the intestinal microbial community remains to be elucidated. Here, we address this relationship using replicate populations of Drosophila melanogaster maintained over multiple generations on three diets differing in the concentration of yeast (the only source of most nutrients). While a 6.5-fold increase in yeast concentration led to a 100-fold increase in the total abundance of gut microbes, it caused a major decrease in their alpha diversity (by 45-60% depending on the diversity measure). This was accompanied by only minor shifts in the taxonomic affiliation of the most common operational taxonomic units (OTUs). Thus, nutrient concentration in host diet mediates a strong negative relationship between the nutrient abundance and microbial diversity in the Drosophila gut ecosystem.

Simple models combining competition, defence and resource availability have broad implications in pelagic microbial food webs

In food webs, interactions between competition and defence control the partitioning of limiting resources. As a result, simple models of these interactions contain links between biogeochemistry, diversity, food web structure and ecosystem function. Working at hierarchical levels, these mechanisms also produce self-similarity and therefore suggest how complexity can be generated from repeated application of simple underlying principles. Reviewing theoretical and experimental literature relevant to the marine photic zone, we argue that there is a wide spectrum of phenomena, including single cell activity of prokaryotes, microbial biodiversity at different levels of resolution, ecosystem functioning, regional biogeochemical features and evolution at different timescales; that all can be understood as variations over a common principle, summarised in what has been termed the 'Killing-the-Winner' (KtW) motif. Considering food webs as assemblages of such motifs may thus allow for a more integrated approach to aquatic microbial ecology.

Trade-off shapes diversity in eco-evolutionary dynamics

We introduce an Interaction- and Trade-off-based Eco-Evolutionary Model (ITEEM), in which species are competing in a well-mixed system, and their evolution in interaction trait space is subject to a life-history trade-off between replication rate and competitive ability. We demonstrate that the shape of the trade-off has a fundamental impact on eco-evolutionary dynamics, as it imposes four phases of diversity, including a sharp phase transition. Despite its minimalism, ITEEM produces a remarkable range of patterns of eco-evolutionary dynamics that are observed in experimental and natural systems. Most notably we find self-organization towards structured communities with high and sustained diversity, in which competing species form interaction cycles similar to rock-paper-scissors games.

Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: (i) How does species diversity relate to the rates of primary and heterotrophic productivity? (ii) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon-based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope tracers that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C-labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose or acetate, respectively. The bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, from energy constraints imposed by changing irradiance over a diel cycle.

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil

The enrichment of H₂-oxidizing bacteria (HOB) by H₂ generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H₂, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H₂ mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H₂ exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H₂ while enhancing community level carbon substrate utilization potential and lowering CH₄ uptake activity in soil. We found that H₂ triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H₂ exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H₂ on soil microbial communities will lead to a better understanding of the H₂ fertilization effect and soil biogeochemical processes.IMPORTANCE An innovative dynamic microcosm chamber system was used to demonstrate that H₂ diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH₄ oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H₂ rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB.

The effect of top-predator presence and phenotype on aquatic microbial communities

The presence of predators can impact a variety of organisms within the ecosystem, including microorganisms. Because the effects of fish predators and their phenotypic differences on microbial communities have not received much attention, we tested how the presence/absence, genotype, and plasticity of the predatory three‐spine stickleback (Gasterosteus aculeatus) influence aquatic microbes in outdoor mesocosms. We reared lake and stream stickleback genotypes on contrasting food resources to adulthood, and then added them to aquatic mesocosm ecosystems to assess their impact on the planktonic bacterial community. We also investigated whether the effects of fish persisted following the removal of adults, and the subsequent addition of a homogenous juvenile fish population. The presence of adult stickleback increased the number of bacterial OTUs and altered the size structure of the microbial community, whereas their phenotype affected bacterial community composition. Some of these effects were detectable after adult fish were removed from the mesocosms, and after juvenile fish were placed in the tanks, most of these effects disappeared. Our results suggest that fish can have strong short‐term effects on microbial communities that are partially mediated by phenotypic variation of fish.

Patterns and multi-scale drivers of phytoplankton species richness in temperate peri-urban lakes

Local species richness (SR) is a key characteristic affecting ecosystem functioning. Yet, the mechanisms regulating phytoplankton diversity in freshwater ecosystems are not fully understood, especially in peri-urban environments where anthropogenic pressures strongly impact the quality of aquatic ecosystems. To address this issue, we sampled the phytoplankton communities of 50 lakes in the Paris area (France) characterized by a large gradient of physico-chemical and catchment-scale characteristics. We used large phytoplankton datasets to describe phytoplankton diversity patterns and applied a machine-learning algorithm to test the degree to which species richness patterns are potentially controlled by environmental factors. Selected environmental factors were studied at two scales: the lake-scale (e.g. nutrients concentrations, water temperature, lake depth) and the catchment-scale (e.g. catchment, landscape and climate variables). Then, we used a variance partitioning approach to evaluate the interaction between lake-scale and catchment-scale variables in explaining local species richness. Finally, we analysed the residuals of predictive models to identify potential vectors of improvement of phytoplankton species richness predictive models. Lake-scale and catchment-scale drivers provided similar predictive accuracy of local species richness (R(2)=0.458 and 0.424, respectively). Both models suggested that seasonal temperature variations and nutrient supply strongly modulate local species richness. Integrating lake- and catchment-scale predictors in a single predictive model did not provide increased predictive accuracy; therefore suggesting that the catchment-scale model probably explains observed species richness variations through the impact of catchment-scale variables on in-lake water quality characteristics. Models based on catchment characteristics, which include simple and easy to obtain variables, provide a meaningful way of predicting phytoplankton species richness in temperate lakes. This approach may prove useful and cost-effective for the management and conservation of aquatic ecosystems.

A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan

Water quality is impacted significantly by urbanization. The delivery of increased nutrient loads to waterways is a primary characteristic of this land use change. Despite the recognized effects of nutrient loading on aquatic systems, the influence of urbanization on the bacterial community composition of these systems is not understood. We used massively-parallel sequencing of bacterial 16S rRNA genes to examine the bacterial assemblages in transect samples spanning the heavily urbanized estuary of Milwaukee, WI to the relatively un-impacted waters of Lake Michigan. With this approach, we found that genera and lineages common to freshwater lake epilimnia were common and abundant in both the high nutrient, urban-impacted waterways, and the low nutrient Lake Michigan. Although the two environments harbored many taxa in common, we identified a significant change in the community assemblage across the urban-influence gradient, and three distinct community features drove this change. First, we found the urban-influenced waterways harbored significantly greater bacterial richness and diversity than Lake Michigan (i.e., taxa augmentation). Second, we identified a shift in the relative abundance among common freshwater lineages, where acI, acTH1, Algoriphagus and LD12, had decreased representation and Limnohabitans, Polynucleobacter, and Rhodobacter had increased representation in the urban estuary. Third, by oligotyping 18 common freshwater genera/lineages, we found that oligotypes (highly resolved sequence clusters) within many of these genera/lineages had opposite preferences for the two environments. With these data, we suggest many of the defined cosmopolitan freshwater genera/lineages contain both oligotroph and more copiotroph species or populations, promoting the idea that within-genus lifestyle specialization, in addition to shifts in the dominance among core taxa and taxa augmentation, drive bacterial community change in urbanized waters.

Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions

To test whether protist grazing selectively affects the composition of aquatic bacterial communities, we combined high-throughput sequencing to determine bacterial community composition with analyses of grazing rates, protist and bacterial abundances and bacterial cell sizes and physiological states in a mesocosm experiment in which nutrients were added to stimulate a phytoplankton bloom. A large variability was observed in the abundances of bacteria (from 0.7 to 2.4 × 10(6) cells per ml), heterotrophic nanoflagellates (from 0.063 to 2.7 × 10(4) cells per ml) and ciliates (from 100 to 3000 cells per l) during the experiment (∼3-, 45- and 30-fold, respectively), as well as in bulk grazing rates (from 1 to 13 × 10(6) bacteria per ml per day) and bacterial production (from 3 to 379 μg per C l per day) (1 and 2 orders of magnitude, respectively). However, these strong changes in predation pressure did not induce comparable responses in bacterial community composition, indicating that bacterial community structure was resilient to changes in protist predation pressure. Overall, our results indicate that peaks in protist predation (at least those associated with phytoplankton blooms) do not necessarily trigger substantial changes in the composition of coastal marine bacterioplankton communities.

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors.

Oceanographic structure drives the assembly processes of microbial eukaryotic communities

Arctic Ocean microbial eukaryote phytoplankton form subsurface chlorophyll maximum (SCM), where much of the annual summer production occurs. This SCM is particularly persistent in the Western Arctic Ocean, which is strongly salinity stratified. The recent loss of multiyear sea ice and increased particulate-rich river discharge in the Arctic Ocean results in a greater volume of fresher water that may displace nutrient-rich saltier waters to deeper depths and decrease light penetration in areas affected by river discharge. Here, we surveyed microbial eukaryotic assemblages in the surface waters, and within and below the SCM. In most samples, we detected the pronounced SCM that usually occurs at the interface of the upper mixed layer and Pacific Summer Water (PSW). Poorly developed SCM was seen under two conditions, one above PSW and associated with a downwelling eddy, and the second in a region influenced by the Mackenzie River plume. Four phylogenetically distinct communities were identified: surface, pronounced SCM, weak SCM and a deeper community just below the SCM. Distance-decay relationships and phylogenetic structure suggested distinct ecological processes operating within these communities. In the pronounced SCM, picophytoplanktons were prevalent and community assembly was attributed to water mass history. In contrast, environmental filtering impacted the composition of the weak SCM communities, where heterotrophic Picozoa were more numerous. These results imply that displacement of Pacific waters to greater depth and increased terrigenous input may act as a control on SCM development and result in lower net summer primary production with a more heterotroph dominated eukaryotic microbial community.

Preliminary evidence for the organisation of a bacterial community by zooplanktivores at the top of an estuarine planktonic food web

As part of a larger investigation, the effect of apex predation on estuarine bacterial community structure, through trophic cascading, was investigated using experimental in situ mesocosms. Through either the removal (filtration) or addition of specific size classes of planktonic groups, four different trophic scenarios were established using estuarine water and its associated plankton. One such treatment represented a "natural" scenario in which stable apex predatory pressure was qualified. Water samples were collected over time from each of the treatments for bacterial community evaluation. These samples were assessed through pyrosequencing of the variable regions 4 and 5 of the bacterial 16S rRNA gene and analysed at the species operational taxonomic unit (OTU) level using a community procedure. The blue-green group dominated the samples, followed by Proteobacteria and Bacteroidetes. Samples were the most similar among treatments at the commencement of the experiment. While the bacterial communities sampled within each treatment changed over time, the deviation from initial appeared to be linked to the treatment trophic scenarios. The least temporal deviation-from-initial in bacterial community was found within the stable apex predatory pressure treatment. These findings are consistent with trophic cascade theory, whereby predators mediate interactions at multiple lower trophic levels with consequent repercussions for diversity.

Bacterial community structure in patagonian Andean Lakes above and below timberline: from community composition to community function

Lakes located above the timberline are remote systems with a number of extreme environmental conditions, becoming physically harsh ecosystems, and sensors of global change. We analyze bacterial community composition and community-level physiological profiles in mountain lakes located in an altitude gradient in North Patagonian Andes below and above the timberline, together with dissolved organic carbon (DOC) characterization and consumption. Our results indicated a decrease in 71 % of DOC and 65 % in total dissolved phosphorus (TDP) concentration as well as in bacteria abundances along the altitude range (1,380 to 1,950 m a.s.l.). Dissolved organic matter (DOM) fluorescence analysis revealed a low global variability composed by two humic-like components (allochthonous substances) and a single protein-like component (autochthonous substances). Lakes below the timberline showed the presence of all the three components, while lakes above the timberline the protein-like compound constituted the main DOC component. Furthermore, bacterial community composition similarity and ordination analysis showed that altitude and resource concentration (DOC and TDP) were the main variables determining the ordination of groups. Community-level physiological profiles showed a mismatch with bacteria community composition (BCC), indicating the absence of a relationship between genetic and functional diversity in the altitude gradient. However, carbon utilization efficiencies varied according to the presence of different compounds in DOM bulk. The obtained results suggest that the different bacterial communities in these mountain lakes seem to have similar metabolic pathways in order to be able to exploit the available DOC molecules.

Global relationship between phytoplankton diversity and productivity in the ocean

The shape of the productivity-diversity relationship (PDR) for marine phytoplankton has been suggested to be unimodal, that is, diversity peaking at intermediate levels of productivity. However, there are few observations and there has been little attempt to understand the mechanisms that would lead to such a shape for planktonic organisms. Here we use a marine ecosystem model together with the community assembly theory to explain the shape of the unimodal PDR we obtain at the global scale. The positive slope from low to intermediate productivity is due to grazer control with selective feeding, which leads to the predator-mediated coexistence of prey. The negative slope at high productivity is due to seasonal blooms of opportunist species that occur before they are regulated by grazers. The negative side is only unveiled when the temporal scale of the observation captures the transient dynamics, which are especially relevant at highly seasonal latitudes. Thus selective predation explains the positive side while transient competitive exclusion explains the negative side of the unimodal PDR curve. The phytoplankton community composition of the positive and negative sides is mostly dominated by slow-growing nutrient specialists and fast-growing nutrient opportunist species, respectively.

Resource availability and spatial heterogeneity control bacterial community response to nutrient enrichment in lakes

The diversity and composition of ecological communities often co-vary with ecosystem productivity. However, the relative importance of productivity, or resource abundance, versus the spatial distribution of resources in shaping those ecological patterns is not well understood, particularly for the bacterial communities that underlie most important ecosystem functions. Increasing ecosystem productivity in lakes has been shown to influence the composition and ecology of bacterial communities, but existing work has only evaluated the effect of increasing resource supply and not heterogeneity in how those resources are distributed. We quantified how bacterial communities varied with the trophic status of lakes and whether community responses differed in surface and deep habitats in response to heterogeneity in nutrient resources. Using ARISA fingerprinting, we found that bacterial communities were more abundant, richer, and more distinct among habitats as lake trophic state and vertical heterogeneity in nutrients increased, and that spatial resource variation produced habitat specific responses of bacteria in response to increased productivity. Furthermore, changes in communities in high nutrient lakes were not produced by turnover in community composition but from additional taxa augmenting core bacterial communities found in lower productivity lakes. These data suggests that bacterial community responses to nutrient enrichment in lakes vary spatially and are likely influenced disproportionately by rare taxa.

Response of bacterioplankton to a glucose gradient in the absence of lysis and grazing

Bacterial utilization of dissolved organic matter plays an important role in marine carbon cycling. In this study, the response of bacterioplankton to a gradient of carbon (glucose) addition was investigated experimentally in a subtropical coastal environment in the absence of top-down control by viruses and flagellates. Bacterial abundance and production were stimulated by glucose addition corresponding to a gradient of glucose. Differences in the extent of stimulation suggested different bacterial life strategies under different nutrient conditions. Bacterial community diversity as revealed by denaturing gradient gel electrophoresis (DGGE) showed a unimodal productivity-diversity (number of DGGE bands) relationship after 3-day incubation. DNA fingerprinting profiling and cluster analysis showed clear and gradual changes in bacterial community structure along the gradient of glucose concentrations, reflecting the competition for carbon supply among bacterial groups. Sequencing analysis of the DGGE bands disclosed the relative abundance of seven bacterial genotypes in the Alteromonadaceae and Roseovarius that gradually decreased with the glucose enrichment while two Vibrio genotypes showed the reverse increasing trend. This suggested that Vibrio was a more successful opportunist at high carbon availability.

Mechanisms determining the fate of dispersed bacterial communities in new environments

Recent work has shown that dispersal has an important role in shaping microbial communities. However, little is known about how dispersed bacteria cope with new environmental conditions and how they compete with local resident communities. To test this, we implemented two full-factorial transplant experiments with bacterial communities originating from two sources (freshwater or saline water), which were incubated, separately or in mixes, under both environmental conditions. Thus, we were able to separately test for the effects of the new environment with and without interactions with local communities. We determined community composition using 454-pyrosequencing of bacterial 16S rRNA to specifically target the active fraction of the communities, and measured several functional parameters. In absence of a local resident community, the net functional response was mainly affected by the environmental conditions, suggesting successful functional adaptation to the new environmental conditions. Community composition was influenced both by the source and the incubation environment, suggesting simultaneous effects of species sorting and functional plasticity. In presence of a local resident community, functional parameters were higher compared with those expected from proportional mixes of the unmixed communities in three out of four cases. This was accompanied by an increase in the relative abundance of generalists, suggesting that competitive interactions among local and immigrant taxa could explain the observed 'functional overachievement'. In summary, our results suggest that environmental filtering, functional plasticity and competition are all important mechanisms influencing the fate of dispersed communities.

Ecological effects on gut bacterial communities in wild bumblebee colonies

1. Animal hosts harbour diverse and often specific bacterial communities (microbiota) in their gut. These microbiota can provide crucial services to the host such as aiding in digestion of food and immune defence. However, the ecological factors correlating with and eventually shaping these microbiota under natural conditions are poorly understood. 2. Bumblebees have recently been shown to possess simple and highly specific microbiota. We here examine the dynamics of these microbiota in field colonies of the bumblebee Bombus terrestris over one season. The gut bacteria were assessed with culture-independent methods, that is, with terminal restriction fragment length profiles of the 16S rRNA gene. 3. To further understand the factors that affect the microbiota, we experimentally manipulated field-placed colonies in a fully factorial experiment by providing additional food or by priming the workers' immune system by injecting heat-killed bacteria. We furthermore looked at possible correlates of diversity and composition of the microbiota for (i) natural infections with the microbial parasites Crithidia bombi and Nosema bombi, (ii) bumblebee worker size, (iii) colony identity, and (iv) colony age. 4. We found an increase in diversity of the microbiota in individuals naturally infected with either C. bombi or N. bombi. Crithidia bombi infections, however, appear to be only indirectly linked with higher microbial diversity when comparing colonies. The treatments of priming the immune system with heat-killed bacteria and additional food supply, as well as host body size, had no effect on the diversity or composition of the microbiota. Host colony identity had only a weak effect on the composition of the microbiota at the level of resolution of our method. We found both significant increases and decreases in the relative abundance of selected bacterial taxa over the season. 5. We present the first study on the ecological dynamics of gut microbiota in bumblebees and identify parasite infections, colony identity and colony age as important factors influencing the diversity and composition of the bacterial communities. The absence of an effect of our otherwise effective experimental treatments suggests a remarkable ability of the host to maintain a homoeostasis in this community under widely different environments.