Evaluating community-environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions

Microeukaryotic plankton communities are keystone components for keeping aquatic primary productivity. Currently, variations in microeukaryotic plankton diversity have often been explained by local ecological factors but not by evolutionary constraints. We used amplicon sequencing of 100 water samples across five years to investigate the ecological preferences of the microeukaryotic plankton community in a subtropical riverine ecosystem. We found that microeukaryotic plankton diversity was less associated with bacterial abundance (16S rRNA gene copy number) than bacterial diversity. Further, environmental effects exhibited a larger influence on microeukaryotic plankton community composition than bacterial community composition, especially at fine taxonomic levels. The evolutionary constraints of microeukaryotic plankton community increased with decreasing taxonomic resolution (from 97% to 91% similarity levels), but not significant change from 85% to 70% similarity levels. However, compared with the bacterial community, the evolutionary constraints were shown to be more affected by environmental variables. This study illustrated possible controlling environmental and bacterial drivers of microeukaryotic diversity and community assembly in a subtropical river, thereby indirectly reflecting on the quality status of the water environment by providing new clues on the microeukaryotic community assembly.

Temperature-mediated microbial carbon utilization in China's lakes

Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes in temperature across large geographic areas. Here, we explored how microbial communities utilized different carbon substrates and the underlying ecological mechanisms along a space-for-time substitution temperature gradient of future climate change. The gradient included 47 lakes from five major lake regions in China spanning a difference of nearly 15°C in mean annual temperatures (MAT). Our results indicated that lakes from warmer regions generally had lower values of variables related to carbon concentrations and greater carbon utilization than those from colder regions. The greater utilization of carbon substrates under higher temperatures could be attributed to changes in bacterial community composition, with a greater abundance of Cyanobacteria and Actinobacteriota and less Proteobacteria in warmer lake regions. We also found that the core species in microbial networks changed with increasing temperature, from Hydrogenophaga and Rhodobacteraceae, which inhibited the utilization of amino acids and carbohydrates, to the CL500-29-marine-group, which promoted the utilization of all almost carbon substrates. Overall, our findings suggest that temperature can mediate aquatic carbon utilization by changing the interactions between bacteria and individual carbon substrates, and the discovery of core species that affect carbon utilization provides insight into potential carbon sequestration within inland water bodies under future climate warming.

Bacterial Community Shifts during Polyp Bail-Out Induction in Pocillopora Corals

Polyp bail-out constitutes both a stress response and an asexual reproductive strategy that potentially facilitates dispersal of some scleractinian corals, including several dominant reef-building taxa in the family Pocilloporidae. Recent studies have proposed that microorganisms may be involved in onset and progression of polyp bail-out. However, changes in the coral microbiome during polyp bail-out have not been investigated. In this study, we induced polyp bail-out in Pocillopora corals using hypersaline and hyperthermal methods. Bacterial community dynamics during bail-out induction were examined using the V5-V6 region of the 16S-rRNA gene. From 70 16S-rRNA gene libraries constructed from coral tissues, 1,980 OTUs were identified. Gammaproteobacteria and Alphaproteobacteria consistently constituted the dominant bacterial taxa in all coral tissue samples. Onset of polyp bail-out was characterized by increased relative abundance of Alphaproteobacteria and decreased abundance of Gammaproteobacteria in both induction experiments, with the shift being more prominent in response to elevated temperature than to elevated salinity. Four OTUs, affiliated with Thalassospira, Marisediminitalea, Rhodobacteraceae, and Myxococcales, showed concurrent abundance increases at the onset of polyp bail-out in both experiments, suggesting potential microbial causes of this coral stress response. IMPORTANCE Polyp bail-out represents both a stress response and an asexual reproductive strategy with significant implications for reshaping tropical coral reefs in response to global climate change. Although earlier studies have suggested that coral-associated microbiomes likely contribute to initiation of polyp bail-out in scleractinian corals, there have been no studies of coral microbiome shifts during polyp bail-out. In this study, we present the first investigation of changes in bacterial symbionts during two experiments in which polyp bail-out was induced by different environmental stressors. These results provide a background of coral microbiome dynamics during polyp bail-out development. Increases in abundance of Thalassospira, Marisediminitalea, Rhodobacteraceae, and Myxococcales that occurred in both experiments suggest that these bacteria are potential microbial causes of polyp bail-out, shedding light on the proximal triggering mechanism of this coral stress response.

Linking niche size and phylogenetic signals to predict future soil microbial relative abundances

Bacteria provide ecosystem services (e.g., biogeochemical cycling) that regulate climate, purify water, and produce food and other commodities, yet their distribution and likely responses to change or intervention are difficult to predict. Using bacterial 16S rRNA gene surveys of 1,381 soil samples from the Biomes of Australian Soil Environment (BASE) dataset, we were able to model relative abundances of soil bacterial taxonomic groups and describe bacterial niche space and optima. Hold out sample validated hypothetical causal networks (structural equation models; SEM) were able to predict the relative abundances of bacterial taxa from environmental data and elucidate soil bacterial niche space. By using explanatory SEM properties as indicators of microbial traits, we successfully predicted soil bacterial response, and in turn potential ecosystem service response, to near-term expected changes in the Australian climate. The methods developed enable prediction of continental-scale changes in bacterial relative abundances, and demonstrate their utility in predicting changes in bacterial function and thereby ecosystem services. These capabilities will be strengthened in the future with growing genome-level data.

Shifts of soil archaeal nitrification and methanogenesis with elevation in water level fluctuation zone of the three Gorges Reservoir, China

The water level fluctuation zone is a unique ecological zone exposed to long-term drying and flooding and plays a critical role in the transport and transformation of carbon and nitrogen materials in reservoir-river systems. Archaea are a vital component of soil ecosystems in the water level fluctuation zones, however, the distribution and function of archaeal communities in responde to long-term wet and dry alternations are still unclear. The community structure of archaea in the drawdown areas at various elevations of the Three Gorges Reservoir was investigated by selecting surface soils (0-5 cm) of different inundation durations at three sites from upstream to downstream according to the flooding pattern. The results revealed that prolonged flooding and drying increased the community diversity of soil archaea, with ammonia-oxidizing archaea being the dominant species in non-flooded regions, while methanogenic archaea were abundant in soils that had been flooded for an extended period of time. Long-term alternation of wetting and drying increases methanogenesis but decreases nitrification. It was determined that soil pH, NO3--N, TOC and TN are significant environmental factors affecting the composition of soil archaeal communities (P = 0.02). Long-term flooding and drying changed the community composition of soil archaea by altering environmental factors, which in turn influenced nitrification and methanogenesis in soils at different elevations. These findings contribute to our understanding of soil carbon and nitrogen transport transformation processes in the water level fluctuation zone as well as the effects of long-term wet and dry alternation on soil carbon and nitrogen cycles. The results of this study can provide a basis for ecological management, environmental management, and long-term operation of reservoirs in water level fluctuation zones.

Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment

Assessments of the ecological health of algal assemblages in streams typically focus on measures of their local diversity and classify individuals by morphotaxonomy. Such assemblages are often connected through various ecological processes, such as dispersal, and may be more accurately assessed as components of regional-, rather than local-scale assemblages. With recent declines in the costs of sequencing and computation, it has also become increasingly feasible to use metabarcoding to more accurately classify algal species and perform regional-scale bioassessments. Recently, zeta diversity has been explored as a novel method of constructing regional bioassessments for groups of streams. Here, we model the use of zeta diversity to investigate whether stream health can be determined by the landscape diversity of algal assemblages. We also compare the use of DNA metabarcoding and morphotaxonomy classifications in these zeta diversity-based bioassessments of regional stream health. From 96 stream samples in California, we used various orders of zeta diversity to construct models of biotic integrity for multiple assemblages of diatoms, as well as hybrid assemblages of diatoms in combination with soft-bodied algae, using taxonomy data generated with both DNA sequencing as well as traditional morphotaxonomic approaches. We compared our ability to evaluate the ecological health of streams with the performance of multiple algal indices of biological condition. Our zeta diversity-based models of regional biotic integrity were more strongly correlated with existing indices for algal assemblages classified using metabarcoding compared to morphotaxonomy. Metabarcoding for diatoms and hybrid algal assemblages involved rbcL and 18S V9 primers, respectively. Importantly, we also found that these algal assemblages, independent of the classification method, are more likely to be assembled under a process of niche differentiation rather than stochastically. Taken together, these results suggest the potential for zeta diversity patterns of algal assemblages classified using metabarcoding to inform stream bioassessments.

Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field

Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species-level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus-level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere) we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere-associated clade. We extended our approach to show that closely related Cercozoa encounter divergent AM fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field-scale is driven by niche-based processes shaped by evolutionary legacy of adaptation to conditions primarily related to soil compartment, followed by soil layer, giving a deeper understanding on the selection pressures that shaped their evolution.

New index of functional specificity to predict the redundancy of ecosystem functions in microbial communities

An ecosystem function is suggested to be more sensitive to biodiversity loss (i.e. low functional redundancy) when focusing on specific-type functions than broad-type functions. Thus far, specific-type functions have been loosely defined as functions performed by a small number of species (facilitative species) or functions involved in utilizing complex substrates. However, quantitative examination of functional specificity remains underexplored. We quantified the functional redundancy of 33 ecosystem functions in a freshwater system from 76 prokaryotic community samples over three years. For each function, we used a sparse regression model to estimate the number of facilitative Amplicon Sequence Variants (ASVs) and to define taxon-based functional specificity. We also used Bertz structural complexity to determine substrate-based functional specificity. We found that functional redundancy increased with the taxon-based functional specificity defined as the proportion of facilitative ASVs ( = facilitative ASV richness/ facilitative ASV richness + repressive ASV (ASVs reducing functioning) richness). When using substrate-based functional specificity, functional redundancy was influenced by Bertz complexity per se and by substrate acquisition mechanisms. Therefore, taxon-based functional specificity is a better predictive index for evaluating functional redundancy than substrate-based functional specificity. These findings provide a framework to quantitatively predict the consequences of diversity losses on ecosystem functioning.

Global taxonomic and phylogenetic assembly of AM fungi

Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly - in particular the roles of dispersal limitation and historical drivers - remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small-subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities - occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil.

The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution

As functional traits are conserved at different phylogenetic depths, the ability to detect community assembly processes can be conditional on the phylogenetic resolution; yet most previous work quantifying their influence has focused on a single level of phylogenetic resolution. Here, we have studied the ecological assembly of bacterial communities from an Antarctic wetland complex, applying null models across different levels of phylogenetic resolution (i.e. clustering ASVs into OTUs with decreasing sequence identity thresholds). We found that the relative influence of the community assembly processes varies with phylogenetic resolution. More specifically, selection processes seem to impose stronger influence at finer (100% sequence similarity ASV) than at coarser (99%–97% sequence similarity OTUs) resolution. We identified environmental features related with the ecological processes and propose a conceptual model for the bacterial community assembly in this Antarctic ecosystem. Briefly, eco‐evolutionary processes appear to be leading to different but very closely related ASVs in lotic, lentic and terrestrial environments. In all, this study shows that assessing community assembly processes at different phylogenetic resolutions is key to improve our understanding of microbial ecology. More importantly, a failure to detect selection processes at coarser phylogenetic resolution does not imply the absence of such processes at finer resolutions.

Abundance-Occupancy Relationships Along Taxonomic Ranks Reveal a Consistency of Niche Differentiation in Marine Bacterioplankton With Distinct Lifestyles

Abundance-occupancy relationships (AORs) are an important determinant of biotic community dynamics and habitat suitability. However, little is known about their role in complex bacterial communities, either within a phylogenetic framework or as a function of niche breadth. Based on data obtained in a field study in the St. Lawrence Estuary, we used 16S rRNA gene sequencing to examine the vertical patterns, strength, and character of AORs for particle-attached and free-living bacterial assemblages. Free-living communities were phylogenetically more diverse than particle-attached communities. The dominant taxa were consistent in terms of their presence/absence but population abundances differed in surface water vs. the cold intermediate layer. Significant, positive AORs characterized all of the surveyed communities across all taxonomic ranks of bacteria, thus demonstrating an ecologically conserved trend for both free-living and particle-attached bacteria. The strength of the AORs was low at the species level but higher at and above the genus level. These results demonstrate that an assessment of the distributions and population densities of finely resolved taxa does not necessarily improve determinations of apparent niche differences in marine bacterioplankton communities at regional scales compared with the information inferred from a broad taxonomic classification.

Inter- and Intra-Annual Bacterioplankton Community Patterns in a Deepwater Sub-Arctic Region: Persistent High Background Abundance of Putative Oil Degraders

Hydrocarbon-degrading bacteria naturally degrade and remove petroleum pollutants, yet baselines do not currently exist for these critical microorganisms in many regions where the oil and gas industry is active. Furthermore, understanding how a baseline community changes across the seasons and its potential to respond to an oil spill event are prerequisites for predicting their response to elevated hydrocarbon exposures. In this study, 16S rRNA gene-based profiling was used to assess the spatiotemporal variability of baseline bacterioplankton community composition in the Faroe-Shetland Channel (FSC), a deepwater sub-Arctic region where the oil and gas industry has been active for the last 40 years. Over a period of 2 years, we captured the diversity of the bacterioplankton community within distinct water masses (defined by their temperature and salinity) that have a distinct geographic origin (Atlantic or Nordic), depth, and direction of flow. We demonstrate that bacterioplankton communities were significantly different across water samples of contrasting origin and depth. Taxa of known hydrocarbon-degrading bacteria were observed at higher-than-anticipated abundances in water masses originating in the Nordic Seas, suggesting these organisms are sustained by an unconfirmed source of oil input in that region. In the event of an oil spill, our results suggest that the response of these organisms is severely hindered by the low temperatures and nutrient levels that are typical for the FSC.IMPORTANCE Oil spills at sea are one of the most disastrous anthropogenic pollution events, with the Deepwater Horizon spill providing a testament to how profoundly the health of marine ecosystems and the livelihood of its coastal inhabitants can be severely impacted by spilled oil. The fate of oil in the environment is largely dictated by the presence and activities of natural communities of oil-degrading bacteria. While a significant effort was made to monitor and track the microbial response and degradation of the oil in the water column in the wake of the Deepwater Horizon spill, the lack of baseline data on the microbiology of the Gulf of Mexico confounded scientists' abilities to provide an accurate assessment of how the system responded relative to prespill conditions. This data gap highlights the need for long-term microbial ocean observatories in regions at high risk of oil spills. Here, we provide the first microbiological baseline established for a subarctic region experiencing high oil and gas industry activity, the northeast Atlantic, but with no apparent oil seepage or spillage. We also explore the presence, relative abundances, and seasonal dynamics of indigenous hydrocarbon-degrading communities. These data will advance the development of models to predict the behavior of such organisms in the event of a major oil spill in this region and potentially impact bioremediation strategies by enhancing the activities of these organisms in breaking down the oil.

Applying the core microbiome to understand host-microbe systems

The host-associated core microbiome was originally coined to refer to common groups of microbes or genes that were likely to be particularly important for host biological function. However, the term has evolved to encompass variable definitions across studies, often identifying key microbes with respect to their spatial distribution, temporal stability or ecological influence, as well as their contribution to host function and fitness. A major barrier to reaching a consensus over how to define the core microbiome and its relevance to biological, ecological and evolutionary theory is a lack of precise terminology and associated definitions, as well the persistent association of the core microbiome with host function. Common, temporal and ecological core microbiomes can together generate insights into ecological processes that act independently of host function, while functional and host-adapted cores distinguish between facultative and near-obligate symbionts that differ in their effects on host fitness. This commentary summarizes five broad definitions of the core microbiome that have been applied across the literature, highlighting their strengths and limitations for advancing our understanding of host-microbe systems, noting where they are likely to overlap, and discussing their potential relevance to host function and fitness. No one definition of the core microbiome is likely to capture the range of key microbes across a host population. Applied together, they have the potential to reveal different layers of microbial organization from which we can begin to understand the ecological and evolutionary processes that govern host-microbe interactions.

Functional and taxonomic biogeography of phytoplankton and zooplankton communities in relation to environmental variation across the contiguous USA

For biomonitoring of aquatic ecosystems, the use of coarse group classifications, either taxonomic or functional, has been proposed as an alternative to more highly resolved taxonomic identification. We tested this proposition for phytoplankton and zooplankton using a pan-United States dataset, which also allows us to investigate biogeographic relationships between plankton groups and environmental variables. We used data from 1010 lakes composing the 2012 US National Lakes Assessment and compared relationships derived using genus-level, more aggregated taxonomic resolution and functional types. We examined responses nationally and by ecoregion. Differences in plankton assemblages among ecoregions were detected, especially at genus-level classification. Our analyses show a gradient of altitude and temperature influencing both phytoplankton and zooplankton, and another gradient of nutrients and anthropogenic activity influencing mostly phytoplankton. The overall variation in the planktonic communities explained by environmental variables ranged from 4 to 22%, but together indicated that aggregated taxonomic classification performed better for phytoplankton; for zooplankton, the performance of different classification types depended on the ecoregion. Our analyses also revealed linkages between particular phytoplankton and zooplankton groups, mainly attributable to similar environmental responses and trophic interactions. Overall, the results support the applicability of coarse classifications to infer general responses of plankton communities to environmental drivers.

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000–2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

Potential Correlation between Dietary Fiber-Suppressed Microbial Conversion of Choline to Trimethylamine and Formation of Methylglyoxal

Dietary interventions alter the formation of the disease-associated metabolite, trimethylamine (TMA), via intestinal microbial TMA lyase activity. Nevertheless, the mechanisms regulating microbial enzyme production are still unclear. Sequencing of the gut bacteria 16S rDNA demonstrated that dietary intervention changed the composition of the gut microbiota and the functional metagenome involved in the choline utilization pathway. Characterization of the functional profile of the metagenomes and metabonomics analysis revealed that a series of Kyoto Encyclopedia of Genes and Genomes orthologous groups and enzyme groups related to accumulation of methylglyoxal (MG) and glycine were enriched in red meat diet-fed animals, whereas fiber-rich diet suppressed glycine formation via the MG-dependent pathway. Our observations suggest associations between choline-TMA lyase expression and MG formation, which are indicative of a novel role of the gut microbiota in choline metabolism and highlight it as a potential target for inhibiting TMA production.

Elevational patterns and hierarchical determinants of biodiversity across microbial taxonomic scales

Microbial biogeography is gaining increasing attention due to recent molecular methodological advance. However, the diversity patterns and their environmental determinants across taxonomic scales are still poorly studied. By sampling along an extensive elevational gradient in subarctic ponds of Finland and Norway, we examined the diversity patterns of aquatic bacteria and fungi from whole community to individual taxa across taxonomic coverage and taxonomic resolutions. We further quantified cross-phylum congruence in multiple biodiversity metrics and evaluated the relative importance of climate, catchment and local pond variables as the hierarchical drivers of biodiversity across taxonomic scales. Bacterial community showed significantly decreasing elevational patterns in species richness and evenness, and U-shaped patterns in local contribution to beta diversity (LCBD). Conversely, no significant species richness and evenness patterns were found for fungal community. Elevational patterns in species richness and LCBD, but not in evenness, were congruent across bacterial phyla. When narrowing down the taxonomic scope towards higher resolutions, bacterial diversity showed weaker and more complex elevational patterns. Taxonomic downscaling also indicated a notable change in the relative importance of biodiversity determinants with stronger local environmental filtering, but decreased importance of climatic variables. This suggested that niche conservatism of temperature preference was phylogenetically deeper than that of water chemistry variables. Our results provide novel perspectives for microbial biogeography and highlight the importance of taxonomic scale dependency and hierarchical drivers when modelling biodiversity and species distribution responses to future climatic scenarios.

A conceptual framework for the phylogenetically constrained assembly of microbial communities

Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs' identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.

Evolutionary constraints on species diversity in marine bacterioplankton communities

Variation in microbial species diversity has typically been explained as the outcome of local ecological factors driving species coexistence, overlooking the roles of evolutionary constraints. Here, we argue that macro-evolutionary niche conservatism and unequal diversification rates among phylum-level lineages are strong determinants of diversity-environment relationships in bacterial systems. That is, apart from stochasticity, environmental effects operate most strongly on phylum composition, which in turn dictates the species diversity of bacterial communities. This concept is demonstrated using bacterioplankton in the surface seawaters of the East China Sea. Furthermore, we show that the species richness of a local bacterioplankton community can generally be estimated based on the relative abundances of phyla and their contributions of species numbers in the global seawater pool-highlighting the important influence of evolutionary constraints on local community diversity.

The effects of contemporary selection and dispersal limitation on the community assembly of acidophilic microalgae

Extremophilic microalgae are primary producers in acidic habitats, such as volcanic sites and acid mine drainages, and play a central role in biogeochemical cycles. Yet, basic knowledge about their species composition and community assembly is lacking. Here, we begin to fill this knowledge gap by performing the first large-scale survey of microalgal diversity in acidic geothermal sites across the West Pacific Island Chain. We collected 72 environmental samples in 12 geothermal sites, measured temperature and pH, and performed rbcL amplicon-based 454 pyrosequencing. Using these data, we estimated the diversity of microalgal species, and then examined the relative contribution of contemporary selection (i.e., local environmental variables) and dispersal limitation on the assembly of these communities. A species delimitation analysis uncovered seven major microalgae (four red, two green, and one diatom) and higher species diversity than previously appreciated. A distance-based redundancy analysis with variation partitioning revealed that dispersal limitation has a greater influence on the community assembly of microalgae than contemporary selection. Consistent with this finding, community similarity among the sampled sites decayed more quickly over geographical distance than differences in environmental factors. Our work paves the way for future studies to understand the ecology and biogeography of microalgae in extreme habitats.

Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient

Global climate and land use change are altering plant and soil microbial communities worldwide, particularly in arctic and alpine biomes where warming is accelerated. The widespread expansion of woody shrubs into historically herbaceous alpine plant zones is likely to interact with climate to affect soil microbial community structure and function; however, our understanding of alpine soil ecology remains limited. This study aimed to (i) determine whether the diversity and community composition of soil fungi vary across elevation gradients and to (ii) assess the impact of woody shrub expansion on these patterns. In the White Mountains of California, sagebrush (Artemisia rothrockii) shrubs have been expanding upwards into alpine areas since 1960. In this study, we combined observational field data with a manipulative shrub removal experiment along an elevation transect of alpine shrub expansion. We utilized next-generation sequencing of the ITS1 region for fungi and joint distribution modelling to tease apart effects of the environment and intracommunity interactions on soil fungi. We found that soil fungal diversity declines and community composition changes with increasing elevation. Both abiotic factors (primarily soil moisture and soil organic C) and woody sagebrush range expansion had significant effects on these patterns. However, fungal diversity and relative abundance had high spatial variation, overwhelming the predictive power of vegetation type, elevation and abiotic soil conditions at the landscape scale. Finally, we observed positive and negative associations among fungal taxa which may be important in structuring community responses to global change.

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing

High-throughput sequencing technology has helped microbial community ecologists explore ecological and evolutionary patterns at unprecedented scales. The benefits of a large sample size still typically outweigh that of greater sequencing depths per sample for accurate estimations of ecological inferences. However, excluding or not sequencing rare taxa may mislead the answers to the questions ‘how and why are communities different?’ This study evaluates the confidence intervals of ecological inferences from high-throughput sequencing data of foliar fungal endophytes as case studies through a range of sampling efforts, sequencing depths, and taxonomic resolutions to understand how technical and analytical practices may affect our interpretations. Increasing sampling size reliably decreased confidence intervals across multiple community comparisons. However, the effects of sequencing depths on confidence intervals depended on how rare taxa influenced the dissimilarity estimates among communities and did not significantly decrease confidence intervals for all community comparisons. A comparison of simulated communities under random drift suggests that sequencing depths are important in estimating dissimilarities between microbial communities under neutral selective processes. Confidence interval analyses reveal important biases as well as biological trends in microbial community studies that otherwise may be ignored when communities are only compared for statistically significant differences.

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve

Invasion by exotic plant species can alter ecosystem function and reduce native plant diversity, but relatively little is known about their effects on belowground microbial communities. Here we investigated the effects of exotic cordgrass (Spartina alterniflora) invasion on the distribution of soil bacterial communities in a mangrove nature reserve of the Jiulong River Estuary, southeast China using high-throughput sequencing of 16S rRNA gene and multivariate statistical analysis. Our results showed that S. alterniflora invasion altered soil properties, and significantly increased soil bacterial taxa richness, primarily by stimulating an increase in conditionally rare or rare taxa, and changes in community composition and function. Abundant, conditionally rare and rare subcommunities exhibited similar response patterns to environment changes, with both conditionally rare and rare taxa showing a stronger response than abundant ones. Habitat generalists were detected among abundant, conditionally rare and rare taxa, whereas habitat specialists were only identified among conditionally rare taxa and rare taxa. In addition, we found that vegetation was the key factor driving these patterns. However, our comparative analysis indicated that both environmental selection, and neutral process, significantly contributed to soil bacterial community assembly. These results could improve the understanding of the microbial processes and mechanisms of cordgrass invasion, and offer empirical data of use in the restoration and management of the mangrove wetlands.

A genomic perspective on stoichiometric regulation of soil carbon cycling

Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5-25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition. Shotgun metagenome data revealed changes in community functions with increasing C turnover, including a shift from aromatic C to carbohydrate utilization accompanied by lower N uptake and P scavenging. Similar patterns of C, N and P acquisition, along with higher ribosomal RNA operon copy numbers, distinguished that microbial taxa positively correlated with C turnover. Considering such tradeoffs in genomic resource allocation patterns among taxa strengthened correlations between microbial community composition and C cycling, suggesting simplified guilds amenable to ecosystem modeling. Our results suggest that patterns of soil C turnover may reflect community-dependent metabolic shifts driven by resource allocation strategies, analogous to growth rate-stoichiometry coupling in animal and plant communities.

Recurrent patterns of microdiversity in a temperate coastal marine environment

Temperate coastal marine environments are replete with complex biotic and abiotic interactions that are amplified during spring and summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond to successional releases of dissolved organic matter as algal cells are lysed. Annual seasonal shifts in the community composition of free-living bacterioplankton follow broadly predictable patterns, but whether similar communities respond each year to bloom disturbance events remains unknown owing to a lack of data sets, employing high-frequency sampling over multiple years. We capture the fine-scale microdiversity of these events with weekly sampling using a high-resolution method to discriminate 16S ribosomal RNA gene amplicons that are >99% identical. Furthermore, we used 2 complete years of data to facilitate identification of recurrent sub-networks of co-varying microbes. We demonstrate that despite inter-annual variation in phytoplankton blooms and despite the dynamism of a coastal–oceanic transition zone, patterns of microdiversity are recurrent during both bloom and non-bloom conditions. Sub-networks of co-occurring microbes identified reveal that correlation structures between community members appear quite stable in a seasonally driven response to oligotrophic and eutrophic conditions.

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

Numerous ecological processes, such as bacteriophage infection and phytoplankton-bacterial interactions, often occur via strain-specific mechanisms. Therefore, studying the causes of microbial dynamics should benefit from highly resolving taxonomic characterizations. We sampled daily to weekly over 5 months following a phytoplankton bloom off Southern California and examined the extent of microdiversity, that is, significant variation within 99% sequence similarity clusters, operational taxonomic units (OTUs), of bacteria, archaea, phytoplankton chloroplasts (all via 16S or intergenic spacer (ITS) sequences) and T4-like-myoviruses (via g23 major capsid protein gene sequence). The extent of microdiversity varied between genes (ITS most, g23 least) and only temporally common taxa were highly microdiverse. Overall, 60% of taxa exhibited microdiversity; 59% of these had subtypes that changed significantly as a proportion of the parent taxon, indicating ecologically distinct taxa. Pairwise correlations between prokaryotes and myoviruses or phytoplankton (for example, highly microdiverse Chrysochromulina sp.) improved when using single-base variants. Correlations between myoviruses and SAR11 increased in number (172 vs 9, Spearman>0.65) and became stronger (0.61 vs 0.58, t-test: P<0.001) when using SAR11 ITS single-base variants vs OTUs. Whole-community correlation between SAR11 and myoviruses was much improved when using ITS single-base variants vs OTUs, with Mantel rho=0.49 vs 0.27; these results are consistent with strain-specific interactions. Mantel correlations suggested >1 μm (attached/large) prokaryotes are a major myovirus source. Consideration of microdiversity improved observation of apparent host and virus networks, and provided insights into the ecological and evolutionary factors influencing the success of lineages, with important implications to ecosystem resilience and microbial function.