Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

Soil communities are intricately linked to ecosystem functioning, and a predictive understanding of how communities assemble in response to environmental change is of great ecological importance. Little is known about the assembly processes governing abundant and rare fungal communities across agro‐ecosystems, particularly with regard to their environmental adaptation. By considering abundant and rare taxa, we tested the environmental thresholds and phylogenetic signals for ecological preferences of fungal communities across complex environmental gradients to reflect their environmental adaptation, and explored the factors influencing their assembly based on the large‐scale soil survey in agricultural fields across eastern China. We found that the abundant taxa exhibited remarkably broader response thresholds and stronger phylogenetic signals for the ecological preferences across environmental gradients compared to the rare taxa. Neutral processes played a key role in shaping the abundant subcommunity compared to the rare subcommunity. Null model analysis revealed that the abundant subcommunity was less clustered phylogenetically and governed primarily by dispersal limitation, while homogeneous selection was the major assembly process in the rare subcommunity. Soil available sulfur was the major factor mediating the balance between stochastic and deterministic processes of both the abundant and rare subcommunities, as indicated by an increase in stochasticity with higher available sulfur concentration. Based on macroecological spatial scale datasets, our study revealed the potential broader environmental adaptation of abundant fungal taxa compared to rare fungal taxa, and identified the factors mediating their distinct community assembly processes in agricultural fields. These results contribute to our understanding of the mechanisms underlying the generation and maintenance of fungal diversity in response to global environmental change.     

Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis

In completely insular microbial communities, evolution of community structure cannot be shaped by the immigration of new members. In addition, when those communities are run in steady state, the influence of environmental factors on their assembly is reduced. Therefore, one would expect similar community structures under steady-state conditions. Yet, in parallel setups, variability does occur. To reveal ecological mechanisms behind this phenomenon, five parallel reactors were studied at the single-cell level for about 100 generations and community structure variations were quantified by ecological measures. Whether community variability can be controlled was tested by implementing soft temperature stressors as potential synchronizers. The low slope of the lognormal rank-order abundance curves indicated a predominance of neutral mechanisms, i.e., where species identity plays no role. Variations in abundance ranks of subcommunities and increase in inter-community pairwise β-diversity over time support this. Niche differentiation was also observed, as indicated by steeper geometric-like rank-order abundance curves and increased numbers of correlations between abiotic and biotic parameters during initial adaptation and after disturbances. Still, neutral forces dominated community assembly. Our findings suggest that complex microbial communities in insular steady-state environments can be difficult to synchronize and maintained in their original or desired structure, as they are non-equilibrium systems.     

Biogeography and ecological diversity patterns of rare and abundant bacteria in oil‐contaminated soils

Revealing the biogeographies and ecologies of rare and abundant microorganisms is crucial to understand ecosystem diversity and function. In this study, we investigated the biogeographic assemblies and ecological diversity patterns of rare and abundant bacteria in long‐term oil‐contaminated soils at intervals of 46–360 km by performing high‐throughput sequencing of 16S rRNA genes. The results clearly revealed distinct distribution patterns for rare and abundant bacteria in soil samples. Rare taxa were unevenly distributed; however, abundant taxa were ubiquitous across all samples. Both rare and abundant subcommunities showed significant distance–decay relationships, and their assemblies were driven by different factors. The rare subcommunity primarily exhibited a spatially structured distribution (i.e., stochastic processes), while edaphic factors (i.e., deterministic processes) largely contributed to the structure of the abundant subcommunity. A network analysis revealed closer relationships between abundant bacteria and their heightened influence on other co‐occurrences in the community compared with rare species. In conclusion, rare microbial taxa may play potential roles in maintaining ecosystem diversity, although they do not appear to be central to microbial networks. Abundant microbes are vital for microbial co‐occurrences in oil‐contaminated soils, and high relative abundance and ubiquitous distribution suggest potential roles in the degradation of organic pollutants.     

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance–decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance–decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems.     

Microbiome subcommunity learning with logistic-tree normal latent Dirichlet allocation

Mixed-membership (MM) models such as latent Dirichlet allocation (LDA) have been applied to microbiome compositional data to identify latent subcommunities of microbial species. These subcommunities are informative for understanding the biological interplay of microbes and for predicting health outcomes. However, microbiome compositions typically display substantial cross-sample heterogeneities in subcommunity compositions—that is, the variability in the proportions of microbes in shared subcommunities across samples—which is not accounted for in prior analyses. As a result, LDA can produce inference, which is highly sensitive to the specification of the number of subcommunities and often divides a single subcommunity into multiple artificial ones. To address this limitation, we incorporate the logistic-tree normal (LTN) model into LDA to form a new MM model. This model allows cross-sample variation in the composition of each subcommunity around some “centroid” composition that defines the subcommunity. Incorporation of auxiliary Pólya-Gamma variables enables a computationally efficient collapsed blocked Gibbs sampler to carry out Bayesian inference under this model. By accounting for such heterogeneity, our new model restores the robustness of the inference in the specification of the number of subcommunities and allows meaningful subcommunities to be identified.     

How habitat heterogeneity shapes bacterial and protistan communities in temperate coastal areas near estuaries

In this study, we investigated microbial communities (bacteria and protist) in two coastal areas near the estuaries of the Liaohe (LH) River and Yalujiang (YLJ) River in the Northwestern Pacific Ocean. Due to the existence of Liaodong Peninsula and different levels of urbanization, geographical segregation and significant environmental heterogeneity were observed between these two areas. There were significantly different regional species pools and biogeographic patterns for both bacterial and protistan communities between LH and YLJ coastal areas. Species turnover was the main mechanism driving β-diversity patterns of both bacterial and protistan communities in each area. In addition, the contributed ratio of nestedness to the β-diversity patterns was significantly higher for protists compared to bacteria. Variation in regional species pools was found to be the dominant driver of differences of bacterial and protistan communities between the LH and YLJ coastal areas. For a single-studied area, local community assembly mechanisms, including heterogeneous selection and dispersal limitation, were found to shape the bacterial and protistan communities through calculation of the β-deviation index. Among them, the relative importance of heterogeneous selection and dispersal limitation on the community assembly varied according to microorganism type and habitat.     

Low functional β-diversity despite high taxonomic β-diversity among tropical estuarine fish communities

The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules.     

Patterns of phylogenetic beta diversity in China's grasslands in relation to geographical and environmental distance

Patterns and determinants of beta (β-) diversity can be used to explore the underlying mechanisms regulating community assembly. Despite being the most commonly used measure of β-diversity, species turnover does not consider the evolutionary differences among species, treating all species equally. Incorporating information on phylogenetic non-independence or relatedness among species in the calculation of β-diversity may substantially advance our understanding of the ecological and evolutionary mechanisms structuring communities. Here, we investigate the relative influence of geographical distance and differences in environmental conditions (environmental distance) on the phylogenetic β-diversity between grassland communities expanding 4000 km across the Tibetan Plateau, the Inner Mongolia Plateau and the Xinjiang Autonomous Region in China. Both observed and standardized effect size of phylogenetic β-diversity were significantly correlated with geographical and environmental distance across all regions. However, the effect of geographical distance on the standardized effect size of phylogenetic β-diversity disappeared when environmental distance was controlled. We also found that within different regions, the effect of environmental distance on both observed and standardized effect size of phylogenetic β-diversity was more significant than geographical distance. Among environmental variables, climate played a more important role in shaping observed phylogenetic β-diversity across and within regions, and standardized effect size of phylogenetic β-diversity across regions. Soil properties played a more important role in shaping standardized effect size of phylogenetic β-diversity within regions. The phylogenetic β-diversity of species from dicot and monocot clades exhibited similar patterns along environmental and geographical distance. The results suggest that at the study scale, phylogeny of grassland communities in China is predominantly structured by environmental filtering, and the dominant environmental factors may be scale-dependent.     

Habitat heterogeneity induced by pyrogenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes

Although pyrogenic organic matter (PyOM) generated during wildfires plays a critical role in post-fire ecosystem recovery, the specific mechanisms by which PyOM controls soil microbial community assembly after wildfire perturbation remain largely uncharacterized. Herein we characterized the effect of PyOM on soil bacterial communities at two independent wildfire-perturbed forest sites. We observed that α-diversity of bacterial communities was the highest in wildfire-perturbed soils and that bacterial communities gradually changed along a sequence of unburnt soil → burnt soil → PyOM. The microbial communities reconstructed from unburnt soil and PyOM resembled the real bacterial communities in wildfire-perturbed soils in their α-diversity and community structure. Bacterial specialists in PyOM and soils clustered in phylogenetic coherent lineages with intra-lineage pH-niche conservatism and inter-lineage pH-niche divergence. Our results suggest that PyOM mediates bacterial community assembly in wildfire-perturbed soils by a combination of environmental selection and dispersal of phylogenetic coherent specialists with habitat preference in the heterogeneous microhabitats of burnt soils with distinct PyOM patches.Subject terms: Forest ecology, Microbial ecology     

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant–mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil–plant continuums (rhizosphere, phyllosphere and endosphere) in the maize–wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop-associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub-community is mainly determined by stochastic processes. In contrast, the rare sub-community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co-occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions.     

Biogeographical patterns of abundant and rare bacterial biospheres in paddy soils across East Asia

Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub-communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub-communities consistently displayed significant distance–decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub-communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%–49.78%) and average annual air temperature (16.59%–46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils.     

The biogeochemical variability of Arctic thermokarst ponds is reflected by stochastic and niche-driven microbial community assembly processes

Shallow thermokarst ponds are a conspicuous landscape element of the Arctic Siberian tundra with high biogeochemical variability. Little is known about how microbes from the regional species pool assemble into local pond communities and how the resulting patterns affect functional properties such as dissolved organic carbon (DOC) remineralization and greenhouse gas (GHG) turnover. We analysed the pelagic microbiomes of 20 ponds in north-eastern Siberia in the context of their physico-chemical properties. Ponds were categorized as polygonal or trough according to their geomorphological origin. The diversity of bacteria and eukaryotic microbes was assessed by ribosomal gene tag sequencing. Null model analysis revealed an important role of stochastic assembly processes within ponds of identical origin, in particular for genotypes only occurring in few systems. Nevertheless, the two pond types clearly represented distinct niches for both the bacterial and eukaryotic microbial communities. Carbon dioxide concentration, indicative of heterotrophic microbial processes, varied greatly, especially in the trough ponds. Methane concentrations were lower in polygonal ponds and were correlated with the estimated abundance of methanotrophs. Thus, the overall functional variability of Arctic ponds reflects the stochastic assembly of their microbial communities. Distinct functional subcommunities can, nevertheless, be related to GHG concentrations.     

Plant functional and phylogenetic turnover correlate with climate and land use in the Western Swiss Alps

Aims Understanding the relative importance of historical and environmental processes in the structure and composition of communities is one of the longest quests in ecological research. Increasingly, researchers are relying on the functional and phylogenetic β-diversity of natural communities to provide concise explanations on the mechanistic basis of community assembly and the drivers of trait variation among species. The present study investigated how plant functional and phylogenetic β-diversity change along key environmental and spatial gradients in the Western Swiss Alps.Methods Using the quadratic diversity measure based on six functional traits—specific leaf area, leaf dry matter content, plant height, leaf carbon content, leaf nitrogen content and leaf carbon to nitrogen content alongside a species-resolved phylogenetic tree—we relate variations in climate, spatial geographic, land use and soil gradients to plant functional and phylogenetic turnover in mountain communities of the Western Swiss Alps.Important findings Our study highlights two main points. First, climate and land-use factors play an important role in mountain plant community turnover. Second, the overlap between plant functional and phylogenetic turnover along these gradients correlates with the low phylogenetic signal in traits, suggesting that in mountain landscapes, trait lability is likely an important factor in driving plant community assembly. Overall, we demonstrate the importance of climate and land-use factors in plant functional and phylogenetic community turnover and provide valuable complementary insights into understanding patterns of β-diversity along several ecological gradients.     

Experimental insights into the importance of ecologically dissimilar bacteria to community assembly along a salinity gradient

The response of local communities to marine–freshwater transitions and the processes that underlie community assembly are unclear, particularly with respect to bacteria that differ in their life strategies. Here, we implemented a transplant experiment where bacterioplankton from three regions of the Baltic Sea with differing salinities (～3, 7 and 28 psu) were exposed to each other's environmental conditions. We found that habitat specialists were more abundant than generalists after exposure to salinity changes, irrespective of their origins. Most specialists that were selected following a salinity change were rare in the starting communities. Selection for generalists, however, was not specifically driven by the recruitment of either rare or abundant members, suggesting that taxon's initial abundance is minor relevant to the growth of generalists. Patterns in phylogenetic relatedness indicated that environmental filtering was the most influential assembly mechanism for specialists, whereas competitive interaction was more important for the assembly of generalists. Altogether, this study shows that large salinity changes promote the establishment of habitat specialists and that deterministic processes vary during community assembly for ecologically dissimilar taxa. We, therefore, propose that distinguishing assembly mechanisms of different community members helps understand and predict community dynamics in response to environmental change.     

Predators temper the relative importance of stochastic processes in the assembly of prey metacommunities

Communities assemble through a combination of stochastic processes, which can make environmentally similar communities divergent (high β-diversity), and deterministic processes, which can make environmentally similar communities convergent (low β-diversity). Top predators can influence both stochasticity (e.g. colonization and extinction events) and determinism (e.g. size of the realized species pool), in community assembly, and thus their net effect is unknown. We investigated how predatory fish influenced the scaling of prey diversity in ponds at local and regional spatial scales. While fish reduced both local and regional richness, their effects were markedly more intense at the regional scale. Underlying this result was that the presence of fish made localities within metacommunities more similar in their community composition (lower β-diversity), suggesting that fish enhance the deterministic, relative to the stochastic, components of community assembly. Thus, the presence of predators can alter fundamental mechanisms of community assembly and the scaling of diversity within metacommunities.     

Damming river shapes distinct patterns and processes of planktonic bacterial and microeukaryotic communities

Planktonic bacterial and microeukaryotic communities play important roles in biogeochemical cycles, but their biogeographic patterns and community assembly processes in large damming rivers still remain unclear. In this study, 16S rRNA and 18S rRNA coding genes were used for sample sequencing analysis of planktonic bacterial and microeukaryotic communities in the upper Yangtze River. The upper Yangtze River was divided into dam-affected zones and river zones based on the influence of dams. The results showed that there were significant differences in the bacterial and microeukaryotic communities between the two zones and that dams significantly reduced the α-diversity of the bacterial communities. Co-occurrence network analysis indicated that networks in the river zone were denser than those in the dam-affected zone. The relationships among species in bacterial networks were more complex than those in microeukaryotic networks. Dispersal limitation and ecological drift were the main processes influencing planktonic bacterial and microeukaryotic communities in the dam-affected zone respectively, whereas the role of deterministic processes increased in the river zone. Anthropogenic activities and hydraulic conditions affected suspended sediment and controlled microbial diversity in the river zone. These results suggest that dams impact planktonic bacteria more strongly than planktonic microeukaryotes, indicating that the distribution patterns and processes of the bacterial and microeukaryotic communities in large rivers are significantly different.     

Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils

Rare biosphere represents the majority of Earth's biodiversity and performs vital ecological functions, yet little is known about its biogeographical patterns and community assembly processes in terrestrial ecosystems. Herein, we investigated the community composition and phylogeny of rare (relative abundance <0.1%) and abundant (>1%) bacteria in dryland grassland soils on the Tibetan Plateau. Results revealed similar biogeographical patterns of rare and abundant bacteria at both compositional and phylogenetic levels, but rare subcommunity was more heavily influenced by stochasticity (72%) than the abundant (57%). The compositional variation of rare bacteria was less explained by environmental factors (41%) than that of the abundant (80%), while the phylogeny of rare bacteria (36%) was more explained than that of the abundant (29%). The phylogeny of rare bacteria was equally explained by local factors (soil and vegetation) and geospatial distance (11.5% and 11.9% respectively), while that of the abundant was more explained by geospatial distance (22.1%) than local factors (11.3%). Furthermore, a substantially tighter connection between the community phylogeny and composition was observed in rare (R² = 0.65) than in abundant bacteria (R² = 0.08). Our study provides novel insights into the assembly processes and biographical patterns of rare and abundant bacteria in dryland soils.     

Illumina Sequencing of 16S rRNA Tag Revealed Spatial Variations of Bacterial Communities in a Mangrove Wetland

The microbial community plays an essential role in the high productivity in mangrove wetlands. A proper understanding of the spatial variations of microbial communities will provide clues about the underline mechanisms that structure microbial groups and the isolation of bacterial strains of interest. In the present study, the diversity and composition of the bacterial community in sediments collected from four locations, namely mudflat, edge, bulk, and rhizosphere, within the Mai Po Ramsar Wetland in Hong Kong, SAR, China were compared using the barcoded Illumina paired-end sequencing technique. Rarefaction results showed that the bulk sediment inside the mature mangrove forest had the highest bacterial α-diversity, while the mudflat sediment without vegetation had the lowest. The comparison of β-diversity using principal component analysis and principal coordinate analysis with UniFrac metrics both showed that the spatial effects on bacterial communities were significant. All sediment samples could be clustered into two major groups, inner (bulk and rhizosphere sediments collected inside the mangrove forest) and outer mangrove sediments (the sediments collected at the mudflat and the edge of the mangrove forest). With the linear discriminate analysis scores larger than 3, four phyla, namely Actinobacteria, Acidobacteria, Nitrospirae, and Verrucomicrobia, were enriched in the nutrient-rich inner mangrove sediments, while abundances of Proteobacteria and Deferribacterias were higher in outer mangrove sediments. The rhizosphere effect of mangrove plants was also significant, which had a lower α-diversity, a higher amount of Nitrospirae, and a lower abundance of Proteobacteria than the bulk sediment nearby.     

浙西南地区沉水植物的区系分布与物种多样性

2007～2008年对浙西南地区的婺江、衢江及瓯江流域沉水植物的种类组成、区系类型及群落特征进行了调查研究。结果表明:(1)该地区共有沉水植物6科8属19种,在属水平上可归纳为3个区系类型,在种水平上可分为7个区系类型,并且在属种水平上的主要分布类型不同。(2)9个典型样地的13个群落类型进行了β-、γ-多样性分析。群落间β-多样性Jaccard指数显示89.8%群落间的相似性低于0.5,各样地的y-多样性则在衢江水域为最高(14种),瓯江水域最低(9种),这与不同水域沉水群落分布的研究结果相一致。并认为该地区沉水植物多样性降低是环境因子与人为干扰共同作用的结果。     

Fungal infection alters the selection,dispersal and drift processes structuring the amphibian skin microbiome

Symbiotic microbial communities are important for host health, but the processes shaping these communities are poorly understood. Understanding how community assembly processes jointly affect microbial community composition is limited because inflexible community models rely on rejecting dispersal and drift before considering selection. We developed a flexible community assembly model based on neutral theory to ask: How do dispersal, drift and selection concurrently affect the microbiome across environmental gradients? We applied this approach to examine how a fungal pathogen affected the assembly processes structuring the amphibian skin microbiome. We found that the rejection of neutrality for the amphibian microbiome across a fungal gradient was not strictly due to selection processes, but was also a result of species‐specific changes in dispersal and drift. Our modelling framework brings the qualitative recognition that niche and neutral processes jointly structure microbiomes into quantitative focus, allowing for improved predictions of microbial community turnover across environmental gradients.