Community Assembly Mechanisms Research Articles

The taxonomical and functional diversity of three groups of aquatic insects in rheocrene karst springs are affected by different environmental factors

Karst springs represent valuable and often the most threatened habitats in the riverine landscape. Unlike other stream habitats, they have several specifics that determine their insularity in the river continuum, e.g., high seasonal thermal and chemical stability. The presented study aimed to find out the taxonomical and functional richness of three groups of aquatic insects (Ephemeroptera, Plecoptera and Trichoptera) in the Western Carpathians karst springs, as well as uncover the mechanism of the EPT community assembly. Low within-site species richness was generally found, however, there was high between-site diversity and thus high total diversity of the studied groups of benthic invertebrates as well. Species richness of the EPT community was higher in larger and colder springs: those with lower concentrations of CO2 and Fe, as well as higher concentrations of SO42−. Analysis of functional richness, as well as functional dispersion, did not reveal any clear assembly mechanism in the spring EPT community; however, both analyses indicated a higher proportion of environmental filtering there. Unlike the taxonomic richness, the functional richness of the EPT community was significantly higher in small and medium springs with higher water temperatures, as well as in springs with the presence of deadwood. Between-site dissimilarities in the functional composition of EPT were significantly correlated with environmental differences of springs, which determined variables such as spring size and temperature, as well as the concentration of CO2 and SiO2.

Reconciling trait based perspectives along a trait-integration continuum.

Trait based ecology has developed fast in the last decades, aiming to both explain mechanisms of community assembly, and predict patterns in nature, such as the effects of biodiversity shifts on key ecosystem processes. This body of work has stimulated the development of several conceptual frameworks and analytical methods, as well as the production of trait databases covering a growing number of taxa and organizational levels (from individuals to guilds). However, this breeding ground of novel concepts and tools currently lacks a general and coherent framework, under which functional traits can help ecologists organize their research aims, and serve as the common currency to unify several scientific disciplines. Specifically, we see a need to bridge the gaps between community ecology, ecosystem ecology, and evolutionary biology, in order to address the most pressing environmental issues of our time. To achieve this integration goal, we define a trait-integration continuum, which reconciles alternative trait definitions and approaches in ecology. This continuum outlines a coherent progression of biological scales, along which traits interact and hierarchically integrate from genetic information, to whole organism fitness-related traits, to trait syndromes and functional groups. Our conceptual scheme proposes that lower-level trait integration is closer to the inference of ecoevolutionary mechanisms determining population and community properties, whereas higher-level trait integration is most suited to the prediction of ecosystem processes. Within these two extremes, trait integration varies on a continuous scale, which relates directly to the inductive-deductive loop that should characterize the scientific method. With our proposed framework, we aim to facilitate scientists in contextualising their research based on the trait-integration levels that matter most to their specific goals. Explicitly acknowledging the existence of a trait-integration continuum is a promising way for framing the appropriate questions, thus obtaining reliable answers and results that are comparable across studies and disciplines.

Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed.

An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy‐to‐measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using the diversity of expressed genes—functional genomic diversity (FGD)—to understand ecological dynamics of a recent and ongoing alpine invasion. We quantified FGD based on transcriptomic data measured for 26 plant species occurring along adjacent invaded and pristine streambeds. We used an RNA‐seq approach to summarize the overall number of expressed transcripts and their annotations to functional categories, and contrasted this with functional trait diversity (FTD) measured from a suite of characters that have been traditionally considered in plant ecology. We found greater FGD and FTD in the invaded community, independent of differences in species richness. However, the magnitude of functional dispersion was greater from the perspective of FGD than from FTD. Comparing FGD between congeneric alien–native species pairs, we did not find many significant differences in the proportion of genes whose annotations matched functional categories. Still, native species with a greater relative abundance in the invaded community compared with the pristine tended to express a greater fraction of genes at significant levels in the invaded community, suggesting that changes in FGD may relate to shifts in community composition. Comparisons of diversity patterns from the community to the species level offer complementary insights into processes and mechanisms driving invasion dynamics. FGD has the potential to illuminate cryptic changes in ecological diversity, and we foresee promising avenues for future extensions across taxonomic levels and macro‐ecosystems.

Direct Evidence for Deterministic Assembly of Bacterial Communities in Full-Scale Municipal Wastewater Treatment Facilities.

In this study, we investigated whether bacterial community composition in full-scale wastewater treatment bioreactors can be better explained by niche- or neutral-based theory (deterministic or stochastic) and whether bioreactor design (continuous flow versus fill and draw) affected community assembly. Four wastewater treatment facilities (one with quadruplicated continuous-flow bioreactors, two with one continuous-flow bioreactor each, and one with triplicate fill-and-draw bioreactors) were investigated. Bioreactor community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Replicate bioreactors at the same wastewater treatment facility had largely reproducible (i.e., deterministic) bacterial community composition, although bacterial community composition in continuous-flow bioreactors was significantly more reproducible (P < 0.001) than in fill-and-draw bioreactors (Bray-Curtis dissimilarity, μ = 0.48 ± 0.06 versus 0.58 ± 0.08). Next, we compared our results to previously used indirect methods for distinguishing between deterministic and stochastic community assembly mechanisms. Synchronicity was observed in the bacterial community composition among bioreactors within the same metropolitan region, consistent with deterministic community assembly. Similarly, a null model-based analysis also indicated that all wastewater bioreactor communities were controlled by deterministic factors and that continuous-flow bioreactors were significantly more deterministic (P < 0.001) than fill-and-draw bioreactors (nearest-taxon index, μ = 3.8 ± 0.6 versus 2.7 ± 0.8). Our results indicate that bacterial community composition in wastewater treatment bioreactors is better explained by deterministic community assembly theory; simultaneously, our results validate previously used but indirect methods to quantify whether microbial communities were assembled via deterministic or stochastic mechanisms. IMPORTANCE Understanding the mechanisms of bacterial community assembly is one of the grand challenges of microbial ecology. In environmental systems, this challenge is exacerbated because replicate experiments are typically impossible; that is, microbial ecologists cannot fabricate multiple field-scale experiments of identical, natural ecosystems. Our results directly demonstrate that deterministic mechanisms are more prominent than stochastic mechanisms in the assembly of wastewater treatment bioreactor communities. Our results also suggest that wastewater treatment bioreactor design is pertinent, such that the imposition of feast-famine conditions (i.e., fill-and-draw bioreactors) nudge bacterial community assembly more toward stochastic mechanisms than the imposition of stringent nutrient limitation (i.e., continuous-flow bioreactors). Our research also validates the previously used indirect methods (synchronous community dynamics and an application of a null model) for characterizing the relative importance of deterministic versus stochastic mechanisms of community assembly.

Little environmental adaptation and high stability of bacterial communities in rhizosphere rather than bulk soils in rice fields

The rhizosphere harbors complex bacterial communities, which are critical for plant growth and health. Significant differences exist between bacterial communities in the rhizosphere and bulk soils, however, limited research has explored co-occurrence patterns, environmental adaptations, and assembly mechanisms of rhizosphere bacterial communities. Using 16S rRNA high-throughput sequencing, we investigated the taxonomic and phylogenetic diversity of bacterial communities in both rhizosphere and bulk soils from a rice cropping experimental system in China. In addition to investigating differences in bacterial composition, we examined co-occurrence patterns, estimated environmental breadth and phylogenetic signals, and analyzed community assembly processes in these environments. Significant differences were observed between rhizosphere composition and bulk soil (p < 0.05) even some bacteria in the rice rhizosphere may come from the bulk soil around roots. The distribution patterns and ecological functions between communities in the rice rhizosphere and bulk soil were also significantly different. Lower β-diversity values among bacterial communities in the rice rhizosphere indicated that they had a higher stability than those in the bulk soils. In addition, rice rhizosphere communities had a wider phylogenetic diversity and lower functional redundancy when compared with bulk soils. Moreover, the results of environmental breadth analysis revealed that communities in bulk soils were more environmentally constrained than rhizosphere communities. Our null model revealed that deterministic processes drove community assembly in bulk soils (59.57%), whereas stochastic processes determined those in the rice rhizosphere (53.85%). Available potassium was decisive in determining the balance between stochasticity and determinism in both communities. Our study provides insights on the mechanisms underlying the assembly and maintenance of bacterial diversity in rice cropping soils, in response to environmental changes.

Rainforest conversion to monocultures favors generalist ants with large colonies

AbstractThe conversion of natural ecosystems to agricultural land is one of the most important drivers of biodiversity decline worldwide, particularly in the tropics. Species loss is typically trait‐associated, leading to filtering of disturbance‐resistant species during community assembly, which affects ecosystem functioning and evolutionary potential of communities. To understand the ecological and phylogenetic impact of rainforest conversion to agricultural systems, we combine analysis of nesting habit, feeding habit, colony size, and body size of canopy ants (Formicidae) with a phylogenetic analysis of species collected in four land‐use systems in Sumatra, Indonesia: (1) lowland tropical rainforest, (2) jungle rubber (extensive rubber agroforest), and smallholder plantations of (3) rubber and (4) oil palm. Canopy ant communities in these land‐use systems differed in trait composition, with a larger proportion of generalist nesting and generalist‐omnivore feeding species in oil palm compared to rainforest and a larger proportion of generalist nesters and species with large colonies (&gt;1000 individuals) in rubber than in rainforest. Traits of canopy ant communities in jungle rubber were more similar to those in rainforest than to those in rubber and oil palm plantations. In rainforest, mean pairwise phylogenetic distance was lower than expected for random community assembly, but did not differ from random in the other land‐use systems. Of the traits nesting habit, feeding habit, and colony size, only feeding habit exhibited phylogenetic signal. Our results show that rainforest conversion to agricultural systems is accompanied by shifts in trait composition of canopy ant communities. Further, our results argue against environmental filtering of closely related canopy ant species as the major community assembly mechanism in plantation systems, but suggest that the Sumatran lowland rainforests harbor recently diverged endemic ant species that are particularly vulnerable to rainforest conversion to agricultural systems. Given the importance of ants for tropical ecosystems, the ecological differences among ant communities along the land‐use gradient might have important consequences for ecosystem functioning and services in plantation systems.

Meadow degradation increases spatial turnover rates of the fungal community through both niche selection and dispersal limitation

The alpine meadow ecosystem, as the main ecosystem of the Qinghai-Tibet Plateau, has been heavily degraded over the past several decades due to overgrazing and climate change. Although soil microorganisms play key roles in the stability and succession of grassland ecosystems, their response to grassland degradation has not been investigated at spatial scale. Here, we systematically analyzed the spatial turnover rates of soil prokaryotic and fungal communities in degraded and undegraded meadows through distance-decay relationship (DDR) and species area relationship (SAR), as well as the community assembly mechanisms behind them. Although the composition and structure of both fungal and prokaryotic communities showed significant changes between undegraded and degraded meadows, steeper spatial turnover rates were only observed in fungi (Degraded Alpine Meadow β = 0.0142, Undegraded Alpine Meadow β = 0.0077, P < 0.05). Mantel tests indicated that edaphic variables and vegetation factors showed significant correlations to the β diversity of fungal community only in degraded meadow, suggesting soil and vegetation heterogeneity both contributed to the variation of fungal community in that system. Correspondingly, a novel phylogenetic null model analysis demonstrated that environmental selection was enhanced in the fungal community assembly process during meadow degradation. Interestingly, dispersal limitation was also enhanced for the fungal community in the degraded meadow, and its relative contribution to other assembly process (i.e. selection and drift) showed a significant linear increase with spatial distance, suggesting that dispersal limitation played a greater role as distance increased. Our findings indicated the spatial scaling of the fungal community is altered during meadow degradation by both niche selection and dispersal limitation. This study provides a new perspective for the assessment of soil microbial responses to vegetation changes in alpine areas.

Dispersal Limitation Expands the Diversity of Coral Microbiome Metacommunity in the South China Sea

The coral microbiome is one of the most complex microbial biospheres. However, the ecological processes shaping coral microbiome community assembly are not well understood. Here, we investigated the abundance, diversity, and community assembly mechanisms of coral-associated microbes from a highly diverse coral metacommunity in the South China Sea. Compared to seawater, the coral microbial metacommunity were defined by highly variable bacterial abundances among individual coral samples, high species evenness but not high species richness, high β-diversity, and a small core microbiome. We used variation partitioning analysis, neutral community model, and null model to disentangle the influences of different ecological processes in coral microbiome assembly. Measured physico-chemical parameters of the surrounding seawater and the spatial factor together explained very little of the variation in coral microbiome composition. Neutral processes only explained a minor component of the variation of coral microbial communities, suggesting a non-stochastic community assembly. Homogeneous and heterogeneous selection, but not dispersal, contributed greatly to the assembly of the coral microbiome. Such selection could be attributed to the within-host environments rather than the local environments. Our results demonstrated that dispersal limitation and host filtering contribute significantly to the assembly of discrete coral microbial regimes and expand the metacommunity diversity.

Both fencing duration and shrub cover facilitate the restoration of shrub-encroached grasslands

Fully understanding community assembly mechanisms is crucial to better predict grassland community dynamic under restoration. The community assembly over time is more complicated in shrub-encroached than in non-encroached degraded grasslands because the presence and size of shrub could regulate community processes and diminish effects of restoration time. However, how shrub size influences community assembly under restoration in shrub-encroached communities remains poorly understood. Therefore, in Caragana microphylla shrub-encroached grasslands in the Inner Mongolia typical steppe region, three plots with different shrub cover (low, medium and high) were set up in each of three sites with different fencing duration (15-, 35- and 39-year fencing). We assessed the assembly mechanisms of shrub-interspace herbaceous communities by estimating standardized effect size (SES) of functional dispersion (FDis) based on the first two principal components (PC1 and PC2) of traits characterizing resource acquisition strategies. According to the SES of FDisPC1, the assembly mechanisms shifted from stochastic processes to competitive exclusion over time of fencing in the plots of low and medium shrub cover and across a shrub cover gradient in the sites of 15-year and 35-year fencing, with the increase of soil moisture, species richness, Shannon-Wiener diversity and relative density of perennial grasses. Competitive exclusion dominated the communities in the site of 39-year fencing and in the plots of high shrub cover. According to the SES of FDisPC2, the competitive exclusion dominated all of the 9 communities investigated in this study. By variance component analysis, shrub cover showed the highest contribution in explaining the variance in community-weighted mean (CWM), and shrub cover and fencing duration showed the first two highest contributions in explaining the variance in SES of FDis. The present findings highlight the significance of shrub cover in influencing the community assembly in shrub-encroached grasslands under restoration in the European-Asian typical steppe region.

Stochasticity overrides deterministic processes in structuring macroinvertebrate communities in a plateau aquatic system

AbstractDeterministic and stochastic processes are two major factors shaping community dynamics, but their relative importance remains unknown for many aquatic systems, including those in the high‐elevation Qinghai–Tibet Plateau. Here, we explored the causes of multidimensional beta diversity patterns (i.e., taxonomic, functional, and phylogenetic) of a macroinvertebrate metacommunity in this large aquatic system by using multiple approaches (i.e., null models, phylogenetic signal testing, and ordination‐based approaches). To obtain insights into community assembly mechanisms, we also analyzed beta diversity in two deconstructed sub‐metacommunities (e.g., different tributaries and the main lake body). We found that most functional traits showed significant phylogenetic signals, indicating that the functional traits were profoundly influenced by evolutionary history. The null models showed randomness of functional and phylogenetic beta diversities for the whole basin and its tributaries, confirming the importance of stochasticity over deterministic processes in controlling community structure. However, both phylogenetic and functional community structures were clustered in the Qinghai Lake, probably reflecting the importance of environmental filtering. Ordination‐based approaches also revealed that both environmental factors and spatial processes accounted for variation in taxonomic, functional, and phylogenetic beta diversity. More specifically, environmental filtering was more important than spatial processes for the functional dimension, but the opposite was true for the taxonomic and phylogenetic dimensions. The paleogeographic history of the Qinghai Lake basin may have contributed substantially to the prevalence of stochastic processes. Overall, this study provides a better understanding of ecological patterns and assembly mechanisms of macroinvertebrate communities across this poorly known high‐elevation aquatic system that is highly sensitive to climate warming.

Seasonal patterns of taxonomic and functional beta diversity in submerged macrophytes at a fine scale.

Spatiotemporal variation in community composition is of considerable interest in ecology. However, few studies have focused on seasonal variation patterns in taxonomic and functional community composition at the fine scale. As such, we conducted seasonal high‐density sampling of the submerged macrophyte community in Hongshan Bay of Erhai Lake in China and used the generalized dissimilarity model (GDM) to evaluate the effects of environmental factors and geographic distance on taxonomic and functional beta diversity as well as corresponding turnover and nestedness components. At the fine scale, taxonomic turnover and nestedness as well as functional turnover and nestedness showed comparable contributions to corresponding taxonomic and functional beta diversity, with different importance across seasons. All taxonomic and functional dissimilarity metrics showed seasonal variation. Of note, taxonomic beta diversity was highest in summer and lowest in winter, while functional beta diversity showed the opposite pattern. Taxonomic and functional turnover showed similar change patterns as taxonomic and functional beta diversity. Taxonomic nestedness was low in summer and high in winter. Functional nestedness was also lower in summer. These results suggest that under extreme environmental conditions, both turnover and nestedness can exist at the fine scale and seasonal community composition patterns in submerged macrophytes should be considered. Future investigations on community assembly mechanisms should pay greater attention to long‐term dynamic characteristics and functional information.

Prokaryotic, Fungal, and Unicellular Eukaryotic Core Communities Across Three Sympatric Marine Sponges From the Southwestern Atlantic Coast Are Dominated Largely by Deterministic Assemblage Processes.

Marine sponges are known to harbor a diverse and complex microbiota; however, a vast majority of surveys have been investigating the prokaryotic communities in the north hemisphere and Australia. In addition, the mechanisms of microbial community assembly are poorly understood in this pivotal player of the ecosystem. Thus, this survey addressed the holobiome of the sponge species in the São Paulo region (Brazil) for the first time and investigated the contribution of neutral and niche processes of prokaryotic, fungal, and unicellular eukaryotic assemblage in three sympatric species Aplysina caissara, Aplysina fulva, and Tedania ignis along with environmental samples. The compositions of the holobiome associated with the sponges and detected in environmental samples were strikingly different. Remarkably, between 47 and 88% of the assigned operational taxonomic units (OTUs) were specifically associated with sponge species. Moreover, around 77, 69, and 53% of the unclassified OTUs from prokaryotic, fungal, and unicellular eukaryotic communities, respectively, showed less than 97% similarity with well-known databases, suggesting that sponges from the southwestern Atlantic coast are an important source of microbial novelty. These values are even higher, around 80 and 61% of the unclassified OTUs, when excluding low abundance samples from fungal and unicellular eukaryotic datasets, respectively. Host species were the major driver shaping the sponge-associated microbial community. Deterministic processes were primarily responsible for the assembly of microbial communities in all sponge species, while neutral processes of prokaryotic and fungal community assembly were also detected in the sympatric A. caissara and T. ignis replicates, respectively. Most of the species-rich sponge-associated lineages from this region are also found in the Northern seas and many of them might play essential roles in the symbioses, such as biosynthesis of secondary metabolites that exhibit antimicrobial and antiviral activities, as well as provide protection against host predation. Overall, in this study the microbiota was assembled by interactions with the host sponge in a deterministic-based manner; closely related sponge species shared a strong phylogenetic signal in their associated prokaryotic and fungal community traits and Brazilian sponges were a reservoir of novel microbial species.

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir

BackgroundFreshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity.ResultsHere, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics.ConclusionsOur findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture.-E3MKQHtp7WR1f_cJEBdqXVideo abstract

Changes of Periphyton Abundance and Biomass Driven by Factors Specific to Flooding Inflow in a River Inlet Area in Erhai Lake, China

Periphyton is an ecological essential in freshwater lakes and rivers. Its abundance and biomass are very dynamic in various habitats and subject to various factors, for example, nutrient and light. Following flooding events, the transitional area adjacent to a river inlet and the shallow lake generates diverse habitats for periphyton with gradients in current velocity, suspended matters, nutrients, and light, which would strongly shape the growth and community of periphyton. In this study, three sampling sites were established around a river inlet in Erhai Lake, China, and a field survey was conducted in the sites from April to August (flooding seasons) in 2019 to investigate the abundance and biomass of periphyton and explore influential factors. The results showed that three study areas have different gradients of current velocity depending on the distance to the river inlet, thereby regulating the concentrations of nutrients and suspended matters, which strongly affected the periphyton community; to be specific, the biomass of periphyton was inhibited by the concentration of suspended matters and high concentrations of silicate mainly reduced the diversity of periphyton. Our results imply that the study on the driving factors of periphyton could help to understand its community assembly mechanism and biomass and species composition of periphyton can provide some reference for trophic state of the lake.

Plant Community Assembly Mechanisms of a Subalpine Meadow Community Along Different Successional Time

The process of community assembly is important to explain species coexistence and the maintenance of species diversity. Succession provides a good opportunity to study the role of the deterministic and stochastic processes during the community species composition. We investigated species composition and environmental factors and calculated the change in species diversity, phylogenetic diversity, net relatedness index, and nearest taxon index along a successional chronosequence, with a series of 0.5 × 0.5 m2 plots (n = 20) from five successional subalpine meadow plant communities (ages 1, 3, 5, 15, and 30) in the Qinghai-Tibetan Plateau. In the plots, we found a significant change in species composition and abiotic environmental factors. Our redundancy analysis showed that soil nitrate nitrogen and soil organic carbon were the key environmental factors that affect the community composition in succession gradient. The community showed an overdispersion phylogenetic structure along with the early and medium succession. The ends of the succession stage showed a random or convergent phylogenetic structure. The results showed that the construction process of plant communities in the early and middle stages of succession was mainly affected by habitat filtering. In the late stage of succession, the process of community construction is more complex, which could be affected by the limiting similarity and neutral driving process. Our findings are important to be used in managing ecological restoration and protection.

Environmental filtering and dispersal limitation jointly shaped the taxonomic and phylogenetic beta diversity of natural forests in southern China.

AimThe mechanisms underlying the maintenance of biodiversity remain to be elucidated. Taxonomic diversity alone remains an unresolved issue, especially in terms of the mechanisms of species co‐existence. We hypothesized that phylogenetic information could help to elucidate the mechanism of community assembly and the services and functions of ecosystems. The aim of this study was to explore the mechanisms driving floral diversity in subtropical forests and evaluate the relative effects of these mechanisms on diversity variation, by combining taxonomic and phylogenetic information.LocationWe examined 35 1‐ha tree stem‐mapped plots across eight national nature reserves in Guangxi Zhuang Autonomous Region, China.TaxonTrees.MethodsWe quantified the taxonomic and phylogenetic β‐diversity between each pair of plots using the (abundance‐based) Rao's quadratic entropy and the (incidence‐based) Sørensen dissimilarity indices. Using a null model approach, we compared the observed β‐diversity with the expected diversity at random and calculated the standard effect size of the observed β‐diversity deviation. Furthermore, we used distance‐based redundancy analysis (dbRDA) to partition the variations in taxonomic and phylogenetic observed β‐diversity and β‐deviation into four parts to assess the environmental and spatial effects.ResultsThe taxonomic β‐deviation was related to and higher than the phylogenetic β‐deviation (r = .74). This indicated that the species turnover between pairwise plots was mainly the turnover of closely related species. Higher taxonomic and phylogenetic β‐deviation were mainly concentrated in the pairwise karst and nonkarst forest plots, indicating that the species in karst forests and nonkarst forests were predominantly from distantly related clades. A large proportions of the variation in taxonomic and phylogenetic β‐deviation were explained by the joint effect of environmental and spatial variables, while the contribution of environmental variables was greater than that of spatial variables, probably owing to the influence of the sampling scale dependence, integrality of sampling size and species pool, and the unique climatic and geomorphic characteristics.Main conclusionsOur study highlights the importance of phylogeny in biodiversity research. The incorporation of taxonomic and phylogenetic information provides a perspective to explore potential underlying mechanisms that have shaped species assemblages and phylogenetic patterns in biodiversity hotspots.

Geographical Distribution of Iron Redox Cycling Bacterial Community in Peatlands: Distinct Assemble Mechanism Across Environmental Gradient.

Microbial-mediated iron (Fe) oxidation and reduction greatly contribute to the biogeochemistry and mineralogy of ecosystems. However, knowledge regarding the composition and distribution patterns of iron redox cycling bacteria in peatlands remains limited. Here, using high-throughput sequencing, we compared biogeographic patterns and assemblies of the iron redox cycling bacterial community between soil and water samples obtained from different types of peatland across four regions in Northeast China. A total of 48 phylotypes were identified as potential iron redox bacteria, which had greater than 97% similarity with Fe(II)-oxidizing bacteria (FeOB) and Fe(III)-reducing bacteria (FeRB). Among them, Rhodoferax, Clostridium, Geothrix, Sideroxydans, Geobacter, Desulfovibrio, and Leptothrix could be used as bioindicators in peatlands for characterizing different hydrological conditions and nutrient demands. Across all samples, bacterial communities associated with iron redox cycling were mainly affected by pH, dissolved organic carbon (DOC), and Fe2+. Distance–decay relationship (DDR) analysis indicated that iron redox cycling bacterial communities in soil, but not in water, were highly correlated with geographic distance. Additionally, null model analysis revealed that stochastic processes substituted deterministic processes from minerotrophic fens to ombrotrophic bogs in soils, whereas deterministic processes were dominant in water. Overall, these observations suggest that bacteria involved in iron redox cycling are widespread in diverse habitats and exhibit distinct patterns of distribution and community assembly mechanisms between soil and water in peatlands.

Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern

The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using “Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)”. The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.

Distinct microhabitats affect the relative balance of ecological processes shaping the spatial distribution of bacterial communities in lakeshore habitats

Abstract The lakeshore habitat, which is an interface zone between lake and land, harbours various organic particles providing nutrient‐rich microhabitats for bacterial colonisation. Revealing the mechanisms maintaining the bacterial diversity generated on these particles is vital for understanding the biogeochemical processes within lakeshore habitats. To date, however, the bacterial communities within lakeshore habitats have been rarely explored, and knowledge of the ecological processes associated with their spatial distribution is limited. Here, we employed amplicon‐based high throughput sequencing technology to investigate the composition, co‐occurrence patterns, spatial distribution, and assembly processes of free‐living and particle‐attached bacterial communities (FLBC vs. PABC) across 29 lakeshore zones within freshwater lakes from two typical regions: Middle–Lower Yangtze River Plain and Yunnan–Kweichow Plateau. We found significant community dissimilarity between both bacterial lifestyles and regions. PABC exhibited higher community dissimilarity between the plain and plateau regions than FLBC did. Furthermore, eight operational taxonomic units were detected as a core bacterial community within the lakeshore habitats across the plain and plateau regions. Network analysis revealed that bacterial taxa preferring a particle‐attached lifestyle exhibited more co‐occurrence associations for both intra‐ and inter‐community than the free‐living lifestyle. Both FLBC and PABC showed significant distance–decay relationships in these two regions. Dispersal limitation was the most important process associated with patterns in the spatial distribution of FLBC and PABC, whereas the relative importance of variable and homogeneous selection differed between the assembly of FLBC and PABC because of differences in their microhabitats. Our results highlight that dispersal limitation may be strongly associated with the spatial distribution of lakeshore bacterial communities at a regional scale. However, lifestyle differences influence the relative balance between the processes of dispersal, selection, and biotic interaction that influence these bacterial communities. This study reveals potential interactions between bacterial taxa with different lifestyles as well as indicating which ecological processes may lie behind the spatial distribution of bacterial communities in lakeshore habitats. Knowledge of potential assembly mechanisms of bacterial communities within different microhabitats help us understand how bacterial communities in different microhabitats are generated and their different roles in biogeochemical processes in lakeshore habitats.

Seasonal variations in soil fungal communities and co-occurrence networks along an altitudinal gradient in the cold temperate zone of China: A case study on Oakley Mountain

Cold temperate forests carry out functions that are essential to global biogeochemical cycling and climate regulation. The biogeography of soil fungi has attracted much attention in recent years; however, the seasonal patterns of soil fungal community structure and diversity along altitudinal gradients under the unique climatic conditions at high latitudes remain unclear, which limits our insight into soil microbial interactions and the mechanisms of community assembly. In this study, Illumina MiSeq sequencing was used to investigate the spatiotemporal changes in soil fungal communities along an altitudinal gradient (from 750 m to 1420 m) on Oakley Mountain in the northern Greater Khingan Mountains. Altitude had significant impacts on the relative abundances of the dominant phyla and classes of soil fungi, and the interaction of altitude and season significantly affected the relative abundances of Ascomycota and Basidiomycota. The number of soil fungal taxa and Faith’s phylogenetic diversity index tended to monotonically decline with increasing elevation. Soil moisture, soil temperature and pH were the main factors affecting fungal community structure in May, July and September, respectively. The soil dissolved organic carbon content significantly shaped the soil fungal community composition along the altitudinal gradient throughout the growing season. Compared to that in May and July, the soil fungal network in September had more nodes and links, a higher average degree and a higher average clustering coefficient. The nine module nodes in the co-occurrence network were all Ascomycota taxa, and the identities of the keystone taxa of soil fungi in the network showed obvious seasonality. Our results demonstrated that altitude has stronger effects than season on soil fungal community structure and diversity at high latitudes. In addition, the co-occurrence network of soil fungi exhibited obvious seasonal succession, which indicated that the keystone taxa of soil fungi exhibit niche differentiation among seasons.