Beta Diversity of Antarctic and Sub-Antarctic Benthic Communities Reveals a Major Role of Stochastic Assembly Processes

Community assembly is the result of both, deterministic and stochastic processes. The former encompasses niche-based local-scale mechanisms such as environmental filtering and biotic interactions; the latter includes ecological drift, probabilistic colonisation, and random extinctions. Using standardised sampling protocols, we show that the spatial variation in species composition (beta diversity) of shallow subtidal macrobenthic communities of sub-Antarctic (Strait of Magellan and Yendegaia Fjord [Beagle Channel]) and Antarctic (Fildes Bay [King George Island, West Antarctic Peninsula]) localities reflects a high contribution of stochastic processes to community assembly. Null model analyses indicated that random sampling from species pools of different sizes drove the observed among-locality differences in incidence- and abundance-based beta diversity. We analysed a normalised stochasticity ratio (NST), which delimits between more deterministic (<50%) and more stochastic (>50%) assembly. NST was notably larger than 50%, with mean values of 69.5% (95% CI = 69.2–69.8%), 62.5% (62.1–62.9%), and 72.8% (72.5–73.2%) in Strait of Magellan, Yendegaia Fjord, and Fildes Bay, respectively. Accordingly, environmental factors, such as depth, seawater temperature, salinity, and underwater light penetration, accounted for a small fraction of the spatial variation in community composition across the three localities. In this region, therefore, stochastic processes could have stronger effects on community assembly than deterministic niche-based factors. As anthropogenic biotic homogenisation continues apace, our study can give useful insights into the major ecological processes in Southern Ocean’ coastal marine communities.

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Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests

10.7287/peerj.preprints.27223v1 ◽

2018 ◽

Author(s):

Pengyu Zhao ◽

Jiabing Bao ◽

Xue Wang ◽

Yi Liu ◽

Cui Li ◽

...

Keyword(s):

Microbial Community ◽

Stochastic Processes ◽

Community Assembly ◽

Soil Microbial Community ◽

Analytical Methods ◽

Community Dynamics ◽

Coniferous Forests ◽

Ecological Processes ◽

Soil Microbial ◽

Microbial Community Assembly

The mechanisms underlying community dynamics, which govern the complicated biogeographical patterns of microbes, have long been a research hotspot in community ecology. However, the mixing of multiple ecological processes and the one-sidedness of analytical methods make it difficult to draw inferences about the community assembly mechanisms. In this study, we investigated the driving forces of the soil microbial community in subalpine coniferous forests of the Loess Plateau in Shanxi, China, by integrating multiple analytical methods. The results of the null model demonstrated that deterministic processes (especially interspecific relationships) were the main driving force of the soil microbial community assembly in this study area, relative to stochastic processes. Based on the results of the net relatedness index (NRI) and nearest taxon index (NTI), we inferred that historical and evolutionary factors, such as climate change and local diversification, may have similar effects on microbial community structure based on the climatic niche conservatism. Based on the results of a functional traits analysis, we found that the effects of ongoing ecological processes on the microbial community assembly varied among sites. Therefore, the functional structures seemed to be more related to ongoing ecological processes, whereas the phylogenetic structures seemed to be more related to historical and evolutionary factors, as well as the tradeoff between deterministic and stochastic processes. The functional and phylogenetic structures were mainly shaped by different ecological processes. By integrating multiple ecological processes, our results provide more details of the mechanisms driving the community assembly

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Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

mSystems ◽

10.1128/msystems.00704-19 ◽

2020 ◽

Vol 5 (1) ◽

Author(s):

Pengfa Li ◽

Weitao Li ◽

Alex J. Dumbrell ◽

Ming Liu ◽

Guilong Li ◽

...

Keyword(s):

Spatial Variation ◽

Fungal Community ◽

Community Assembly ◽

Soil Depth ◽

Environmental Filtering ◽

Its Region ◽

Dispersal Limitation ◽

Fungal Communities ◽

Subtropical China ◽

Soil Layers

ABSTRACT Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, “everything is everywhere, but the environment selects,” although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths. IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.

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Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests

10.7287/peerj.preprints.27223 ◽

2018 ◽

Author(s):

Pengyu Zhao ◽

Jiabing Bao ◽

Xue Wang ◽

Yi Liu ◽

Cui Li ◽

...

Keyword(s):

Microbial Community ◽

Stochastic Processes ◽

Community Assembly ◽

Soil Microbial Community ◽

Analytical Methods ◽

Community Dynamics ◽

Coniferous Forests ◽

Ecological Processes ◽

Soil Microbial ◽

Microbial Community Assembly

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Stochastic processes dominate community assembly in cichlid communities in Lake Tanganyika

10.1101/039503 ◽

2016 ◽

Cited By ~ 1

Author(s):

Thijs Janzen ◽

Adriana Alzate ◽

Moritz Muschick ◽

Fons van der Plas ◽

Rampal S. Etienne

Keyword(s):

Stochastic Processes ◽

Community Assembly ◽

Environmental Conditions ◽

Lake Tanganyika ◽

Environmental Gradients ◽

Cichlid Fish ◽

Species Traits ◽

Ecological Processes ◽

African Great Lakes ◽

Community Dissimilarity

ABSTRACTThe African Great Lakes are characterized by an extraordinary diversity of endemic cichlid fish species. The cause of this diversity is still largely unknown. Most studies have tried to solve this question by focusing on macro-evolutionary processes, such as speciation. However, the ecological processes determining local cichlid diversity have so far been understudied, even though knowledge on these might be crucial for understanding larger scale biodiversity patterns.Using trait, environmental and abundance data of cichlid fishes along 36 transects, we have studied how differences in local environmental conditions influence cichlid community assembly in the littoral of Lake Tanganyika, Zambia. We investigated changes in average trait values and in trait-based community assembly processes along three key environmental gradients.Species diversity and local abundance decreased with increasing sand cover and diet-associated traits changed with depth. Analyses on within-community trait diversity patterns indicated that cichlid community assembly was mainly driven by stochastic processes, to a smaller extent by processes that limit the similarity among co-existing species and least by filtering processes that limit the range of species traits occurring in an environment. Despite, the low impact of habitat filtering processes, we find community dissimilarity to increase with increasing environmental difference.Our results suggest that local environmental conditions determine cichlid abundance, while the predominance of stochastic community assembly across all environments explains why the communities with the highest abundances contain most species.

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Differentiation of Environmental Conditions Promotes Variation of Two Quercus wutaishanica Community Assembly Patterns

Forests ◽

10.3390/f11010043 ◽

2019 ◽

Vol 11 (1) ◽

pp. 43

Author(s):

Mao Wang ◽

Jinshi Xu ◽

Yongfu Chai ◽

Yaoxin Guo ◽

Xiao Liu ◽

...

Keyword(s):

Loess Plateau ◽

Community Assembly ◽

Local Community ◽

Environmental Filtering ◽

Local Environment ◽

Qinling Mountains ◽

Forest Communities ◽

The Loess Plateau ◽

Ecological Processes ◽

Phylogenetic Structure

Two contradictory niche-based processes, environmental filtering and competitive exclusion, are important ecological processes in community assembly. Quercus wutaishanica forests are the climax communities in the Qinling Mountains and the Loess Plateau, China. Since these areas are characterized by different climate and evolutionary histories, these forests could be a suitable study system to test the phylogenetic niche conservatism hypothesis. We compared variation in community assembly of two distinct Q. wutaishanica forest communities and analyzed how the variations are formed. Quercus wutaishanica forest communities had significantly different species pool, phylogenetic structure and phylogenetic diversity between the two regions that were driven by inconsistency in environment conditions and evolutionary history at the local scale. Soil ammonium nitrogen, soil water content, and nitrate nitrogen play a major role in phylogenetic beta diversity patterns. The effect of environmental filtering on community assembly was more significant on the Loess Plateau than in the Qinling Mountains. Our study also found that local environment is important in mediating the patterns of phylogenetic structure. These findings provide insights into the mechanisms of local community assembly.

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Key Community Assembly Processes Switch between Scales in Shaping Beta Diversity in Two Primary Forests, Southwest China

Forests ◽

10.3390/f11101106 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1106

Author(s):

Mengesha Asefa ◽

Han-Dong Wen ◽

Min Cao ◽

Yue-Hua Hu

Keyword(s):

Community Assembly ◽

Beta Diversity ◽

Spatial Scales ◽

Process Models ◽

Small Scale ◽

Life Stages ◽

Relative Importance ◽

Vegetation Types ◽

Ecological Processes ◽

Environmental Selection

Environmental and dispersal-based processes have been widely investigated for the understanding of community assembly. However, the relative importance of these ecological processes across spatial scales, life history stages and forest types needs to be largely studied. We test the variability of ecological processes in shaping tree community composition across life stages and spatial scales, and in particular, the hypothesis that dispersal limitation dominates at smaller scales and early life stages, but environmental filtering at larger scales and later life stages. We used spatially explicit point process models to estimate the relative importance of environmental and dispersal processes and their combined effect on beta diversity across spatial scales and life stages in tropical and subtropical forests. These models fit the observed species distribution pattern and generated realizations of the fitted models for each species. We found that the importance of environmental and dispersal processes did not shift with life stages or vegetation types, but did with spatial scales. Dispersal provided the best explanation of large-scale patterns, but dispersal combined with environmental selection was superior for small-scale patterns. In conclusion, we confirm the importance of spatial scale for the effects and identification of community assembly mechanisms. Our results also suggest that the importance of both dispersal and environmental processes for community assembly could be pervasive across life stages and vegetation types. The generality of these findings should be tested further in different vegetation types and life stages to assess whether specific ecological processes have consistent effects on community structure across life stages and vegetation types.

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Inferring community assembly processes from trait diversity across environmental gradients

Journal of Tropical Ecology ◽

10.1017/s0266467416000262 ◽

2016 ◽

Vol 32 (4) ◽

pp. 290-299 ◽

Cited By ~ 6

Author(s):

Yong Shen ◽

Shi-Xiao Yu ◽

Ju-Yu Lian ◽

Hao Shen ◽

Hong-Lin Cao ◽

...

Keyword(s):

Environmental Factors ◽

Soil Fertility ◽

Functional Diversity ◽

Community Assembly ◽

Environmental Gradients ◽

Environmental Filtering ◽

Competitive Interactions ◽

Dry Matter Content ◽

Ecological Processes ◽

Trait Diversity

Abstract:Environmental filtering and competitive interactions are important ecological processes in community assembly. The contribution of the two processes to community assembly can be evaluated by shifts in functional diversity patterns. We examined the correlations between functional diversity of six traits (leaf chlorophyll concentration, dry matter content, size, specific leaf area, thickness and wood density) and environmental gradients (topography and soil) for 92 species in the 20-ha Dinghushan forest plot in China. A partial Mantel test showed that most of the community-weighted mean trait values changed with terrain convexity and soil fertility, which implied that environmental filtering was occurring. Functional diversity of many traits significantly increased with increasing terrain convexity and soil fertility, which was associated with increased light and below-ground resources respectively. These results suggest that co-occurring species are functionally convergent in regions of strong abiotic stress under the environmental filtering, but functionally divergent in more benign environments due to resource partitioning and competitive interactions. Single-trait diversity and multivariate functional diversity had different relationships with environmental factors, indicating that traits were related to different niche axes, and associated with different ecological processes, which demonstrated the importance of focusing niche axes in traits selection. Between 9% and 41% of variation in functional diversity of different traits was explained by environmental factors in stepwise multiple regression models. Terrain convexity and soil fertility were the best predictors of functional diversity, which contributed 30.5% and 29.0% of total R2to the model. These provided essential evidence that different environmental factors had distinguishing impacts on regulating diversity of traits.

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Phylogenetic and Functional Traits Verify the Combined Effect of Deterministic and Stochastic Processes in the Community Assembly of Temperate Forests along an Elevational Gradient

Forests ◽

10.3390/f12050591 ◽

2021 ◽

Vol 12 (5) ◽

pp. 591

Author(s):

Wensong Zhou ◽

Yuxin Zhang ◽

Shuang Zhang ◽

Basil N. Yakimov ◽

Keming Ma

Keyword(s):

Stochastic Processes ◽

Functional Traits ◽

Community Assembly ◽

Woody Plants ◽

Elevational Gradient ◽

Combined Effect ◽

Abiotic Environment ◽

Spatial Factors ◽

Assembly Mechanism ◽

Deterministic Processes

Explaining community assembly mechanisms along elevational gradients dominated by deterministic processes or stochastic processes is a pressing challenge. Many studies suggest that phylogenetic and functional diversity are significant indicators of the process. In this study, we analyzed the structure and beta diversity of phylogenetic and functional traits along an elevational gradient and discussed the effects of environmental and spatial factors. We found that the phylogenetic and functional traits showed inconsistent changes, and their variations were closely related to the abiotic environment. The results suggested that the community assembly of woody plants was obviously affected by the combined effect of deterministic processes and the stochastic hypothesis (primarily by the latter). Phylogenetic and functional traits had a certain relationship but changed according to different rules. These results enhance our understanding of the assembly mechanism of forest communities by considering both phylogenetic and functional traits.

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Assembly processes of gastropod community change with horizontal and vertical zonation in ancient Lake Ohrid: a metacommunity speciation perspective

Biogeosciences ◽

10.5194/bg-13-2901-2016 ◽

2016 ◽

Vol 13 (10) ◽

pp. 2901-2911 ◽

Cited By ~ 9

Author(s):

Torsten Hauffe ◽

Christian Albrecht ◽

Thomas Wilke

Keyword(s):

Community Composition ◽

Community Assembly ◽

Environmental Filtering ◽

Dispersal Limitation ◽

Species Interaction ◽

Relative Importance ◽

Lake Depth ◽

Ancient Lake ◽

Lake Ohrid ◽

Speciation Model

Abstract. The Balkan Lake Ohrid is the oldest and most diverse freshwater lacustrine system in Europe. However, it remains unclear whether species community composition, as well as the diversification of its endemic taxa, is mainly driven by dispersal limitation, environmental filtering, or species interaction. This calls for a holistic perspective involving both evolutionary processes and ecological dynamics, as provided by the unifying framework of the “metacommunity speciation model”.The current study used the species-rich model taxon Gastropoda to assess how extant communities in Lake Ohrid are structured by performing process-based metacommunity analyses. Specifically, the study aimed (1) to identifying the relative importance of the three community assembly processes and (2) to test whether the importance of these individual processes changes gradually with lake depth or discontinuously with eco-zone shifts.Based on automated eco-zone detection and process-specific simulation steps, we demonstrated that dispersal limitation had the strongest influence on gastropod community composition. However, it was not the exclusive assembly process, but acted together with the other two processes – environmental filtering and species interaction. The relative importance of the community assembly processes varied both with lake depth and eco-zones, though the processes were better predicted by the latter.This suggests that environmental characteristics have a pronounced effect on shaping gastropod communities via assembly processes. Moreover, the study corroborated the high importance of dispersal limitation for both maintaining species richness in Lake Ohrid (through its impact on community composition) and generating endemic biodiversity (via its influence on diversification processes). However, according to the metacommunity speciation model, the inferred importance of environmental filtering and biotic interaction also suggests a small but significant influence of ecological speciation. These findings contribute to the main goal of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) deep drilling initiative – inferring the drivers of biotic evolution – and might provide an integrative perspective on biological and limnological dynamics in ancient Lake Ohrid.

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Deterministic Selection Dominates Microbial Community Assembly in Termite Mounds Across a Large Spatial Area

10.21203/rs.3.rs-34782/v1 ◽

2020 ◽

Author(s):

Qing-Lin Chen ◽

Hang-Wei Hu ◽

Zhen-Zhen Yan ◽

Chao-Yu Li ◽

Bao-Anh Thi Nguyen ◽

...

Keyword(s):

Microbial Community ◽

Stochastic Processes ◽

Microbial Communities ◽

Fungal Community ◽

Community Assembly ◽

Distance Decay ◽

Termite Mounds ◽

Deterministic Processes ◽

Microbial Community Assembly

Abstract Background: Termites are ubiquitous insects in tropical and subtropical habitats, where they construct massive mounds from soil, their saliva and excreta. Termite mounds harbor an enormous amount of microbial inhabitants, which regulate multiple ecosystem functions such as mitigating methane emissions and increasing ecosystem resistance to climate change. However, we lack a mechanistic understanding about the role of termite mounds in modulating the microbial community assembly processes, which are essential to unravel the biological interactions of soil fauna and microorganisms, the major components of soil food webs. We conducted a large-scale survey across a >1500 km transect in northern Australia to investigate biogeographical patterns of bacterial and fungal community in 134 termite mounds and the relative importance of deterministic versus stochastic processes in microbial community assembly. Results: Microbial alpha (number of phylotypes) and beta (changes in bacterial and fungal community composition) significantly differed between termite mounds and surrounding soils. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungal communities had a stronger distance-decay relationship (slope = -1.91) than bacteria (slope = -0.21). Based on the neutral community model (fitness < 0.7) and normalized stochasticity ratio index (NST) with a value below the 50% boundary point, deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited significantly weaker impacts on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), probably due to the wider habitat niche breadth and higher potential migration rate of bacteria. The abundance of antibiotic resistance genes (ARGs) was negatively correlated with bacterial/fungal biomass ratios, indicating that ARG content might be an important biotic factor that drove the biogeographic pattern of microbial communities in termite mounds. Conclusions: Deterministic processes play a more important role than stochastic processes in shaping the microbial community assembly in termite mounds, an unique habitat ubiquitously distributed in tropical and subtropical ecosystems. An improved understanding of the biogeographic patterns of microorganisms in termite mounds is crucial to decipher the role of soil faunal activities in shaping microbial community assembly, with implications for their mediated ecosystems functions and services.

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