Integrating succession and community assembly perspectives

Testing the sequence of successional processes in miniature ecosystems

Dispersal, environmental filtering, and biotic interactions define the species inventory of local communities. Along successional gradients, these assembly processes are predicted to sequentially vary in their relative importance with dispersal as the dominating process early in succession, followed by environmental filtering and biotic interactions at later stages. While observational data from field studies supported this prediction, controlled experiments confirming a sequence of successional processes are still lacking. We designed miniature ecosystems to explicitly test these assumptions under controlled laboratory conditions. Our "Ecosystems on a Plate" (EsoaP) are 3D-printed customized microplates with 24 connected wells allowing us to track dispersal, niche filtering, and biotic interactions among bacteria and plants in time and space. Within EsoaPs, we created heterogeneous habitat landscapes by well-specific nutrient levels or by providing plant seedlings as mutualistic partners in a checkerboard pattern. Bacteria of a single strain were released in one well and subsequently distributed themselves within the plates. We measured the spatial distribution of bacterial abundances at two time points as a function of abiotic or biotic heterogeneity. Bacterial abundance distribution confirmed a shift from initial dispersal-dominated processes to later niche filtering and biotic interactions as more important processes. Our approach follows the principles of open science as the affordable availability of 3D printers as well as shared STL files makes EsoaPs disseminatable and accessible to all levels of society, facilitating future experimental research.

IMPORTANCE

Hypotheses regarding the underlying processes of ecological successions have primarily emerged from and have been tested in observational studies, lacking substantial support through controlled experiments. The design of such experiments should focus on testing contemporary ecological theories at the intersection of community assembly and successional research. To achieve this, we developed and employed 3D-printed "Ecosystems on a Plate" (EsoaP) within controlled laboratory settings. EsoaPs surmount several limitations of nanoscale instruments that had hindered their application in ecologically meaningful research. By sharing 3D printing designs, experimental protocols, and data openly, we facilitate reproducibility of our experiments by researchers across diverse ecological disciplines. Moreover, our approach facilitates cost-effective replication of experiments, democratizing access to tools for ecological research, and thus holds the potential to serve as a model for future studies and educational purposes.

Species pool, local assembly processes: Disentangling the mechanisms determining bacterial α- and β-diversity during forest secondary succession

Across ecology, and particularly within microbial ecology, there is limited understanding how the generation and maintenance of diversity. Although recent work has shown that both local assembly processes and species pools are important in structuring microbial communities, the relative contributions of these mechanisms remain an important question. Moreover, the roles of local assembly processes and species pools are drastically different when explicitly considering the potential for saturation or unsaturation, yet this issue is rarely addressed. Thus, we established a conceptual model that incorporated saturation theory into the microbiological domain to advance the understanding of mechanisms controlling soil bacterial diversity during forest secondary succession. Conceptual model hypotheses were tested by coupling soil bacterial diversity, local assembly processes and species pools using six different forest successional chronosequences distributed across multiple climate zones. Consistent with the unsaturated case proposed in our conceptual framework, we found that species pool consistently affected α-diversity, even while local assembly processes on local richness operate. In contrast, the effects of species pool on β-diversity disappeared once local assembly processes were taken into account, and changes in environmental conditions during secondary succession led to shifts in β-diversity through mediation of the strength of heterogeneous selection. Overall, this study represents one of the first to demonstrate that most local bacterial communities might be unsaturated, where the effect of species pool on α-diversity is robust to the consideration of multiple environmental influences, but β-diversity is constrained by environmental selection.

Community assembly of the human piercing microbiome

Predicting how biological communities respond to disturbance requires understanding the forces that govern their assembly. We propose using human skin piercings as a model system for studying community assembly after rapid environmental change. Local skin sterilization provides a 'clean slate' within the novel ecological niche created by the piercing. Stochastic assembly processes can dominate skin microbiomes due to the influence of environmental exposure on local dispersal, but deterministic processes might play a greater role within occluded skin piercings if piercing habitats impose strong selection pressures on colonizing species. Here we explore the human ear-piercing microbiome and demonstrate that community assembly is predominantly stochastic but becomes significantly more deterministic with time, producing increasingly diverse and ecologically complex communities. We also observed changes in two dominant and medically relevant antagonists (Cutibacterium acnes and Staphylococcus epidermidis), consistent with competitive exclusion induced by a transition from sebaceous to moist environments. By exploiting this common yet uniquely human practice, we show that skin piercings are not just culturally significant but also represent ecosystem engineering on the human body. The novel habitats and communities that skin piercings produce may provide general insights into biological responses to environmental disturbances with implications for both ecosystem and human health.

The collapse and re-establishment of stability regulate the gradual transition of bacterial communities from macrophytes- to phytoplankton-dominated types in a large eutrophic lake

Eutrophic lakes often exhibit two alternative types: macrophytes-dominated (MD) and phytoplankton-dominated (PD). However, the nature of bacterial community types that whether the transition from the MD to the PD types occurs in a gradual or abrupt manner remains hotly debated. Further, the theoretical recognition that stability regulates the transition of bacterial community types remains qualitative. To address these issues, we divided the transition of bacterial communities along a trophic gradient into 12 successional stages, ranging from the MD to the PD types. Results showed that 12 states were clustered into three distinct regimes: MD type, intermediate transitional type and PD type. Bacterial communities were not different between consecutive stages, suggesting that the transition of alternative types occurs in a continuous gradient. At the same time, the stability of bacterial communities was significantly lower in the intermediate type than in the MD or PD types, highlighting that the collapse and re-establishment of community stability regulate the transition. Further, our results showed that the high complexity of taxon interactions and strong stochastic processes disrupt the stability. Ultimately, this study enables deeper insights into understanding the alternative types of microbial communities in the view of community stability.

Adaptive Relationships in Hemi-Boreal Forests: Tree Species Responses to Competition, Stress, and Disturbance

European Union forest policy calls for closer-to-nature forest management, but natural disturbances and forest succession are ecological phenomena that are difficult to characterize and integrate into sustainable forest management practices. Therefore, the aim of this study is to explore the adaptive properties of Lithuania's hemi-boreal forest ecosystems. To accomplish this, we first reviewed (i) the potential natural forest communities, (ii) the successional dynamics, and (iii) adaptive strategies of forest trees, and second, we synthesised the adaptive relationships using these three reviews. The results firstly identified that Lithuania's potential natural forests are broadly divided into two climatically based zonal formations: (i) mesophytic and hygromesophytic coniferous and broadleaved forests and (ii) mesophytic deciduous broadleaved and coniferous-broadleaved forests. Secondly, the review of successional dynamics showed that each tree species can be categorised into various end communities and plant functional groups. Using the differences in tree establishment and phenological development modes we identified four forest dynamic types of tree adaptive strategies: stress-resistant ruderals, competitive stress-sensitive ruderals, ruderal stress-sensitive competitors, and stress-resistant competitors. Such functional redundancy leads to a variety of tree responses to competition, stress, and disturbance, which reduces the risk of loss of forest ecosystem functioning. Finally, the synthesised review on the adaptive relationships of each forest tree community shows both the niche position of each hemi-boreal forest tree species and how they should be managed in the organization of plant communities. We believe that this research can serve as a guide for future relevant research and the development of appropriate methods for sustainable forest management.

Exploring the Frequency and Distribution of Ecological Non-monotonicity in Associations among Ecosystem Constituents

Complex links between biotic and abiotic constituents are fundamental for the functioning of ecosystems. Although non-monotonic interactions and associations are known to increase the stability, diversity, and productivity of ecosystems, they are frequently ignored by community-level standard statistical approaches. Using the copula-based dependence measure qad, capable of quantifying the directed and asymmetric dependence between variables for all forms of (functional) relationships, we determined the proportion of non-monotonic associations between different constituents of an ecosystem (plants, bacteria, fungi, and environmental parameters). Here, we show that up to 59% of all statistically significant associations are non-monotonic. Further, we show that pairwise associations between plants, bacteria, fungi, and environmental parameters are specifically characterized by their strength and degree of monotonicity, for example, microbe-microbe associations are on average stronger than and differ in degree of non-monotonicity from plant-microbe associations. Considering directed and non-monotonic associations, we extended the concept of ecosystem coupling providing more complete insights into the internal order of ecosystems. Our results emphasize the importance of ecological non-monotonicity in characterizing and understanding ecosystem patterns and processes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10021-023-00867-9.

Accuracy of mutual predictions of plant and microbial communities vary along a successional gradient in an alpine glacier forefield

Receding glaciers create virtually uninhabited substrates waiting for initial colonization of bacteria, fungi and plants. These glacier forefields serve as an ideal ecosystem for studying transformations in community composition and diversity over time and the interactions between taxonomic groups in a dynamic landscape. In this study, we investigated the relationships between the composition and diversity of bacteria, fungi, and plant communities as well as environmental factors along a successional gradient. We used random forest analysis assessing how well the composition and diversity of taxonomic groups and environmental factors mutually predict each other. We did not identify a single best indicator for all taxonomic and environmental properties, but found specific predictors to be most accurate for each taxon and environmental factor. The accuracy of prediction varied considerably along the successional gradient, highlighting the dynamic environmental conditions along the successional gradient that may also affect biotic interactions across taxa. This was also reflected by the high accuracy of predictions of plot age by all taxa. Next to plot age, our results indicate a strong importance of pH and temperature in structuring microbial and plant community composition. In addition, taxonomic groups predicted the community composition of each other more accurately than environmental factors, which may either suggest that these groups similarly respond to other not measured environmental factors or that direct interactions between taxa shape the composition of their communities. In contrast, diversity of taxa was not well predicted, suggesting that community composition of one taxonomic group is not a strong driver of the diversity of another group. Our study provides insights into the successional development of multidiverse communities shaped by complex interactions between taxonomic groups and the environment.

Succession of the Abandoned Rice Fields Restores the Riparian Forest

The vegetation changes in the abandoned rice fields with different abandonment histories were analyzed across the country of South Korea. The successional process was confirmed by changes in vegetation profiles and species composition. The vegetation profile showed the process of starting with grassland, passing through the shrub stage, and turning into a tree-dominated forest. DCA ordination based on vegetation data showed that the process began with grasslands consisting of Persicaria thunbergii, Juncus effusus var. decipiens, Phalaris arundinacea, etc., then partially went through shrubland stages consisting of Salix gracilistyla, S. integra, young Salix koreensis, etc., and ultimately changed to a Salix koreensis dominated forest. In order to study the relationship between the succession process of the abandoned rice paddies and riparian vegetation, information on riparian vegetation was collected in the same watershed as the abandoned rice paddies investigated. Riparian vegetation tended to be distributed in the order of grasslands consisting of Phragmites japonica, Miscanthus sacchariflorus, P. arundinacea, etc., shrubland dominated by Salix gracilistyla, S. integra, etc., and a S. koreensis community dominated forest by reflecting the flooding regime as far away from the waterway. The result of stand ordination based on the riparian vegetation data also reflected the trend. From this result, we confirmed that the temporal sequence of the vegetation change that occurred in the abandoned rice fields resembled the spatial distribution of the riparian vegetation. Consequently, succession of the abandoned rice fields restored the riparian forest, which has almost disappeared in Korea and other Asian countries that use rice as their staple food.

Model-checking ecological state-transition graphs

Model-checking is a methodology developed in computer science to automatically assess the dynamics of discrete systems, by checking if a system modelled as a state-transition graph satisfies a dynamical property written as a temporal logic formula. The dynamics of ecosystems have been drawn as state-transition graphs for more than a century, ranging from state-and-transition models to assembly graphs. Model-checking can provide insights into both empirical data and theoretical models, as long as they sum up into state-transition graphs. While model-checking proved to be a valuable tool in systems biology, it remains largely underused in ecology apart from precursory applications. This article proposes to address this situation, through an inventory of existing ecological STGs and an accessible presentation of the model-checking methodology. This overview is illustrated by the application of model-checking to assess the dynamics of a vegetation pathways model. We select management scenarios by model-checking Computation Tree Logic formulas representing management goals and built from a proposed catalogue of patterns. In discussion, we sketch bridges between existing studies in ecology and available model-checking frameworks. In addition to the automated analysis of ecological state-transition graphs, we believe that defining ecological concepts with temporal logics could help clarify and compare them.

Succession comprises a sequence of threshold-induced community assembly processes towards multidiversity

Research on successions and community assembly both address the same processes such as dispersal, species sorting, and biotic interactions but lack unifying concepts. Recent theoretical advances integrated both research lines proposing a sequence of stochastic and deterministic processes along successional gradients. Shifts in ecosystem states along successional gradients are predicted to occur abruptly once abiotic and biotic factors dominate over dispersal as main driver. Considering the multidiversity composed of five organismal groups including plants, animals, and microbes, our results imply that stochastic, likely dispersal-dominated, processes are replaced by rather deterministic processes such as environmental filtering and biotic interactions after around 60 years of succession in a glacier forefield. The niche-based character of later successional processes is further supported by a decline in multi-beta-diversity. Our results may update concepts of community assembly by considering multiple taxa, help to bridge the gap between research on successions and community assembly, and provide insights into the emergence of multidiverse and complex ecosystems.

Ecological Linkages between a Biofilm Ecosystem and Reactor Performance: The Specificity of Biofilm Development Phases

In biofilm-based engineered ecosystems, the reactor performance was closely linked to interspecies interactions within a biofilm ecosystem, whereas the ecological processes underpinning such linkage were still unenlightened. Herein, the principles of community succession and assembly were integrated to capture the ecological laws of biofilm development by molecular ecological networks and assembly model analysis based on the 16S rRNA sequencing analysis and metagenomics in a well-controlled moving bed biofilm reactor. At the initial colonization phase (days 0-2, driven by initial colonizers), interspecific cooperation (74.18%) facilitated initial biofilm formation, whereas some pioneers, and keystone species disappeared at later phases. At the accumulation phase (days 3-30, rapid biofilm development), interspecific cooperation (81.41 ± 5.07%) contributed to rapid biofilm development and keystone species were mainly involved in quorum sensing or positively correlated with extracellular polymeric substance production. At the maturation phase (days 31-106, a well-adapted quasi-equilibrium state), increased interspecific competition (32.74 ± 4.77%) and higher small-world property facilitated the rapid information transportation and pollutant treatment, and keystone species were positively correlated with the removal of COD and NH₄⁺-N. Homogenizing dispersal diminished the contemporary community dissimilarities, while turnover but rather nestedness governed the temporal variations in the biofilm succession period. This study highlighted the specificity of ecological processes at distinct biofilm development phases, which would advance our understanding on the development-to-function linkages in biofilm-based treatment processes.

Plant Diversity and Agroecosystem Function in Riparian Agroforests: Providing Ecosystem Services and Land-Use Transition

Achieving biologically diverse agricultural systems requires a commitment to changes in land use. While in-field agrobiodiversity is a critical route to such a transition, riparian systems remain an important, yet understudied, pathway to achieve key diversity and ecosystem services and targets. Notably, at the interface of agricultural landscapes and aquatic systems, the diversification of riparian buffers with trees reduces the non-point source pollution in waterways. However, in riparian agroforestry systems, little is known about herbaceous community patterns and, importantly, the herbaceous community’s role in governing carbon (C) and nitrogen (N) cycling. Our study investigated herbaceous community taxonomic and phylogenetic diversity patterns in riparian (i) grasslands (GRASSLAND), (ii) rehabilitated agroforests (AGROFOREST-REHAB), and (iii) remnant forests (AGROFOREST-NATURAL). We then determined the biodiversity-ecosystem function relationships between community functional diversity metrics, C and N cycling, and greenhouse gas fluxes. We observed significant differences in taxonomic and phylogenetic diversity among riparian buffer types. We found that herbaceous plant communities in riparian agroforestry systems expressed plant trait syndromes associated with fast-growing, resource acquiring strategies, while grassland buffer plants exhibited slow-growing, resource conserving strategies. Herbaceous communities with high functional diversity and resource acquiring trait syndromes, such as those in the agroforestry riparian systems, were significantly correlated with lower rates of soil CO2 efflux and N mineralization, both of which are key fluxes related to ecosystem service delivery. Our findings provide further evidence that functionally diverse, and not necessarily taxonomically diverse, plant communities are strongly correlated to positive ecosystem processes in riparian agroforestry systems, and that these communities contribute to the transition of agricultural lands toward biologically and functionally diverse landscapes.

Flooding and hydrologic connectivity modulate community assembly in a dynamic river-floodplain ecosystem

Braided river floodplains are highly dynamic ecosystems, where aquatic communities are strongly regulated by the hydrologic regime. So far, however, understanding of how flow variation influences assembly mechanisms remains limited. We collected benthic chironomids and oligochaetes over a year across a lateral connectivity gradient in the semi-natural Tagliamento River (Italy). Four bankfull flood events occurred during the study, allowing the assessment of how flooding and hydrologic connectivity mediate the balance between stochastic and deterministic community assembly. While invertebrate density and richness were positively correlated with connectivity, diversity patterns showed no significant correlation. Species turnover through time increased with decreasing connectivity. Contrary to expectations, hydrologic connectivity did not influence the response of community metrics (e.g. diversity, density) to floods. Invertebrate composition was weakly related to connectivity, but changed predictably in response to floods. Multivariate ordinations showed that faunal composition diverged across the waterbodies during stable periods, reflecting differential species sorting across the lateral gradient, but converged again after floods. Stable hydrological periods allowed communities to assemble deterministically with prevalence of non-random beta-diversity and co-occurrence patterns and larger proportion of compositional variation explained by local abiotic features. These signals of deterministic processes declined after flooding events. This occurred despite no apparent evidence of flood-induced homogenisation of habitat conditions. This study is among the first to examine the annual dynamic of aquatic assemblages across a hydrologic connectivity gradient in a natural floodplain. Results highlight how biodiversity can exhibit complex relations with hydrologic connectivity. However, appraisal of the assembly mechanisms through time indicated that flooding shifted the balance from deterministic species sorting across floodplain habitats, towards stochastic processes related to organisms redistribution and the likely resetting of assembly to earlier stages.

Change in fish functional diversity and assembly rules in the course of tidal marsh restoration

Functional trait theory provides a mechanistic framework to understand change in community composition and community assembly through time and space. Despite this, trait-based approaches have seldom been used in ecological restoration. Succession theory predicts that habitat complexity and resource availability will increase with restoration time, leading to increased functional dissimilarity among coexisting species. However, in the case of tidal marsh restoration, it is not clear whether reestablishing the harsh abiotic conditions typical of estuaries will initiate successional trajectories. We investigated monotonic changes in the functional structure of fish communities and shifts in assembly mechanisms, with tidal restoration time. A five-level gradient of ‘intertidal habitat naturalness’ was constructed from a set of artificialized (dyked), restored (with different ages) and natural intertidal sites, and used as a surrogate for restoration progress. The fish ecophases were described using ten functional traits related to food acquisition and swimming ability. The trends in six functional dimensions (identity, richness, evenness, dispersion, originality and specialization) were investigated along the naturalness gradient. Consistenly with succession theory, functional specialization, dispersion and, less markedly, richness increased with intertidal naturalness meaning that restored and natural intertidal habitats supplied fish with specific foraging and dwelling conditions absent from dyked marshes. Community assembly patterns varied with respect to traits and differed at both ends of the naturalness gradient. Dyked marshes were more affected by trait convergence possibly due to limiting resources. Environmental filtering was detected all along the naturalness gradient although the traits affected varied depending on the naturalness level of habitats. Environmental filtering tended to decrease in restored and natural intertidal habitats. Increased naturalness restored the attractivity of benthic habitats as feeding or settling grounds, promoted shelter-seeking vs. free-swimming strategists and favoured ecophases with carnivorous diets, feeding on microinvertebrates and benthic low-mobility macroinvertebrates. Approaches based on functional trait diversity have the potential to question and refine the theoretical frame of ecological restoration and to assist managers in their efforts to restore tidal wetlands.

Past is prologue: host community assembly and the risk of infectious disease over time

Infectious disease risk is often influenced by host diversity, but the causes are unresolved. Changes in diversity are associated with changes in community structure, particularly during community assembly; therefore, by incorporating change over time, host community assembly may provide a framework to resolve causation. In turn, community assembly can be driven by many processes, including resource enrichment. To test the hypothesis that community assembly causally links host diversity to future disease, we experimentally manipulated host diversity and resource supply to hosts, then allowed communities to assemble for 2 years (surveyed 2012-2014). Initially, host diversity increased disease. Subsequently, host diversity did not directly alter disease. However, host diversity determined the trajectory of host community assembly, altering colonisation by exotic host species and richness-independent host phylogenetic diversity, which together reversed the initial increase in disease. Ultimately, incorporating the temporal dimension of community assembly revealed novel mechanisms linking host diversity to future disease.

The role of breeding system in community dynamics: Growth and mortality in forests of different successional stages

Plant sexual systems appear to play an important role in community assembly: Dioecious species are found to tend to have a higher propensity to colonize communities in early successional stages. Here, we test two demographic hypotheses to explain this pattern in temperate forests. First, we test demographic differences between hermaphrodite and dioecious species in stressful younger successional stages: Previous theory predicts that hermaphrodite seed production is more harmed in stressful environments than that of dioecious populations leading to an advantage for females of dioecious species. Second, in primary forest, we hypothesized that dioecious species would show demographic advantage over monomorphic ones. We used data from two temperate forest plots in Northeast China surveyed over 10 years to compare the rates of growth and mortality of tree species with contrasting breeding systems in both secondary and primary forests. We assessed the effect of breeding system on the growth-mortality trade-off, while controlling for other traits usually considered as correlates of growth and mortality rates. We show that in the secondary forest, dioecious species showed weak advantage in demographic rates compared with monomorphic species; dioecious species showed considerably both lower relative growth and mortality rates compared to the hermaphrodites in the primary forest over 10 years, consistent with a priori predictions. Hermaphrodites showed strong growth-mortality trade-offs across forest stages, even when possibly confounding factors had been accounted for. These results suggest that sexual system influences community succession and assembly by acting on the rates of growth and mortality, and the trade-off between them. As vegetation develops, the demographic differences between breeding systems are much larger. Our results demonstrate the association between breeding system, succession, and community assembly and that this relationship is succession-stage dependent. Our findings support the suggestion that the demographic advantage of dioecious species facilitates the coexistence of sexual systems in primary forest.

Beta Diversity Patterns of Post-fire Forests in Central Yunnan Plateau, Southwest China: Disturbances Intensify the Priority Effect in the Community Assembly

Post-fire succession is an ideal case for studying effects of disturbance on community assembly, and the key is to disentangle the contributions of assembly processes to the variation of community composition, namely beta diversity, and the contingent scales. The central Yunnan Plateau of Southwest China is characterized by monsoon related seasonal drought, and frequent forest fires. We sampled five fire sites burned in different years and a middle aged forest, measured species composition dissimilarity and its species turnover and nestedness components, within each fire site and across all sites. Results indicated species turnover as the primary component of beta diversity within all communities. There was no trend of change with year-since-fire (YSF) in beta diversity among early post-fire communities, but beta diversity in the middle aged community was significantly higher. Species turnover patterns across fire sites revealed a weak dispersal limit effect, which was stronger at lower than upper slope position for woody plants, and reverse for herbs. At the site scale, the species dissimilarity and turnover both enlarged with increasing slope position difference, especially in the middle-aged community, but the species nestedness had no consistent trend among sites, except a decreasing trend in the middle-aged forest. (Partial) Mantel tests indicated habitat filtering [primarily indicating total nitrogen (TN) and slope position] played a much stronger role than dispersal limit and YSF (indicating competition intensity) for the post-fire forest assembly at the landscape scale, for both woody and herbaceous layers. However, at the site scale, Mantel tests indicated a diminishing effect of soil nutrient filtering with increasing YSF, while effects of topography and spatial distance in the middle aged community was stronger. This divergence suggests the primary assembly mechanism gradually shift away from the soil constraint. While the seasonal drought and the mountain topography dominate the environmental legacy, our results imply that fires may reinforce a priority effect in the forests assembly in this region, by creating a habitat filtering (e.g., moisture and nitrogen limitation) effect on species composition in post-fire communities.

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.