Stochastic Community Assembly: Does It Matter in …

1 Stochastic Community assembly : does ItMatter in Microbial Ecology?Jizhong Zhou,a,c,dDaliang Ninga,bInstitute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of CivilEngineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USAa; ConsolidatedCore Laboratory, University of Oklahoma, Norman, Oklahoma, USAb; Earth and Environmental Sciences,Lawrence Berkeley National Laboratory, Berkeley, California, USAc; State Key Joint Laboratory of EnvironmentSimulation and Pollution Control, School of Environment, Tsinghua University, Beijing, VERSUS DETERMINISM: HISTORICAL ECOLOGICAL COMPONENTS OF ECOLOGICAL Fundamental Ecological Contingency and Contemporary View from Ecology and PATTERNS TO PROCESSES.

2 APPROACHES TO INFER Ecological Stochasticity by Multivariate Stochasticity by Neutral-Theory-Based Process Ecological Stochasticity by Null Model APPROACHES FOR TESTING THE IMPORTANCE OF Community assembly Quantitative Assumptions of the Statistical REMARKS AND FUTURE the mechanisms controlling Community diversity, functions,succession, and biogeography is a central, but poorly understood, topic in ecology, par-ticularly in microbial ecology. Although Stochastic processes are believed to play non-negligible roles in shaping Community structure, their importance relative to determinis-tic processes is hotly debated.

3 The importance of ecological stochasticity in shapingmicrobial Community structure is far less appreciated. Some of the main reasons forsuch heavy debates are the difficulty in defining stochasticity and the diverse methodsused for delineating stochasticity. Here, we provide a critical review and synthesis ofdata from the most recent studies on Stochastic Community assembly in microbial ecol-ogy. We then describe both Stochastic and deterministic components embedded in vari-ous ecological processes, including selection, dispersal, diversification, and drift.

4 We alsodescribe different approaches for inferring stochasticity from observational diversity pat-terns and highlight experimental approaches for delineating ecological stochasticity inmicrobial communities. In addition, we highlight research challenges, gaps, and futuredirections for microbial Community assembly assembly , ecological drift, ecological processes, ecologicalstochasticity, microbial communitiesPublished11 October 2017 CitationZhou J, Ning D. 2017. Stochasticcommunity assembly : does it Matter inmicrobial ecology?

5 Microbiol Mol Biol Rev81 2017 American Society Rights to Jizhong 2017 Volume 81 Issue 4 Molecular Biology Reviews on October 11, 2017 by from INTRODUCTIONB iodiversity, a measure of the variety of life found on Earth (1,2), is a central topicinecology and for society, because the dramatic loss in biodiversity could alter thefunctions and services provided by ecosystems (3,4). Since the last century, variousfacetsof biodiversity have been intensively examined across space, time, and ecologicalgradients from different perspectives ( , taxonomic, phylogenetic, and functionaldiversity).

6 Various fundamental biodiversity patterns have been observed in ecology, , latitudinal diversity patterns (5 9), species abundance distributions (SADs) (10 12),species-arearelationships (SARs) (13 16), distance-decay relationships (17 20), andspecies-timerelationships (19,21 25). However, the mechanisms and factors control-lingsuch diversity patterns remain unclear and highly controversial. Traditional niche-based theory hypothesizes that deterministic factors such as species traits, interspeciesinteractions ( , competition, predation, mutualisms, and trade-offs), and environmen-tal conditions ( , pH, temperature, salt, and moisture) govern Community structure,which are often referred to as deterministic processes (26,27).

7 In contrast, neutraltheoryassumes that Community structures are independent of species traits andgoverned by Stochastic processes of birth, death, colonization, extinction, and specia-tion (28,29). Although, recently, it has been generally accepted that both deterministicandstochastic processes occur simultaneously in the assembly of local communities(30 33), a central debate is on their relative importance in controlling communitystructure,succession, and biogeography (34 37).Microorganismsare the most diverse group of life on Earth, inhabiting almost everyimaginable environment (38).

8 Although it is well known that microbial biodiversity isextremelyhigh (12,39 43), why and how such high diversity is generated and main-tainedare long-standing puzzles to microbiologists. Various deterministic factors, suchas changes in environmental conditions (44 48), habitat conditions in hosts (49,50),carbonand nutrient resource heterogeneity (40,51), species traits and/or interspeciesinteractions(52 54), and plant diversity (55 60), are important in governing microbialcommunitystructure. However, they are alone not sufficient to explain the extremelyhigh diversity of microbial communities observed in nature.

9 Numerous studies ( ,13,14,61 63) revealed that substantial amounts of variation in microbial communitystructurecould not be explained by environmental and/or distance effects despiteextensive measurements of all routinely measured environmental variables. It is be-lieved that in many cases, considerable amounts of the microbial Community variationobserved could result from Stochastic processes of Community assembly throughhistorical contingency ( , priority effects), ecological drift, and/or dispersal limitation(29,31,32,35,36,62,64 66).

10 However, the importance of Stochastic processes incontrollingmicrobial biodiversity has been recognized only in some recent studies (33,35,36,67,68). Partly due to the small organism size, vast diversity of microbialcommunities,and uncultivated status for the majority of microorganisms, the mecha-nisms underlying microbial Community structure, succession, and biogeography aremuch less understood in general, compared to the ecology of macroorganisms (35).Alongwith the rapid advance and application of large-scale high-throughput met-agenomics technologies in the last decade (69), mechanisms underlying microbialcommunityassembly have received great attention, especially within the last severalyears, with more emphasis on stochasticity (Fig.)