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      At the Nexus of History, Ecology, and Hydrobiogeochemistry: Improved Predictions across Scales through Integration

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          Abstract

          To improve predictions of ecosystem function in future environments, we need to integrate the ecological and environmental histories experienced by microbial communities with hydrobiogeochemistry across scales. A key issue is whether we can derive generalizable scaling relationships that describe this multiscale integration.

          ABSTRACT

          To improve predictions of ecosystem function in future environments, we need to integrate the ecological and environmental histories experienced by microbial communities with hydrobiogeochemistry across scales. A key issue is whether we can derive generalizable scaling relationships that describe this multiscale integration. There is a strong foundation for addressing these challenges. We have the ability to infer ecological history with null models and reveal impacts of environmental history through laboratory and field experimentation. Recent developments also provide opportunities to inform ecosystem models with targeted omics data. A major next step is coupling knowledge derived from such studies with multiscale modeling frameworks that are predictive under non-steady-state conditions. This is particularly true for systems spanning dynamic interfaces, which are often hot spots of hydrobiogeochemical function. We can advance predictive capabilities through a holistic perspective focused on the nexus of history, ecology, and hydrobiogeochemistry.

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          Most cited references18

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          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.
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            Quantifying community assembly processes and identifying features that impose them.

            Spatial turnover in the composition of biological communities is governed by (ecological) Drift, Selection and Dispersal. Commonly applied statistical tools cannot quantitatively estimate these processes, nor identify abiotic features that impose these processes. For interrogation of subsurface microbial communities distributed across two geologically distinct formations of the unconfined aquifer underlying the Hanford Site in southeastern Washington State, we developed an analytical framework that advances ecological understanding in two primary ways. First, we quantitatively estimate influences of Drift, Selection and Dispersal. Second, ecological patterns are used to characterize measured and unmeasured abiotic variables that impose Selection or that result in low levels of Dispersal. We find that (i) Drift alone consistently governs ∼25% of spatial turnover in community composition; (ii) in deeper, finer-grained sediments, Selection is strong (governing ∼60% of turnover), being imposed by an unmeasured but spatially structured environmental variable; (iii) in shallower, coarser-grained sediments, Selection is weaker (governing ∼30% of turnover), being imposed by vertically and horizontally structured hydrological factors;(iv) low levels of Dispersal can govern nearly 30% of turnover and be caused primarily by spatial isolation resulting from limited exchange between finer and coarser-grain sediments; and (v) highly permeable sediments are associated with high levels of Dispersal that homogenize community composition and govern over 20% of turnover. We further show that our framework provides inferences that cannot be achieved using preexisting approaches, and suggest that their broad application will facilitate a unified understanding of microbial communities.
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              Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.

              Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages--which provide a larger spatiotemporal scale relative to within stage analyses--revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended--and experimentally testable--conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.
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                Author and article information

                Journal
                mSystems
                mSystems
                msys
                msys
                mSystems
                mSystems
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2379-5077
                10 April 2018
                Mar-Apr 2018
                : 3
                : 2
                : e00167-17
                Affiliations
                [a ]Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA
                Author notes
                Address correspondence to James.Stegen@ 123456pnnl.gov .

                Conflict of Interest Disclosures: J.C.S. has nothing to disclose.

                Citation Stegen JC. 2018. At the nexus of history, ecology, and hydrobiogeochemistry: improved predictions across scales through integration. mSystems 3:e00167-17. https://doi.org/10.1128/mSystems.00167-17.

                Author information
                https://orcid.org/0000-0001-9135-7424
                Article
                mSystems00167-17
                10.1128/mSystems.00167-17
                5895879
                29657967
                9f5916d2-356c-4064-9d9a-225e4371bee2
                Copyright © 2018 Stegen.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 31 October 2017
                : 16 February 2018
                Page count
                Figures: 4, Tables: 1, Equations: 0, References: 21, Pages: 9, Words: 4454
                Categories
                Perspective
                Ecological and Evolutionary Science
                Special Issue
                Custom metadata
                March/April 2018

                biogeochemistry,ecological theory,ecosystem interfaces,historical contingency,hydrology,microbial communities,perturbation,resilience,scaling theory,succession

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