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      Understanding Microbiome Stability in a Changing World

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          Abstract

          Microbiomes underpin biogeochemical processes, sustain the bases of food webs, and recycle carbon and nutrients. Thus, microbes are frontline players in determining ecosystem responses to environmental change.

          ABSTRACT

          Microbiomes underpin biogeochemical processes, sustain the bases of food webs, and recycle carbon and nutrients. Thus, microbes are frontline players in determining ecosystem responses to environmental change. My research team and I investigate the causes and consequences of microbiome stability. Our primary objective is to understand the responses of complex microbiomes to stressors associated with environmental change. This work is important because Earth is changing rapidly and drastically, and these changes are expected to have serious consequences for ecosystems, their inhabiting organisms, and their microbiomes. Therefore, we aim to understand the repercussions of alterations to microbiome structure and functions and to use this information to predict the responses of microbiomes to stressors. This research is critical to prepare for, respond to, and potentially moderate environmental change. We anticipate that the results of our research will contribute toward these goals and will broadly inform management or manipulation of microbiomes toward desired functions.

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          Most cited references11

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          Diversity is the question, not the answer

          Local diversity (within-sample or alpha diversity) is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity or invasibility, are much more nuanced. I argue that diversity without context provides limited insights into the mechanisms underpinning community patterns. I provide examples from traditional and microbial ecology to discuss common complications and assumptions about within-sample diversity that may prevent us from digging deeper into the more specific mechanisms underpinning community outcomes. I suggest that measurement of diversity should serve as a starting point for further inquiry of ecological mechanisms rather than an 'answer' to community outcomes.
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            Temporal patterns of rarity provide a more complete view of microbial diversity.

            Recently, conditionally rare taxa (CRTs)--those taxa that are typically in very low abundance but occasionally achieve prevalence--were shown to contribute to patterns of microbial diversity because their collective dynamics explained a large proportion of temporal variability in microbial community structure. Here the benefits and challenges of characterizing the presence and interpreting the role of CRTs are further explored, along with questions about CRT ecology. We also introduce a conceptual model for thinking about microbial taxa as dynamic components along the dimensions of occurrence and abundance. Accounting for CRTs in interpretations of microbial ecological dynamics is essential if we are to understand community stability and ecoevolutionary interactions.
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              Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

              Press disturbances are stressors that are extended or ongoing relative to the generation times of community members, and, due to their longevity, have the potential to alter communities beyond the possibility of recovery. They also provide key opportunities to investigate ecological resilience and to probe biological limits in the face of prolonged stressors. The underground coal mine fire in Centralia, Pennsylvania has been burning since 1962 and severely alters the overlying surface soils by elevating temperatures and depositing coal combustion pollutants. As the fire burns along the coal seams to disturb new soils, previously disturbed soils return to ambient temperatures, resulting in a chronosequence of fire impact. We used 16S rRNA gene sequencing to examine bacterial and archaeal soil community responses along two active fire fronts in Centralia, and investigated the influences of assembly processes (selection, dispersal and drift) on community outcomes. The hottest soils harbored the most variable and divergent communities, despite their reduced diversity. Recovered soils converged toward similar community structures, demonstrating resilience within 10–20 years and exhibiting near-complete return to reference communities. Measured soil properties (selection), local dispersal, and neutral community assembly models could not explain the divergences of communities observed at temperature extremes, yet beta-null modeling suggested that communities at temperature extremes follow niche-based processes rather than null. We hypothesize that priority effects from responsive seed bank transitions may be key in explaining the multiple equilibria observed among communities at extreme temperatures. These results suggest that soils generally have an intrinsic capacity for robustness to varied disturbances, even to press disturbances considered to be ‘extreme', compounded, or incongruent with natural conditions.
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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
                20 March 2018
                Mar-Apr 2018
                : 3
                : 2
                : e00157-17
                Affiliations
                [a ]Michigan State University Department of Microbiology and Molecular Genetics and Department of Plant, Soil and Microbial Sciences, Michigan State Plant Resilience Institute, Program in Ecology, Evolutionary Biology, and Behavior, East Lansing, Michigan, USA
                Author notes
                Address correspondence to shadeash@ 123456msu.edu .

                Conflict of Interest Disclosures: A.S. reports grants from the National Science Foundation, the DOE Great Lakes Bioenergy Research Center, and the National Institutes of Health as well as funding from Michigan State University and the Michigan State University Plant Resilience Institute during the conduct of the study.

                Citation Shade A. 2018. Understanding microbiome stability in a changing world. mSystems 3:e00157-17. https://doi.org/10.1128/mSystems.00157-17.

                Author information
                https://orcid.org/0000-0002-7189-3067
                Article
                mSystems00157-17
                10.1128/mSystems.00157-17
                5881018
                29629411
                863b1de0-4acb-4d7e-9faf-63a7f916e2b2
                Copyright © 2018 Shade.

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

                History
                : 31 October 2017
                : 2 January 2018
                Page count
                Figures: 1, Tables: 0, Equations: 0, References: 11, Pages: 4, Words: 2201
                Categories
                Perspective
                Ecological and Evolutionary Science
                Special Issue
                Custom metadata
                March/April 2018

                centralia,disturbance ecology,diversity reservoir,dormancy,environmental change,microbial ecology,rare biosphere,stability,structure-function,temporal dynamics

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