The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities
Open accessAbstract
Microbial community structure is highly sensitive to natural (e.g., drought, temperature, fire) and anthropogenic (e.g., heavy metal exposure, land-use change) stressors. However, despite an immense amount of data generated, systematic, cross-environment analyses of microbiome responses to multiple disturbances are lacking. Here, we present the Microbiome Stress Project, an open-access database of environmental and host-associated 16S rRNA amplicon sequencing studies collected to facilitate cross-study analyses of microbiome responses to stressors. This database will comprise published and unpublished datasets re-processed from the raw sequences into exact sequence variants using our standardized computational pipeline. Our database will provide insight into general response patterns of microbiome diversity, structure, and stability to environmental stressors. It will also enable the identification of cross-study associations between single or multiple stressors and specific microbial clades. Here, we present a proof-of-concept meta-analysis of 606 microbiomes (from nine studies) to assess microbial community responses to: (1) one stressor in one environment: soil warming across a variety of soil types, (2) a range of stressors in one environment: soil microbiome responses to a comprehensive set of stressors (incl. temperature, diesel, antibiotics, land use change, drought, and heavy metals), (3) one stressor across a range of environments: copper exposure effects on soil, sediment, activated-sludge reactors, and gut environments, and (4) the general trends of microbiome stressor responses. Overall, we found that stressor exposure significantly decreases microbiome alpha diversity and increases beta diversity (community dispersion) across a range of environments and stressor types. We observed a hump-shaped relationship between microbial community resistance to stressors (i.e., the average pairwise similarity score between the control and stressed communities) and alpha diversity. We used Phylofactor to identify microbial clades and individual taxa as potential bioindicators of copper contamination across different environments. Using standardized computational and statistical methods, the Microbiome Stress Project will leverage thousands of existing datasets to build a general framework for how microbial communities respond to environmental stress.
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Complex microbial consortia perform more complex activities (versatility) and tolerate more variation in the environment (robustness) as compared to pure cultures.
“In general, it can be stated that complex microbial consortia perform more complex activities (versatility) and tolerate more variation in the environment (robustness) as compared to pure cultures [9,13,14,15].”
From Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking (2025) · cites this paper as [13]
In Results and Discussion (Results of the Pilot Study; page unavailable), the paper reports that resistance to stressors rises with diversity only at lower diversity levels and falls at higher levels. That finding runs contrary to the claim's general assertion that more complex consortia are more robust. The paper does not compare consortia with pure cultures or assess their relative versatility. (LLM, conf=0.82)
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“In general, it can be stated that complex microbial consortia perform more complex activities (versatility) and tolerate more variation in the environment (robustness) as compared to pure cultures [9,13–15].”
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- Authors
- Rocca, J. D., Simonin, M., Blaszczak, J. R., Ernakovich, J. G., Gibbons, S. M., Midani, F. S., & Washburne, A. D.
- Affiliations
- Duke University (US)
- University of New Hampshire (US)
- University of Washington (US)
- Corresponding author
- Rocca, Jennifer D.
- Simonin, Marie
- ORCID
- Venue
- Frontiers in Microbiology
- Publisher
- Frontiers Media SA
- Published
- 2019-01-10
- Volume
- 9
- Pages
- 3272-3272
- ISSN
- 1664-302X (ISSN-L)
- PMC
- PMC6335337
- OpenAlex
- W2910998269
- Cited by
- 213
- References
- 76
- Citations by year
- 2026: 24 · 2025: 30 · 2024: 24 · 2023: 25 · 2022: 33 · 2021: 37 · 2020: 28 · 2019: 12
- FWCI
- 1.97
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Microbiology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Science Foundation (1754512)
- Washington Research Foundation
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
- Physical Sciences › Environmental Science › Nature and Landscape Conservation › Ecology and Vegetation Dynamics Studies
- Keywords
- environmental stressors, microbial community response, soil microbiome, copper contamination, bioindicators, 16S rRNA amplicon sequencing, meta-analysis database, alpha diversity, beta diversity, community resistance, heavy metals, drought, land use change, diesel fuel, antibiotics, soil warming, gut microbiota, activated sludge
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