Regional biogeography versus intra-annual dynamics of the root and soil microbiome
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Abstract
Background: Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil). Results: To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community. Conclusions: Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.
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Romero, I., Bodenhausen, N., Wille, L., Kurmann, M., Studer, B., Hohmann, P., Messmer, M., & Gfeller, V. (2026) · Plant and Soil · doi:10.1007/s11104-026-08723-0
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Soil Pathobiome in Agroecosystems and Forests
Jędryczka, M., Bełka, M., Berg, G., Hannula, S. E., Koczyk, G., Nannipieri, P., Pietramellara, G., & Frąc, M. (2026) · Plant Pathology · doi:10.1111/ppa.70261
- Authors
- Bell-Dereske, L. P., Benucci, G. M. N., da Costa, P. B., Bonito, G., Friesen, M. L., Tiemann, L. K., & Evans, S. E.
- Affiliations
- Great Lakes Bioenergy Research Center (US)
- Washington State University (US)
- ORCID
- Venue
- Environmental Microbiome
- Published
- 2023-06-07
- Volume
- 18
- Issue
- 1
- Pages
- 50-50
- ISSN
- 2524-6372 (ISSN-L)
- PMC
- PMC10245661
- OpenAlex
- W4379769152
- Cited by
- 14
- References
- 83
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 3
- FWCI
- 2.21
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Environmental Microbiome (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- U.S. Department of Energy (DE-SC0014108, DE-SC0018409)
- U.S. National Science Foundation (DEB 1832042)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
- Keywords
- root microbiome, soil microbiome, switchgrass, perennial cropping systems, nitrogen addition, bacterial community assembly, fungal community assembly, nitrogen-fixing bacteria, saprotrophic fungi, Great Lakes region
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