Shifts in vegetation impact estuary microbiomes
11 affiliations
- 1Department of Interdisciplinary Life Sciences, The University of Texas at Austin, Austin, Texas, USA
- 2Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
- 3Department of Marine Science, The University of Texas at Austin, Austin, Texas, USA
- 4Genomics and Bioinformatics Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Gainesville, Florida, USA
- 5Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
- 6Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute, Berkeley, California, USA
- 7Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- 8Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- 9University of South Alabama, Mobile, Alabama, USA
- 10Dauphin Island Sea Lab, Dauphin Island, Alabama, USA
- 11Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
Abstract
Coastal wetlands, including mangrove-cordgrass mosaics, are among Earth’s most effective carbon stores sequestering >1 Pg C/year. Rapid sea level rise, warming, and storm intensification are now reshaping these habitats. Vegetation type influences root exudates, sediment redox profiles, and organic matter quality. However, the impacts of vegetation on microbe–virus networks that mediate carbon burial and nutrient cycling remain unclear. Here, we sampled coastal sediment profiles in patches of cordgrass (dominated by Sporobolus alterniflorus), black mangrove (Avicennia germinans), and seagrass on the Texas Gulf Coast. We obtained 491 bacterial and archaeal metagenome assembled genomes (MAGs) and 1,097 viral MAGs (vMAGs) from 55 surface sediment samples spanning day and night during summer and fall. Phylogenetic and comparative analyses revealed dominant lineages across the distinct vegetation types, organized into metabolic guilds based on similar protein compositions, revealing contrasting and complementary sulfur, iron, and nitrogen cycling pathways that regulate greenhouse gas emissions and encode genes important for carbon metabolism. Inference from virus–host linkages revealed that dominant lineages were infected, and viral communities have genes for organic carbon degradation, potentially shaping the microbial community dynamics in this ecosystem. This spatio-temporal characterization of estuary ecotone microbiomes provides a framework to better understand the diversity and metabolism of these productive coastal ecosystems.
IMPORTANCE: Coastal wetlands are among the most effective environments for storing carbon and regulating climate. As sea level rise and changing weather patterns drive shifts in coastal vegetation, these vulnerable ecosystems are undergoing rapid transformation. Yet, little is known about the microbes that regulate carbon storage and nutrient cycling. Here, we characterized microbial and viral communities associated with coastal wetland sediments along the Texas Gulf Coast. We identified key microbial groups responsible for key carbon, sulfur, nitrogen, and iron cycling and showed that vegetation type influences their distribution and ecological roles. We also found that viruses interact with dominant microbial groups and carry genes linked to carbon processing, suggesting an important role in shaping ecosystem function. These findings provide insights into the mechanisms that sustain coastal wetlands and help predict how shifts in vegetation may affect nutrient cycling and ecosystem resilience in the future.
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BibTeX
@article{aitolo2026shifts,
title = {{Shifts in vegetation impact estuary microbiomes}},
author = {Georgina L. Aitolo and Ian M. Rambo and Rachel E. Weisend and Megan M. Mullis and Susannah Tringe and James C. Kosmopoulos and Karthik Anantharaman and Brandi Kiel Reese and Brett J. Baker and Valerie De Anda},
journal = {mSystems},
year = {2026},
month = sep,
doi = {10.1128/msystems.01071-26},
url = {https://doi.org/10.1128/msystems.01071-26},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Shifts in vegetation impact estuary microbiomes
AU - Georgina L. Aitolo
AU - Ian M. Rambo
AU - Rachel E. Weisend
AU - Megan M. Mullis
AU - Susannah Tringe
AU - James C. Kosmopoulos
AU - Karthik Anantharaman
AU - Brandi Kiel Reese
AU - Brett J. Baker
AU - Valerie De Anda
PY - 2026
DA - 2026/09/30
JO - mSystems
DO - 10.1128/msystems.01071-26
UR - https://doi.org/10.1128/msystems.01071-26
AB - Coastal wetlands, including mangrove-cordgrass mosaics, are among Earth’s most effective carbon stores sequestering >1 Pg C/year. Rapid sea level rise, warming, and storm intensification are now reshaping these habitats. Vegetation type influences root exudates, sediment redox profiles, and organic matter quality. However, the impacts of vegetation on microbe–virus networks that mediate carbon burial and nutrient cycling remain unclear. Here, we sampled coastal sediment profiles in patches of cordgrass (dominated by Sporobolus alterniflorus), black mangrove (Avicennia germinans), and seagrass on the Texas Gulf Coast. We obtained 491 bacterial and archaeal metagenome assembled genomes (MAGs) and 1,097 viral MAGs (vMAGs) from 55 surface sediment samples spanning day and night during summer and fall. Phylogenetic and comparative analyses revealed dominant lineages across the distinct vegetation types, organized into metabolic guilds based on similar protein compositions, revealing contrasting and complementary sulfur, iron, and nitrogen cycling pathways that regulate greenhouse gas emissions and encode genes important for carbon metabolism. Inference from virus–host linkages revealed that dominant lineages were infected, and viral communities have genes for organic carbon degradation, potentially shaping the microbial community dynamics in this ecosystem. This spatio-temporal characterization of estuary ecotone microbiomes provides a framework to better understand the diversity and metabolism of these productive coastal ecosystems. IMPORTANCE: Coastal wetlands are among the most effective environments for storing carbon and regulating climate. As sea level rise and changing weather patterns drive shifts in coastal vegetation, these vulnerable ecosystems are undergoing rapid transformation. Yet, little is known about the microbes that regulate carbon storage and nutrient cycling. Here, we characterized microbial and viral communities associated with coastal wetland sediments along the Texas Gulf Coast. We identified key microbial groups responsible for key carbon, sulfur, nitrogen, and iron cycling and showed that vegetation type influences their distribution and ecological roles. We also found that viruses interact with dominant microbial groups and carry genes linked to carbon processing, suggesting an important role in shaping ecosystem function. These findings provide insights into the mechanisms that sustain coastal wetlands and help predict how shifts in vegetation may affect nutrient cycling and ecosystem resilience in the future.
SN - 2379-5077
ER -