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Soil depth shapes microbial community composition and function in a freshwater wetland

ABSTRACT: Wetland microbiomes play a crucial role in the global carbon cycle by modulating soil organic carbon (SOC) and greenhouse gas (GHG) emissions. Understanding how microbial communities respond to environmental changes is essential for predicting wetland carbon fluxes under future climate scenarios. Here, we investigated the biogeochemistry of a temperate lacustrine wetland across four seasons and three soil depths, integrating greenhouse gas flux measurements, porewater metabolite profiles, metagenomics, metabolomics, and metaproteomics. While seasonal shifts in GHG fluxes and porewater chemistry were evident, microbial community composition and function were primarily structured by soil depth, suggesting resilience to short-term seasonal fluctuations. Depth-correlated microbial taxa and metabolic pathways revealed distinct stratification: surface soils were enriched in metabolically versatile Gammaproteobacteria capable of oxygen and nitrate respiration, as well as methane and sulfur oxidation, whereas deeper layers favored strict anaerobic metabolism, with increasing abundances of Anaerolinea and Methanomicrobia. Metabolomics showed an enrichment of purine nucleotides and amino acids at the surface, while deeper soils accumulated amino sugars and phenolic compounds, highlighting differences in carbon processing. Metaproteomics confirmed active metabolic pathways, linking functional potential to microbial activity. By integrating multi-omics with biogeochemical measurements, this study provides a system-level view of wetland microbial function and resilience, contributing to predictive models of wetland carbon cycling under future climate change. The work (proposal:https://doi.org/10.46936/10.25585/60000490) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Wetland Soils Microbiome

SUBMITTER: Mari Winkler

PROVIDER: MSV000098292 | MassIVE | Mon Jun 23 14:02:00 BST 2025

REPOSITORIES: MassIVE

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Project description:Wetland microbiomes play a crucial role in the global carbon cycle by modulating soil organic carbon (SOC) and greenhouse gas (GHG) emissions. Understanding how microbial communities respond to environmental changes is essential for predicting wetland carbon fluxes under future climate scenarios. Here, we investigated the biogeochemistry of a temperate lacustrine wetland across four seasons and three soil depths, integrating greenhouse gas flux measurements, porewater metabolite profiles, metagenomics, metabolomics, and metaproteomics. While seasonal shifts in GHG fluxes and porewater chemistry were evident, microbial community composition and function were primarily structured by soil depth, suggesting resilience to short-term seasonal fluctuations. Depth-correlated microbial taxa and metabolic pathways revealed distinct stratification: surface soils were enriched in metabolically versatile Gammaproteobacteria capable of oxygen and nitrate respiration, as well as methane and sulfur oxidation, whereas deeper layers favored strict anaerobic metabolism, with increasing abundances of Anaerolinea and Methanomicrobia. Metabolomics showed an enrichment of purine nucleotides and amino acids at the surface, while deeper soils accumulated amino sugars and phenolic compounds, highlighting differences in carbon processing. Metaproteomics confirmed active metabolic pathways, linking functional potential to microbial activity. By integrating multi-omics with biogeochemical measurements, this study provides a system-level view of wetland microbial function and resilience, contributing to predictive models of wetland carbon cycling under future climate change. The work (proposal:https://doi.org/10.46936/10.25585/60000490) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

Project description:Soils are a huge reservoir of organic C, and the efflux of CO2 from soils is one of the largest fluxes in the global C cycle. Out of all natural environments, soils probably contain the greatest microbial biomass and diversity, which classifies them as one of the most challenging habitats for microbiologists (Mocali and Benedetti, 2010). Until today, it is not well understood how soil microorganisms will respond to a warmer climate. Warming may give competitive advantage to species adapted to higher temperatures (Rinnan et al., 2009). The mechanisms behind temperature adaptations of soil microbes could be shifts within the microbial community. How microbial communities will ultimately respond to climate change, however, is still a matter of speculation. As a post-genomic approach in nature, metaproteomics allows the simultaneous examination of various protein functions and responses, and therefore is perfectly suited to investigate the complex interplay between respiration dynamics, microbial community architecture, and ecosystem functioning in a changing environment (Bastida et al., 2012). Thereby we will gain new insights into responses to climate change from a microbial perspective. Our study site was located at 910 m a.s.l. in the North Tyrolean Limestone Alps, near Achenkirch, Austria The 130 year-old mountain forests consist of Norway spruce (Picea abies) with inter-spread of European beech (Fagus sylvatica) and silver fir (Abies alba). Three experimental plots with 2 × 2 m warmed- and control- subplots were installed in 2004. The temperature difference between control and warmed plots was set to 4 °C at 5 cm soil depth. Soil was warmed during snow-free seasons. In order to extract proteins from forest soil samples, the SDS–phenol method was adopted as previously described by Keiblinger et al. (2012). Protein extractions were performed from each subplot soil samples. The abundance of protein-assigned microbial phylogenetic and functional groups, were calculated based on the normalized spectral abundance factor (NSAF, Zybailov et al., 2006).

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Soil depth shapes microbial community composition and function in a freshwater wetland

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