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Experimental erosion of microbial diversity decreases soil CH$_4$ consumption rates


Schnyder, Elvira; Bodelier, Paul L E; Hartmann, Martin; Henneberger, Ruth; Niklaus, Pascal A (2023). Experimental erosion of microbial diversity decreases soil CH$_4$ consumption rates. Ecology, 104(12):e4178.

Abstract

Biodiversity‐ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH$_{4}$) cycle by removing atmospheric CH$_{4}$ and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution‐to‐extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 10$^{1}$–10$^{7}$‐fold, preincubated under a high CH$_{4}$ atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH$_{4}$ consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH$_{4}$ consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log‐dilution. CH$_{4}$ consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.

Abstract

Biodiversity‐ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH$_{4}$) cycle by removing atmospheric CH$_{4}$ and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution‐to‐extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 10$^{1}$–10$^{7}$‐fold, preincubated under a high CH$_{4}$ atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH$_{4}$ consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH$_{4}$ consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log‐dilution. CH$_{4}$ consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
08 Research Priority Programs > Global Change and Biodiversity
Dewey Decimal Classification:570 Life sciences; biology
Scopus Subject Areas:Life Sciences > Ecology, Evolution, Behavior and Systematics
Uncontrolled Keywords:Ecology, Evolution, Behavior and Systematics
Language:English
Date:1 December 2023
Deposited On:24 Jan 2024 15:11
Last Modified:30 Jun 2024 01:37
Publisher:Ecological Society of America
ISSN:1939-9170
OA Status:Hybrid
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1002/ecy.4178
PubMed ID:37782571
  • Content: Published Version
  • Language: English
  • Licence: Creative Commons: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)