Experimental erosion of microbial diversity decreases soil CH4 consumption rates

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 (CH4) cycle by removing atmospheric CH4 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 101 to 107-fold, and pre-incubated under a high CH4 atmosphere for the microbial communities to recover to approximately equal size. Then, the samples were incubated for 86 days at constant or diurnally-cycling temperature. Our hypotheses were that (1) CH4 consumption would decrease as methanotrophic diversity was lost, and that (2) this effect would be more pronounced under variable environmental conditions (here: variable temperature). We followed net CH4 consumption by gas chromatography. Microbial community composition was determined four times by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). We found that the richness of operational taxonomic units (OTU) of methanotrophic and non-methanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of taxonomic units lost. This effect was independent of community size, which we determined by quantitative PCR, and consistent over the study period. The temperature treatment (constant vs. cycling temperature) did not affect any of these results. The diversity effects we found occurred in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects we report resemble the ones for higher organisms, suggesting that BEF-relationships are universal across taxa and spatial scales.