Experimental erosion of microbial diversity decreases soil CH₄ consumption rates

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 (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, pre‐incubated under a high CH4 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) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperature. Net CH4 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 non‐methanotrophic bacteria decreased approximately linearly with log‐dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. 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 also resemble the ones for higher organisms, suggesting that BEF‐relationships are universal across taxa and spatial scales.

Treasures of Italian Microbial Culture Collections: An Overview of Preserved Biological Resources, Offered Services and Know-How, and Management

“…The reduction of microbial resources is also a consequence of the extensive use of commercial starters in large-scale industrial and artisanal fermented foods and beverages [2]. The erosion of microbial biodiversity means not only the mere loss of species or biotypes but also the vanishing of potential biological tools that can be exploited to face problems such as the big challenges of the day [13]. In this framework, on one side, an increased knowledge of the ecological roles and functions of microorganisms and, on the other side, the safeguard of biological resources in microbial Culture Collections (CCs) can be considered strategic for developing new sustainable biotechnologies.…”