Unifying meta-genomic and -transcriptomic data with metabolomics to help infer ecosystem processes in a thawing permafrost

Abstract:

Unifying meta-genomic and -transcriptomic data with metabolomics in microbiome research can help infer ecosystem processes by shedding the light on how microbial communities’ function in a variety of environments, including permafrost peatlands. Permafrost thaw results in microbial decomposition of sequestered organic matter and production of greenhouse gases, but the geochemical transformations involved in this process are poorly characterized. Continued climate change could shift metabolic transformations and change how organisms exploit the metabolic resources that are available to them, thus altering the systems feedback strength. Therefore, understanding microbial decomposition pathways is relevant to improving models prediction of carbon storage and re-emission with permafrost thaw. To link thaw-induced changes in soil microbial processes with methane metabolism, environmental metabolomic (FTICR MS, GC MS and NMR) data were co-analysed with meta-genomic and -transcriptomic data from active layer (the unfrozen portion of the soil column) samples spanning a thaw gradient from a site of discontinuous permafrost peatland located in Stordalen Mire, Sweden. The diversity of metabolic transformations was significantly correlated with microbial diversity and increased after thaw. Furthermore, the ratio of monosaccharides to fermentation products decreased significantly across the thaw gradient, reflecting a shift from a substrate-restricted and/or reduced metabolic repertoire to an active microbial community. Increased methane emissions across the thaw gradient were associated with an increase in the abundance and expression of methanogenic pathways and methanogenesis-associated metabolites. Acetoclastic methanogenesis in the bog was found to be potentially limited by the rates of diversity transformation acetogenesis, potentially related to the acidic environment Sphagnum mosses create. We propose that unification of environmental metabolomics with metacommunity can help improve our understanding of the relationships between molecular-scale functional biology and ecosystem-scale environmental processes by revealing the mechanisms that drive methane emissions in permafrost ecosystems.