Structure and function of the peatland prokaryotic microbiome

Abstract Peatlands are vital long-term carbon sinks but also sources of trace greenhouse gases, with the balance largely governed by microbial processes. However, the structure and function of peatland microbial communities are currently poorly characterised beyond the local scale, limiting our understanding of their response to climate change. Here, we present a large-scale analysis of the peatland prokaryotic microbiome by leveraging a curated dataset of 109 publicly available metagenomes from 20 near-natural peatland sites worldwide. Despite limitations in the publicly available data, including geographic coverage and sampling depth, our analysis indicates that dominant vegetation and peatland type are the strongest predictors of peatland microbiome taxonomy and function. We show that obligate hydrogenotrophic methanogens of the family Bog-38, previously reported to be prevalent in diverse high methane-flux habitats, are abundant in northern peatlands but occur only at low abundance in tropical peatlands, suggesting a limited contribution to methane cycling in these ecosystems. In contrast to northern peatlands, the tropical peatland microbiome exhibits a broad metabolic potential for multiple key peatland biogeochemical processes, including methanogenesis and denitrification, across all depths. Intriguingly, we observe an impaired potential for complete denitrification in a significant proportion of the northern fen metagenomes, with potential implications for nitrous oxide emissions as a greenhouse gas. Overall, our study uncovers large-scale patterns and ecological drivers of the peatland prokaryotic microbiome based on existing metagenomic data, enhancing our understanding of its response to climate change and highlighting major data gaps for future research.