Assessing the phylogenetic diversity of nifH-containing organisms at deep-sea methane seeps and non-seep sediments

Abstract:

Methane seeps host methane-cycling and nitrogen-fixing microorganisms, where their activity regulates sediment methane emission and sustains community productivity, respectively. Previous molecular studies and stable isotope tracer experiments have demonstrated that consortia of anaerobic methanotrophic archaea and Deltaproteobacteria are key drivers of both processes. Interestingly, additional nifH sequences from unknown source organisms have also been recovered. Here, we analyze the previously published sequences from five globally-distributed deep-sea methane seeps using the new R package PPIT (Phylogenetic Placement for Inferring Taxonomy) to assess the full phylogenetic diversity of nifH-containing organisms at methane seeps. We infer a taxonomically diverse community of nifH-containing organisms, including Euryarchaeota, Gammaproteobacteria, and Firmicutes. We also compare the phylogenetic diversity of nifH sequences recovered from methane seeps to that from non-seeps to understand the distribution of potential methane seep diazotrophs in the broader marine benthos. Our results suggest that methane seeps host a greater taxonomic diversity of diazotrophs than previously recognized and highlights the value of reexamining collections of previously published environmental sequencing data using current tools and updated reference databases.