Eitel, E. M. | Search bioRxiv

bioRxiv2025

Cycling of sulfur redox intermediates drives microbial activity in the sulfate-methane transition zone of cold methane seeps

Microbial sulfate reduction is a cornerstone of marine sediment biogeochemistry, driving carbon remineralization and fueling the anaerobic oxidation of methane (AOM). Yet in zones of high methane flux, sulfate limitations may constrain the sulfate-reducing bacteria (SRB) and anaerobic methanotrophic archaea (ANME) that typically perform AOM. Although often overlooked, sulfur redox intermediates are readily utilized by diverse microorganisms, potentially driving AOM in sulfate-limited zones. To resolve the microbial mechanisms underlying cryptic sulfur cycling in such sediments, Monterey Canyon cold methane seeps were investigated through an integrated geochemical, isotopic, and metatranscriptomic approach. High-resolution electrochemical measurements confirmed intense sulfide production in seep sites, and long-term anoxic incubations were conducted with sediment from the SMTZ amended with elemental sulfur, thiosulfate, or sulfate as the sole sulfur source, with or without methane. Over 650 days, sulfide accumulation was greatest in elemental sulfur treatments, followed by thiosulfate and sulfate; in all cases methane addition enhanced sulfide production. Isotopic measurements showed modest S-isotope fractionation indicating that the large fractionations typical of slow sulfate reduction were muted by additional sulfur transformations. In elemental sulfur treatments, isotopic and geochemical patterns suggested that disproportionation was unlikely. Metatranscriptomes revealed broad expression of sox genes and abundant dsr/apr across treatments, along with thiosulfate-linked phs upregulation. While ANME-2c and SEEP-SRB2 activity increased with methane, transcriptomic and isotopic data together highlighted the roles of Desulfocapsaceae, Desulfobulbaceae, and Sulfurovaceae lineages in mediating sulfur transformations. Taken together, these results demonstrate how cryptic sulfur cycling may sustain microbial communities in sulfate-depleted deep-sea sediments and contribute to AOM.

ecology↗

bioRxiv2024

CABO-16S : A Combined Archaea, Bacteria, Organelle 16S database for amplicon analysis of prokaryotes and eukaryotes in environmental samples

Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by either the burden of additional sequencing required to obtain both 16S and 18S rRNA sequences or the introduction of multiple biases induced by the use of "universal" primers. Organellar 16S rRNA sequences are automatically amplified and sequenced along with prokaryote 16S rRNA, and may provide an alternative method to identify eukaryotic microorganisms. CABO-16S combines bacterial and archaeal sequences from the SILVA database with 16S rRNA sequences of plastids and other organelles from the PR2 database to enable identification of all 16S rRNA sequences. Comparison of CABO-16S with SILVA 138.2 results in equivalent taxonomic classification of mock communities and increased classification of diverse environmental samples. In particular, identification of phototrophic eukaryotes in shallow seagrass environments, marine waters, and lake waters was increased. CABO-16S also provides the framework to add curated datasets of specialized sequences for further classification of clades which are not currently included in other databases. Addition of sequences obtained from Sanger sequencing of methane seep sediments and curated sequences of the polyphyletic SEEP-SRB1 clade resulted in differentiation of syntrophic and non-syntrophic SEEP-SRB1 in hydrothermal vent sediments. Such additions may simplify analysis of communities contributing to the anaerobic oxidation of methane, and highlight the potential benefit of amending existing training sets with curated sequences when studying extreme or unique environments underrepresented in existing databases.

microbiology↗