Linked metatranscriptomic and geochemical data indicate microbial succession in naturally reduced aquifer sediments dominated by H2-oxidizing Comamonadaceae

Abstract:

In this study, we sought to better understand what natural organic matter fuels heterotrophic microbial communities in the anoxic subsurface at the Rifle (CO) site and what genes may be diagnostic of that activity. We conducted a 20-day microcosm experiment with naturally reduced zone (NRZ) sediments and collected replicate samples every 5 days for omics (metagenome and metatranscriptome) and biogeochemical measurements (e.g., continuous CO₂ production, H₂, CH₄, acetate, DOC, Fe(II), sulfate, NH₄⁺, spectroscopic analyses of sediment OM). No electron donors were added other than the NRZ sediment, which is enriched in organic matter relative to typical Rifle aquifer material. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with a N₂headspace.

Biogeochemical measurements indicate that the decomposition of native organic matter occurred in different phases, including depletion of DOC and release of CO₂ during the first week of incubation, followed by a pulse of acetogenesis and methanogenesis after 2 weeks (with acetogenesis dominating carbon flux after 2 weeks). While H₂ remained below detection levels throughout the study, a peak of [NiFe] uptake hydrogenase, acetyl-CoA synthetase, urease, and nitrate reductase transcripts belonging to the Comamonadaceae family occurred at day 15. Some members of Comamonadaceae are facultative H₂-oxidizing chemolithoautotrophs and fix carbon via the acetogenic Wood-Ljungdahl pathway. Comamonadaceae plateaued at 73% of the metagenome at this time and represented 69% of the metatranscriptome, succeeding the S-oxidizing Sulfurimonas genus. Sulfurimonas species were the dominant group at day 0, accounting for 43% of the metagenome and 25% of the metatranscriptome, decreasing to 11% in both the metagenome and metatranscriptome by day 10. Less abundant but still present were transcripts for genes involved in cellulose degradation (glycosyl hydrolases), and glycolysis (phosphofructokinase), consistent with plant biomass degradation. Although further analysis will be required to elucidate the complex and dynamic biogeochemical interactions occurring in this system, it is clear that dramatic metabolic changes occurred over time that markedly altered the nature and magnitude of carbon flux.