Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

Abstract

The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

“…Our survey of 18 metagenome assemblies from the North Pond crustal aquifer (Tully et al, 2018) using the FeGenie library confirmed the presence of previously reported iron oxidases (Figure 1) (Tully et al, 2018;Seyler et al, 2020), which we phylogenetically linked to Zetaproteobacteria (cyc2) and Rhodospirillaceae (foxE) (Supplementary File 2). Linking cyc2 to Zetaproteobacteria is important because this gene is highly diverse and is often encoded by taxa not known to be capable of iron oxidation; thus, only a handful of cyc2 genes have been experimentally shown to be iron oxidases (Castelle et al, 2008;Jeans et al, 2008;Barco et al, 2015;McAllister et al, 2020a;Keffer et al, 2021).…”

“…The Impact of Shifting Redox Conditions on Iron Cycling in the North Pond Aquifer Recent work, including metagenomic, metatranscriptomic, and colonization/poised-electrode experiments, provide evidence for iron oxidation within the North Pond aquifer. Metagenomic (Tully et al, 2018) and metatranscriptomic (Seyler et al, 2020) studies revealed the presence of genes associated with iron oxidation, specifically, cyc2 [encoding an outer membrane porincytochrome fusion; (Appia-Ayme et al, 1998;Castelle et al, 2008;Barco et al, 2015;He et al, 2017, Keffer et al, 2021] and foxE (encoding a periplasmic cytochrome; Croal et al, 2007;Pereira et al, 2017). Tully et al (2018) also reconstructed metagenomeassembled genomes (MAGs) affiliated with the iron-oxidizing Zetaproteobacteria, which are known to adapt to fluctuating O 2 concentrations and advective flow regimes (Chiu et al, 2017;Blackwell et al, 2020), further solidifying the presence and significant contribution that iron-oxidizing bacteria make to the aquifer community.…”

Multiple carbon incorporation strategies support microbial survival in cold subseafloor crustal fluids

“…Given the lack of electron donors that could be paired with chemolithotrophy in our incubations, it is unlikely that rock-driven autotrophy is occurring in our experiments. Metagenomic and metatranscriptomic analysis of the same 2017 North Pond fluids used in our experiments showed more transcription of organotrophic genes than autotrophic genes across all sampling horizons, suggesting a microbial community utilizing organic carbon ( 28 ). Carbon fixation transcripts were most abundant in 1383C Middle and Deep where we also detected the highest rates of bicarbonate incorporation.…”

Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments

“…Gene abundances were normalized into transcripts per million (TPM) counts. The TPM values could be applied to metagenomes to remove the effects of total read counts and gene lengths when comparing the abundances of genes between samples [ 44 ].…”