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

Abstract

The rock-hosted 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 that is representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. The data suggest that the microbial community in this subseafloor habitat is motile, chiefly heterotrophic or mixotrophic, and capable of using alternative electron acceptors such as nitrate and thiosulfate, in addition to oxygen. 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. Together, our results indicate the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust, and is also metabolically flexible, with the ability to switch from autotrophy to heterotrophy, as well as function under low oxygen conditions. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.

Depth-related Variability of Biological Nitrogen Fixation and Diazotrophic Communities in Mangrove Sediments

“…Gene abundances were normalized into transcripts permillion (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 [46].…”

Microbial populations are shaped by dispersal and recombination in a low biomass subseafloor habitat

“…The crustal aquifer beneath the sediments of North Pond is accessible through two circulation obviation retrofit kits (CORKs) installed in 2011, providing direct access to the fluids circulating within the aquifer, while preventing exchange with the overlaying water and sediment environments 15,16 . Repeated sampling in 2012, 2014, and 2017, including an eight sample in situ time-series collected from 2012-2014, has revealed a dynamic microbial community with a high degree of functional redundancy in a complex hydrological system depleted in dissolved organic carbon (DOC) 6,17–19 . The aquifer microbial communities are distinct from bottom seawater, and there are multiple lines of genetic evidence to suggest that the microbial community within the aquifer is motile and metabolically flexible, with the ability to carry out both autotrophic and organotrophic pathways 6,17,20 .…”

“…Repeated sampling in 2012, 2014, and 2017, including an eight sample in situ time-series collected from 2012-2014, has revealed a dynamic microbial community with a high degree of functional redundancy in a complex hydrological system depleted in dissolved organic carbon (DOC) 6,17–19 . The aquifer microbial communities are distinct from bottom seawater, and there are multiple lines of genetic evidence to suggest that the microbial community within the aquifer is motile and metabolically flexible, with the ability to carry out both autotrophic and organotrophic pathways 6,17,20 . The North Pond subseafloor microbial community is low biomass 6,20 (10 3 -10 4 cells ml -1 ) and incubation experiments suggest the North Pond microbial community is growth-limited and that increasing temperature and enrichment with DOC result in rapid growth (E. Trembath-Reichert, S. R. Shah Walter, M. A. Fontánez, P. D. Carter, P. R. Girguis, J.…”