Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt

Abstract

Although little is known regarding microbial life within our planet's rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

“…Sample collection methods are described elsewhere 11 . Briefly, during R/V Atlantis cruise ATL18-07 (28 June 2011-14 July 2011) samples of basement crustal fluids were collected from CORK observatories located in 3.5 million-year-old ocean crust east of the Juan de Fuca spreading center.…”

“…Borehole fluid nucleic acids were extracted using a modified phenol/chloroform lysis and purification method and is described in detail elsewhere 11 . The samples used in this study correspond to samples SSF21–22 (U1362A) and SSF23–24 (U1362B) labelled by Jungbluth et al 11 .…”

“…The samples used in this study correspond to samples SSF21–22 (U1362A) and SSF23–24 (U1362B) labelled by Jungbluth et al 11 . Library preparation and sequencing was conducted by the Department of Energy Joint Genome Institute as part of the Community Science Program.…”

“…The U1362A and U1362B borehole fluid GFMs were comprised of many of the same microbial lineages described previously using SSU rRNA sequencing 8,11 , including bacterial groups Chloroflexi (11), Nitrospirae (8), Acetothermia (OP1; 7), EM3 (5), Aminicenantes (OP8; 4), Gammaproteobacteria (4), and Deltaproteobacteria (4), and archaeal groups Archaeoglobi (21), Bathyarchaeota (MCG; 9), and Marine Benthic Group E (MBG-E; 3) (Table 5 (available online only) and Supplementary Table 1). In this study, we identified the first near-complete genomes from archaeal and bacterial lineages THSCG, MBG-E, and EM3 and, based on the warm, subsurface and hydrothermally-associated environments from which these groups tend to be found, propose the names Geothermarchaeota, Hydrothermarchaeota, and Hydrothermae, respectively.…”

Viruses in the Oceanic Basement

“…DNA was extracted from filters using a phenol-chloroform extraction protocol (20). As described in detail elsewhere (25), metagenome sequencing of the resulting environmental DNA was performed by the Joint Genome Institute (JGI) using an Illumina HiSeq-2000 platform, resulting in 170 million and 168 million sequence reads from boreholes U1362A and U1362B, respectively.…”