Microbial Residents of the Atlantis Massif’s Shallow Serpentinite Subsurface

Abstract

The Atlantis Massif rises 4,000 m above the seafloor near the Mid-Atlantic Ridge and consists of rocks uplifted from Earth’s lower crust and upper mantle. Exposure of the mantle rocks to seawater leads to their alteration into serpentinites. These aqueous geochemical reactions, collectively known as the process of serpentinization, are exothermic and are associated with the release of hydrogen gas (H2), methane (CH4), and small organic molecules. The biological consequences of this flux of energy and organic compounds from the Atlantis Massif were explored by International Ocean Discovery Program (IODP) Expedition 357, which used seabed drills to collect continuous sequences of shallow (<16 m below seafloor) marine serpentinites and mafic assemblages. Here, we report the census of microbial diversity in samples of the drill cores, as measured by environmental 16S rRNA gene amplicon sequencing. The problem of contamination of subsurface samples was a primary concern during all stages of this project, starting from the initial study design, continuing to the collection of samples from the seafloor, handling the samples shipboard and in the lab, preparing the samples for DNA extraction, and analyzing the DNA sequence data. To distinguish endemic microbial taxa of serpentinite subsurface rocks from seawater residents and other potential contaminants, the distributions of individual 16S rRNA gene sequences among all samples were evaluated, taking into consideration both presence/absence and relative abundances. Our results highlight a few candidate residents of the shallow serpentinite subsurface, including uncultured representatives of the Thermoplasmata, Acidobacteria, Acidimicrobia, and Chloroflexi. IMPORTANCE The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites.

Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland

“…Among the abundant ASVs detected in the borehole fluids, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database release 138 has been previously detected in serpentinite-hosted systems ( Merino et al, 2020 ). Uncharacterized Thermoplasmata are also detected in serpentinite subsurface deposits ( Motamedi et al, 2020 ), yet numerous sequences assigned to this class from the SE-01 borehole fluid samples showed less than 90% of sequence similarity with the first match on the NCBI Nucleotide collection database (AB327321). These results suggest that all the latter taxa could be endemic in the Surtsey subsurface deposits and perhaps could be common in other oceanic or continental subsurface habitats, as well.…”

Potential microbial contamination from drilling lubricants into subseafloor rock cores

“…357 and are described in detail in Motamedi et al (2020). Briefly, core subsamples identified for microbiological analyses were immediately retrieved from the drill upon its return to the ship deck, wrapped in acid-washed and autoclaved teflon, and stored at −80 • C. Core samples were then shipped to the Kochi Core Center (Japan) for further processing and subsampling under sterile conditions (Früh-Green et al, 2017b;Orcutt et al, 2017). Please see Früh-Green et al (2017a for more details on lithology and other details of the recovered cores.…”

“…IODP Exp. 357 employed the use of the synthetic tracer PFC (Smith et al, 2000b) mixed into flushing seawater in an effort to assess the level of contamination introduced into the cores (Orcutt et al, 2017).…”

Metabolic strategies shared by basement residents of the Lost City hydrothermal field

“…However, these biofilms form in mixing zones where warm, anoxic hydrothermal fluids vent into cold, oxic seawater. These conditions may not be representative of subseafloor environments within the Atlantis Massif where habitats are probably confined to sparsely distributed fractures and channels within rocks that have limited exposure to seawater (Früh-Green et al, 2018; Motamedi et al, 2020). In particular, dissolved inorganic carbon is provided by ambient seawater to chimney biofilm communities, while its availability is severely limited in subseafloor habitats dominated by the products of serpentinization.…”