Microbial ecology in the sediment-covered ocean basement of the Juan de Fuca Ridge

Abstract

Investigations of microbial life inside of the deep seafloor and most reviews on the topic have focused on sediments and largely ignore the prospect of a biosphere inside the basaltic crust underlying the global system of ocean basins. This is despite the potential global importance of biogeochemical cycling that may be occurring in situ within the uppermost igneous ocean crust; a location that is predicted to be one of the most habitable subsurface environments due to its porosity, hydrothermal circulation, and expected chemical disequilibria. Sedimentation processes occuring over geologic time scales cause a majority of the global seafloor to be covered by thick and relatively impermeable blankets that prevent access to the underlying basaltic seafloor. As a result, studies of microorganisms inside the basaltic crust have traditionally been restricted to the exposed seafloor or to locations where hydrothermal fluids exiting the seafloor act as "windows" into the subsurface. However, these traditional methods for observing basaltic rock seafloor microorganisms are inadequate because ocean crust is hydrogeologically active until up to ~65 million years old and a majority of flow is likely to occur over long time scales and deep within the sediment-covered basement. Seafloor observatories that penetrate through sediments and into basement rock provide the infrastructure needed to collect samples from one of the planet's most remote environments. The broad goals of this study were to estimate the concentrations of microbial biomass and explore the microbial diversity in anoxic, deep subseafloor crustal fluids. Building on the first characterizations of microbial life in the aging ocean basement, discrete fluid samples were collected and analysed here from new borehole observatories that are the first to incorporate dedicated stainless steel or Teflon-coated fluid delivery lines running along the exterior of the reactive iron casing. Biofouling-resistant materials used during the construction of the seafloor observatory fluid delivery lines permit collection of pristine samples that can be used for estimation of the in situ microbial biomass and reveal a range of cellular abundances that are, on average, roughly an order of magnitude lower that those found in bottom seawater. The cellular abundances reported here will help to constrain estimates of biomass inside the global seafloor and elucidate partitioning between the basaltic crustal and marine sediment communities, and furthermore, underscore the difficulties associated with collecting uncontaminated samples from the deep subsurface. Sampling from a combination of older and newer borehole observatories has revealed novel microbial diversity and community structure from the seafloor that is distinct from overlying sediments and varies with the alteration state of the basement fluids. Microorganisms detected were largely from uncultivated groups, which means one can only speculate about the metabolic lifestyle for these organisms; however, comparisons to distant relatives indicate that a combination of autotrophic and heterotrophic lifestyles and active iron-and sulfur-cycling processes are present in the deep subseafloor. Temporal variation over annual timescales in the types of microorganisms collected from a single borehole observatory was observed and is the first instance of microbial community turnover observed in the deep subseafloor. A distinct bacterial lineage of Firmicutes first retrieved in 1998 during the first study of this kind was detected here again from a neighboring borehole location, which is consistent with the inferred hydrogeologic connectivity of the system and implies that the subseafloor crust likely has some permanent and widespread residents. Phylogenetic groups of microorganisms identified here extend previous observations by identifying additional lineages that may truly exist in the deep subseafloor, and provide a foundation for future studies exploring important topics relating to the community metabolic potential and contribution to active global geochemical cycling.