AbstractThe permeability, connectivity, and reactivity of fluid reservoirs in oceanic crust are poorly constrained, yet these reservoirs are pathways for about a quarter of the Earth's heat loss and seawater‐rock exchange within them impact ocean chemical cycles. We present results from the second‐ever cross‐hole tracer experiment within oceanic crust and the first conducted during a single expedition and in slow‐spreading crust west of the Mid‐Atlantic Ridge at North Pond. Here we employed boreholes that were drilled by the Integrated Ocean Drilling Program (IODP Sites U1382 and U1383) that were instrumented and sealed. A cesium‐salt solution and bottom seawater tracer experiment provided a measure of the minimum Darcy fluid velocity (2 to 41 m d‐1) within the upper volcanic crust, constraining the minimum permeability of 10‐11 to 10‐9 m2. We also document chemical heterogeneities in crustal fluid compositions, rebound from drilling disturbances, and nitrification within the basaltic crust, based on systematic differences in borehole fluid compositions over a 5‐year period. These results also show heterogeneous fluid compositions with depth in the borehole, indicating that hydrothermal circulation is not vigorous enough to homogenize the fluid composition in the upper permeable basaltic basement, at least not on the time scale of 5 years. Our work verifies the potential for future manipulative experiments to characterize hydrologic, biogeochemical, and microbial process within the upper basaltic crust.
AbstractGenus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea.
AbstractInterest in extracting mineral resources from the seafloor through deep‐sea mining has accelerated in the past decade, driven by consumer demand for various metals like zinc, cobalt, and rare earth elements. While there are ongoing studies evaluating potential environmental impacts of deep‐sea mining activities, these focus primarily on impacts to animal biodiversity. The microscopic spectrum of seafloor life and the services that this life provides in the deep sea are rarely considered explicitly. In April 2018, scientists met to define the microbial ecosystem services that should be considered when assessing potential impacts of deep‐sea mining, and to provide recommendations for how to evaluate and safeguard these services. Here, we indicate that the potential impacts of mining on microbial ecosystem services in the deep sea vary substantially, from minimal expected impact to loss of services that cannot be remedied by protected area offsets. For example, we (1) describe potential major losses of microbial ecosystem services at active hydrothermal vent habitats impacted by mining, (2) speculate that there could be major ecosystem service degradation at inactive massive sulfide deposits without extensive mitigation efforts, (3) suggest minor impacts to carbon sequestration within manganese nodule fields coupled with potentially important impacts to primary production capacity, and (4) surmise that assessment of impacts to microbial ecosystem services at seamounts with ferromanganese crusts is too poorly understood to be definitive. We conclude by recommending that baseline assessments of microbial diversity, biomass, and, importantly, biogeochemical function need to be considered in environmental impact assessments of deep‐sea mining.
AbstractInternational Ocean Discovery Program (IODP) Expedition 385T aimed to take advantage of a transit of the R/V JOIDES Resolution from Antofagasta, Chile, to San Diego, California (USA), to accomplish new sampling and data collection from legacy borehole observatories in Deep Sea Drilling Project (DSDP) and Ocean Drilling Program (ODP) Holes 504B and 896A on the southern flank of the Costa Rica Rift. In addition, the US Science Support Program organized the participation of 3 Outreach Officers to evaluate the performance of the JOIDES Resolution Outreach Officer program as well as 2 educators and 12 undergraduate students for a shipboard “JR Academy.” Our scientific objectives were to collect (1) new Formation MicroScanner logs from Hole 504B for improving lithologic interpretations of crustal architecture at this archetype deep oceanic crust hole and (2) fluid samples from both holes for evaluating the crustal deep biosphere in deep and warm oceanic crust. These operations in Holes 504B and 896A have direct relevance to Challenges 5, 6, 9, 10, 13, and 14 of the IODP 2013–2023 Science Plan. Accomplishing both of these scientific objectives required the removal of old wireline CORK observatories, including associated inflatable packers that were installed in the cased boreholes in 2001. The fluid sampling plan also included testing a new Multi-Temperature Fluid Sampler. Despite successfully removing the CORK wellhead platforms from both holes, we were unable to remove the packers stuck in casing at both locations after 48 h of milling operations in Hole 504B and 2 h of milling operations in Hole 896A, thus precluding accomplishing any of the scientific objectives of the expedition. We provide an assessment of the final state of the holes and recommendations for possible future operations.
AbstractInternational Ocean Discovery Program (IODP) Expedition 385T will revisit two Deep Sea Drilling Project (DSDP) and Ocean Drilling Program (ODP) legacy sites—Holes 504B and 896A on the Costa Rica Rift flank—to advance lithostratigraphic, hydrogeological, and deep biosphere studies of upper oceanic crust. Hole 504B has served as a standard reference site for upper oceanic crust for decades despite low core recovery during drilling operations. Hole 896A serves as an analog site of crustal alteration for examining biogeography in the crustal deep biosphere. During Expedition 385T, we will advance lithostratigraphic records of in situ crustal architecture through Formation MicroScanner (FMS) logging, with priority for these operations in Hole 504B. The new logs from Hole 504B will reveal whether unrecovered intervals are highly fractured and/or brecciated and whether alteration style and intensity are correlated to volcanic architecture, which will allow for assessment of the hypothesis that hydrothermal alteration and mineralization style are spreading-rate dependent. We will also advance crustal hydrogeological and deep biosphere research through temperature logging and water sampling in both holes, with priority for these operations in Hole 896A. The new FMS-based lithostratigraphy coupled with new fluid assessment will also allow for improvements on the thermal limits of microbial life and seawater-basalt reactions. These operations in Holes 504B and 896A have direct relevance to Challenges 5, 6, 9, 10, 13, and 14 of the IODP 2013–2023 Science Plan. To achieve these data and sample recoveries from these legacy sites, existing wireline observatories installed in both holes will be removed and the remaining cased holes will be left open for possible future installation of next-generation observatories. The expedition will be implemented as an abbreviated (10 operational days) expedition with no new coring.
AbstractThe Methanosarcinales, a lineage of cytochrome-containing methanogens, have recently been proposed to participate in direct extracellular electron transfer interactions within syntrophic communities. To shed light on this phenomenon, we applied electrochemical techniques to measure electron uptake from cathodes by Methanosarcina barkeri, which is an important model organism that is genetically tractable and utilizes a wide range of substrates for methanogenesis. Here, we confirm the ability of M. barkeri to perform electron uptake from cathodes and show that this cathodic current is linked to quantitative increases in methane production. The underlying mechanisms we identified include, but are not limited to, a recently proposed association between cathodes and methanogen-derived extracellular enzymes (e.g., hydrogenases) that can facilitate current generation through the formation of reduced and diffusible methanogenic substrates (e.g., hydrogen). However, after minimizing the contributions of such extracellular enzymes and using a mutant lacking hydrogenases, we observe a lower-potential hydrogen-independent pathway that facilitates cathodic activity coupled to methane production in M. barkeri. Our electrochemical measurements of wild-type and mutant strains point to a novel and hydrogenase-free mode of electron uptake with a potential near −484 mV versus standard hydrogen electrode (SHE) (over 100 mV more reduced than the observed hydrogenase midpoint potential under these conditions). These results suggest that M. barkeri can perform multiple modes (hydrogenase-mediated and free extracellular enzyme-independent modes) of electrode interactions on cathodes, including a mechanism pointing to a direct interaction, which has significant applied and ecological implications.
AbstractThis chapter presents an overview of the motivation for the volume, emphasizing why studying deep carbon is relevant to the goal of understanding carbon quantities, movements, forms, and origins. It contains brief highlights of the new instruments, cross-cutting research initiatives, and deep carbon science over the past decade (spurred in large part by the international Deep Carbon Observatory) that have expanded our understanding of carbon on Earth.
AbstractWork aboard E/V Nautilus and at the Inner Space Center in 2018 may assist in the search for extraterrestrial life, as exploration of iron-rich hydrothermal vent systems on Lō‘ihi Seamount (Figure 1) informs the design of future science-focused missions across our solar system. From August 21 to September 12, 2018, this research program was conducted by the SUBSEA (Systematic Underwater Biogeochemical Science and Exploration Analog) team, which is supported by NASA’s Science Mission Directorate and NOAA’s Office of Ocean Exploration and Research. Our mission comprises three research elements: science, operations, and technology. Both natural and social sciences anchor the SUBSEA program, providing the basis for the operations and technology domains to design and implement their studies and supporting capabilities.
AbstractMethanogenic archaea can be integrated into a sustainable, carbon-neutral cycle for producing organic chemicals from C1 compounds if the rate, yield, and titer of product synthesis can be improved using metabolic engineering. However, metabolic engineering techniques are limited in methanogens by insufficient methods for controlling cellular protein levels. We conducted a systematic approach to tune protein levels in Methanosarcina acetivorans C2A, a model methanogen, by regulating transcription and translation initiation. Rationally designed core promoter and ribosome binding site mutations in M. acetivorans C2A resulted in a predicable change in protein levels over a 60 fold range. The overall range of protein levels was increased an additional 3 fold by introducing the 5′ untranslated region of the mcrB transcript. This work demonstrates a wide range of precisely controlled protein levels in M. acetivorans C2A, which will help facilitate systematic metabolic engineering efforts in methanogens.
AbstractThe oceanic magnesium budget is important to our understanding of Earth’s carbon cycle, because similar processes control both (e.g., weathering, volcanism, and carbonate precipitation). However, dolomite sedimentation and low-temperature hydrothermal circulation remain enigmatic oceanic Mg sinks. In recent years, magnesium isotopes (δ26Mg) have provided new constraints on the Mg cycle, but the lack of data for the low-temperature hydrothermal isotope fractionation has hindered this approach. Here we present new δ26Mg data for low-temperature hydrothermal fluids, demonstrating preferential 26Mg incorporation into the oceanic crust, on average by εsolid-fluid ≈ 1.6‰. These new data, along with the constant seawater δ26Mg over the past ~20 Myr, require a significant dolomitic sink (estimated to be 1.5–2.9 Tmol yr−1; 40–60% of the oceanic Mg outputs). This estimate argues strongly against the conventional view that dolomite formation has been negligible in the Neogene and points to the existence of significant hidden dolomite formation.
Stable isotope compositions of methane (δ13C and δD) and of short-chain alkanes are commonly used to trace the origin and fate of carbon in the continental crust. In continental sedimentary systems, methane is typically produced through thermogenic cracking of organic matter and/or through microbial methanogenesis. However, secondary processes such as mixing, migration or biodegradation can alter the original isotopic and composition of the gas, making the identification and the quantification of primary sources challenging. The recently resolved methane ‘clumped’ isotopologues Δ13CH3D and Δ12CH2D2 are unique indicators of whether methane is at thermodynamic isotopic equilibrium or not, thereby providing insights into formation temperatures and/or into kinetic processes controlling methane generation processes, including microbial methanogenesis.
In this study, we report the first systematic use of methane Δ13CH3D and Δ12CH2D2 in the context of continental sedimentary basins. We investigated sedimentary formations from the Southwest Ontario and Michigan Basins, where the presence of both microbial and thermogenic methane was previously proposed. Methane from the Silurian strata coexist with highly saline brines, and clumped isotopologues exhibit large offsets from thermodynamic equilibrium, with Δ12CH2D2 values as low as −23‰. Together with conventional δ13C and δD values, the variability in Δ13CH3D and Δ12CH2D2 to first order reflects a mixing relationship between near-equilibrated thermogenic methane similar to gases from deeper Cambrian and Middle Ordovician units, and a source characterized by a substantial departure from equilibrium that could be associated with microbial methanogenesis. In contrast, methane from the Devonian-age Antrim Shale, associated with less saline porewaters, reveals Δ13CH3D and Δ12CH2D2 values that are approaching low temperature thermodynamic equilibrium. While microbial methanogenesis remains an important contributor to the methane budget in the Antrim Shale, it is suggested that Anaerobic Oxidation of Methane (AOM) could contribute to reprocessing methane isotopologues, yielding Δ13CH3D and Δ12CH2D2 signatures approaching thermodynamic equilibrium.