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1. Expedition 376 Scientific Prospectus: Brothers Arc Flux

   https://doi.org/10.14379/iodp.sp.376.2017  

   de Ronde, C.E.J. ; Humphris, S.E. ; Höfig, T.W. ( June 2017 , Scientific prospectus)

   null (Ed.)

   Almost two-thirds of Earth’s submarine volcanism is expressed in the ocean basins along the ~65,000 km long mid-ocean-ridge (MOR) system, but the remaining third takes place along intraoceanic arcs and seamounts. The 22,000 km long intraoceanic arc system appears to surpass the MOR system in terms of both the frequency of hydrothermal activity, with several sites per 100 km of arc, and the range in chemical composition of the fluids being discharged. Hydrothermal systems hosted by submarine arc volcanoes differ substantially from those in spreading environments in that they commonly contain a large component of magmatic fluid. Our primary scientific goal is to discover the fundamental underlying processes that develop as a consequence of this difference. A magmatic-hydrothermal signature, coupled with the shallow depths of arc volcanoes and their high-volatile contents, strongly influences the chemistry of fluids and the resulting mineralization and likely has important consequences for the biota associated with these systems. Because of the high metal contents and very acidic fluids, these hydrothermal systems are also thought to be important analogs of many porphyry copper and epithermal gold deposits mined today on land. Drilling at Brothers volcano on the Kermadec arc will provide the missing link (i.e., the third dimension) in our understanding of mineral deposit formation along arcs, the subseafloor architecture of these volcanoes and their related permeability, as well as the relationship between the discharge of magmatic fluids and the deep biosphere. Expedition 376 will drill and log two caldera sites, one on the rim of the caldera and a second inside the caldera, and a third site at the summit of a volcanic cone, located inside the caldera at Brothers. These sites represent discharge zones of geochemically distinct fluids that are variably affected by magmatic volatile input, allowing us to directly address the consequences of magma degassing for metal transport to the seafloor and its effect on the functioning of microbial communities. Drilling will provide access to critical zones dominated by magma degassing and high-temperature hydrothermal circulation over depth intervals regarded as crucial, not only in the development of multiphase mineralizing systems but also in identifying subsurface microbially habitable environments. The specific objectives of Expedition 376 are • To characterize the subvolcano, magma chamber–derived volatile phase to test model-based predictions that this is either a single-phase gas or two-phase brine-vapor; • To determine the subseafloor distribution of base and precious metals and metalloids and the reactions that have taken place along pathways to the seafloor; • To quantify the mechanisms and extent of fluid-rock interaction and consequences for mass transfer of metals and metalloids into the ocean and the role of magmatically derived carbon and sulfur species in mediating these fluxes; and • To assess the diversity, extent, and metabolic pathways of microbial life in an extreme, metal-toxic, and acidic volcanic environment. 

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2. Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems

   https://doi.org/10.3389/fmicb.2021.714920  

   Hoffert, Michael ; Anderson, Rika E. ; Reveillaud, Julie ; Murphy, Leslie G. ; Stepanauskas, Ramunas ; Huber, Julie A. ( August 2021 , Frontiers in Microbiology)

   Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus lineages and their transcripts were more abundant than others in individual vent sites, indicating differential fitness among lineages. The relative abundances of lineages represented by SAGs in each of the samples matched phylogenetic relationships based on single-copy universal genes, and genes related to nitrogen fixation and the CRISPR/Cas immune system were among those differentiating the clades. Lineages possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems. 

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3. Globally‐distributed microbial eukaryotes exhibit endemism at deep‐sea hydrothermal vents

   https://doi.org/10.1111/mec.16745  

   Hu, Sarah K. ; Smith, Amy R. ; Anderson, Rika E. ; Sylva, Sean P. ; Setzer, Michaela ; Steadmon, Maria ; Frank, Kiana L. ; Chan, Eric W. ; Lim, Darlene S. S. ; German, Christopher R. ; et al ( November 2022 , Molecular Ecology)

   Single‐celled microbial eukaryotes inhabit deep‐sea hydrothermal vent environments and play critical ecological roles in the vent‐associated microbial food web. 18S rRNA amplicon sequencing of diffuse venting fluids from four geographically‐ and geochemically‐distinct hydrothermal vent fields was applied to investigate community diversity patterns among protistan assemblages. The four vent fields include Axial Seamount at the Juan de Fuca Ridge, Sea Cliff and Apollo at the Gorda Ridge, all in the NE Pacific Ocean, and Piccard and Von Damm at the Mid‐Cayman Rise in the Caribbean Sea. We describe species diversity patterns with respect to hydrothermal vent field and sample type, identify putative vent endemic microbial eukaryotes, and test how vent fluid geochemistry may influence microbial community diversity. At a semi‐global scale, microbial eukaryotic communities at deep‐sea vents were composed of similar proportions of dinoflagellates, ciliates, Rhizaria, and stramenopiles. Individual vent fields supported distinct and highly diverse assemblages of protists that included potentially endemic or novel vent‐associated strains. These findings represent a census of deep‐sea hydrothermal vent protistan communities. Protistan diversity, which is shaped by the hydrothermal vent environment at a local scale, ultimately influences the vent‐associated microbial food web and the broader deep‐sea carbon cycle.

    

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4. Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes

   https://doi.org/10.1038/s41396-023-01421-0  

   Zhou, Zhichao ; Tran, Patricia Q. ; Adams, Alyssa M. ; Kieft, Kristopher ; Breier, John A. ; Fortunato, Caroline S. ; Sheik, Cody S. ; Huber, Julie A. ; Li, Meng ; Dick, Gregory J. ; et al ( January 2023 , The ISME Journal)

   Abstract In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and their characteristics are determined by geochemical sources from vents, e.g., hydrothermal inputs, nutrients, and trace metals. However, the impacts of plume biogeochemistry on the oceans are poorly constrained due to a lack of integrated understanding of microbiomes, population genetics, and geochemistry. Here, we use microbial genomes to understand links between biogeography, evolution, and metabolic connectivity, and elucidate their impacts on biogeochemical cycling in the deep sea. Using data from 36 diverse plume samples from seven ocean basins, we show that sulfur metabolism defines the core microbiome of plumes and drives metabolic connectivity in the microbial community. Sulfur-dominated geochemistry influences energy landscapes and promotes microbial growth, while other energy sources influence local energy landscapes. We further demonstrated the consistency of links among geochemistry, function, and taxonomy. Amongst all microbial metabolisms, sulfur transformations had the highest MW-score, a measure of metabolic connectivity in microbial communities. Additionally, plume microbial populations have low diversity, short migration history, and gene-specific sweep patterns after migrating from background seawater. Selected functions include nutrient uptake, aerobic oxidation, sulfur oxidation for higher energy yields, and stress responses for adaptation. Our findings provide the ecological and evolutionary bases of change in sulfur-driven microbial communities and their population genetics in adaptation to changing geochemical gradients in the oceans. 

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5. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

   https://doi.org/10.1128/mbio.02918-23  

   Zhang, Irene H. ; Borer, Benedict ; Zhao, Rui ; Wilbert, Steven ; Newman, Dianne K. ; Babbin, Andrew R. ( March 2024 , mBio)

   Giovannoni, Stephen J. (Ed.)

   Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.

    

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