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1. 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 inmore »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.« less
2. 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)

   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., themore »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.« less
3. Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

   https://doi.org/10.1038/s41396-021-00898-x  

   Tran, Patricia Q. ; Bachand, Samantha C. ; McIntyre, Peter B. ; Kraemer, Benjamin M. ; Vadeboncoeur, Yvonne ; Kimirei, Ismael A. ; Tamatamah, Rashid ; McMahon, Katherine D. ; Anantharaman, Karthik ( February 2021 , The ISME Journal)

   Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted tomore »bring increased stratification and anoxia to freshwater lakes.

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4. 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. ; German, Christopher R. ; et al ( January 2023 , 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.
5. Microbial epibiotic community of the deep-sea galatheid squat lobster Munidopsis alvisca

   https://doi.org/10.1038/s41598-022-06666-x  

   Leinberger, Janina ; Milke, Felix ; Christodoulou, Magdalini ; Poehlein, Anja ; Caraveo-Patiño, Javier ; Teske, Andreas ; Brinkhoff, Thorsten ( February 2022 , Scientific Reports)

   Life at hydrothermal vent sites is based on chemosynthetic primary producers that supply heterotrophic microorganisms with substrates and generate biomass for higher trophic levels. Often, chemoautotrophs associate with the hydrothermal vent megafauna. To investigate attached bacterial and archaeal communities on deep-sea squat lobsters, we collected ten specimens from a hydrothermal vent in the Guaymas Basin (Gulf of California). All animals were identified asMunidopsis alviscavia morphological and molecular classification, and intraspecific divergence was determined. Amplicon sequencing of microbial DNA and cDNA revealed significant differences between microbial communities on the carapaces ofM. alviscaand those in ambient sea water. Major epibiotic bacterial taxa were chemoautotrophicGammaproteobacteria, such asThiotrichaceaeandMethylococcaceae, while archaea were almost exclusively represented by sequences affiliated withCa. Nitrosopumilus. In sea water samples, Marine Group II and III archaea and organoheterotrophicAlphaproteobacteria,FlavobacteriiaandPlanctomycetaciawere more dominant. Based on the identified taxa, we assume that main metabolic processes, carried out byM. alviscaepibiota, include ammonia, methane and sulphide oxidation. Considering thatM. alviscacould benefit from sulphide detoxification by its epibiota, and that attached microbes are supplied with a stable habitat in proximity to substrate-rich hydrothermal fluids, a mutualistic host-microbe relationship appears likely.