Advancing subsurface biosphere and paleoclimate research: ECORD–ICDP–DCO–J-DESC–MagellanPlus Workshop Series Program Report

The proper pre-drilling preparation, on-site acquisition and post-drilling preservation of high-qualitysubsurface samples are crucial to ensure significant progress in the scientifically and societally important areasof subsurface biosphere and paleoclimate research. Two of the four research themes of IODP and ICDPand one of the four research areas of the Deep Carbon Observatory (DCO) focus on the subsurface biosphere.Increasing understanding of paleoclimate is a central goal of IODP and incorporated within the scope of theIMPRESS program, the successor of the IMAGES program. Therefore, the goal of our IODP–ICDP–DCO–JDESC–MagellanPlus-sponsored workshop was to help advance deep biosphere and paleoclimate research byidentifying needed improvements in scientific drilling planning and available technology, sample collection andinitial analysis, and long-term storage of subsurface samples and data. Success in these areas will (a) avoidbiological and other contamination during drilling, sampling, storage and shipboard/shore-based experiments;(b) build a repository and database of high-quality subsurface samples for microbiological and paleoclimate researchavailable for the scientific community world-wide over the next decades; and (c) standardize, as much aspossible, microbiological and paleoclimate drilling, sampling and storage workflows to allow results and datato be comparable across both space and time. A result of this workshop is the development and suggested implementationof new advanced methods and technologies to collect high-quality samples and data for the deepbiosphere and paleoclimate scientific communities to optimize expected substantial progress in these fields. Themembers of this workshop will enhance communication within the scientific drilling community by crafting ahandbook focused on pre-drilling, drilling and post-drilling operations

Design by immersion: A transdisciplinary approach to problem-driven visualizations

While previous work exists on how to conduct and disseminate insights from problem-driven visualization work and design studies, the literature does not address how to accomplish these goals in transdisciplinary teams in ways that advance all disciplines involved. In this paper we introduce and define a new methodological paradigm we call design by immersion, which provides an alternative perspective on problem-driven visualization work. Design by immersion embeds transdisciplinary experiences at the center of the visualization process by having visualization researchers participate in the work of the target domain (or domain experts participate in visualization research). Based on our own combined experiences of working on cross-disciplinary, problem-driven visualization projects, we present six case studies that expose the opportunities that design by immersion enables, including (1) exploring new domain-inspired visualization design spaces, (2) enriching domain understanding through personal experiences, and (3) building strong transdisciplinary relationships. Furthermore, we illustrate how the process of design by immersion opens up a diverse set of design activities that can be combined in different ways depending on the type of collaboration, project, and goals. Finally, we discuss the challenges and potential pitfalls of design by immersion

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin

In deep ocean hypersaline basins, the combination of high salinity, unusual ionic composition and anoxic conditions represents significant challenges for microbial life. We used geochemical porewater characterization and DNA sequencing based taxonomic surveys to enable environmental and microbial characterization of anoxic hypersaline sediments and brines in the Orca Basin, the largest brine basin in the Gulf of Mexico. Full-length bacterial 16S rRNA gene clone libraries from hypersaline sediments and the overlying brine were dominated by the uncultured halophilic KB1 lineage, Deltaproteobacteria related to cultured sulfate-reducing halophilic genera, and specific lineages of heterotrophic Bacteroidetes. Archaeal clones were dominated by members of the halophilic methanogen genus Methanohalophilus, and the ammonia-oxidizing Marine Group I (MG-I) within the Thaumarchaeota. Illumina sequencing revealed higher phylum- and subphylum-level complexity, especially in lower-salinity sediments from the Orca Basin slope. Illumina and clone library surveys consistently detected MG-I Thaumarchaeota and halotolerant Deltaproteobacteria in the hypersaline anoxic sediments, but relative abundances of the KB1 lineage differed between the two sequencing methods. The stable isotopic composition of dissolved inorganic carbon and methane in porewater, and sulfate concentrations decreasing downcore indicated methanogenesis and sulfate reduction in the anoxic sediments. While anaerobic microbial processes likely occur at low rates near their maximal salinity thresholds in Orca Basin, long-term accumulation of reaction products leads to high methane concentrations and reducing conditions within the Orca Basin brine and sediments

The Enduring Questions: What's for Dinner? Where's My Knife? …and Can I Use My Fingers? (Unanswered) Questions Related to Organic Matter and Microbes in Marine Sediments

Heterotrophic microbial communities play key roles in processing and remineralizing organic matter in marine sediments: they are the “final gatekeepers” that determine the types and quantity of organicmatter that is ultimately buried in sediments—processes important to our understanding of past global environments, as well as to the production of petroleum products that still fuel much of modern society. These communities’ capabilities also help us understand the energetic and metabolic boundaries of life. Work over the past decades has revealed much information about sedimentary microbial communities: their overall composition (Bacteria and Archaea), the sequence of terminal respiration processes occurring with progressive burial depth in sediments, and the depth to which they can be detected; research on the members and metabolism in the “deep biosphere” has assumed a central position in organic geochemistry, environmental microbiology, and molecular ecology (Orcutt et al., 2013; D’Hondt et al., 2019)

Microbial conversion of inorganic carbon to dimethyl sulfide in anoxic lake sediment (Plußsee, Germany)

In anoxic environments, volatile methylated sulfides like methanethiol (MT) and dimethyl sulfide (DMS) link the pools of inorganic and organic carbon with the sulfur cycle. However, direct formation of methylated sulfides from reduction of dissolved inorganic carbon has previously not been demonstrated. When studying the effect of temperature on hydrogenotrophic microbial activity, we observed formation of DMS in anoxic sediment of Lake Plußsee at 55 °C. Subsequent experiments strongly suggested that the formation of DMS involves fixation of bicarbonate via a reductive pathway in analogy to methanogenesis and engages methylation of MT. DMS formation was enhanced by addition of bicarbonate and further increased when both bicarbonate and H<sub>2</sub> were supplemented. Inhibition of DMS formation by 2-bromoethanesulfonate points to the involvement of methanogens. Compared to the accumulation of DMS, MT showed the opposite trend but there was no apparent 1:1 stoichiometric ratio between both compounds. Both DMS and MT had negative δ<sup>13</sup>C values of −62‰ and −55‰, respectively. Labeling with NaH<sup>13</sup>CO<sub>3</sub> showed more rapid incorporation of bicarbonate into DMS than into MT. The stable carbon isotopic evidence implies that bicarbonate was fixed via a reductive pathway of methanogenesis, and the generated methyl coenzyme M became the methyl donor for MT methylation. Neither DMS nor MT accumulation were stimulated by addition of the methyl-group donors methanol and syringic acid or by the methyl-group acceptor hydrogen sulphide. The source of MT was further investigated in a H<sub>2</sub><sup>35</sup>S labeling experiment, which demonstrated a microbially-mediated process of hydrogen sulfide methylation to MT that accounted for only <10% of the accumulation rates of DMS. Therefore, the major source of the <sup>13</sup>C-depleted MT was neither bicarbonate nor methoxylated aromatic compounds. Other possibilities for isotopically depleted MT, such as other organic precursors like methionine, are discussed. This DMS-forming pathway may be relevant for anoxic environments such as hydrothermally influenced sediments and fluids and sulfate-methane transition zones in marine sediments

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment

Editorial: Current Topics in Marine Organic Biogeochemical Research

Complex and incompletely understood chemical, biological and physical processes affect the delivery, transport, and storage of organic matter (OM) in the ocean. Atmospheric and climate-relevant gases, primarily carbon dioxide, are closely linked to the production and flux of organic matter within the ocean via the biological pump. Marine and continental OM is transformed in the water column, some is transported to the sediments where a fraction is stored over geological time, and some marine OM is released to the atmosphere. These functions are intimately linked to global nutrient cycles and ecosystem processes. Perhaps indicative of how the field has matured, the multidisciplinary nature of ocean carbon studies and the importance of biological processes in organic carbon cycling has resulted in a morphing of “marine organic geochemistry” into “marine organic biogeochemistry.” Marine organic biogeochemistry now provides a molecular-level window onto the functioning and scale of processes that control the behavior of OM in the ocean. New sampling tools, analytical methods, and data handling capabilities have been applied to marine chemistry since the 1970s; and in tandem with coordinated, international and interdisciplinary research programs, this has led to explosive growth of marine organic biogeochemistry

Intact polar lipids in the water column of the eastern tropical North Pacific: abundance and structural variety of non-phosphorus lipids

Intact polar lipids (IPLs) are the main building blocks of cellular membranes and contain chemotaxonomic, ecophysiological and metabolic information, making them valuable biomarkers in microbial ecology and biogeochemistry. This study investigates IPLs in suspended particulate matter (SPM) in the water column of the eastern tropical North Pacific Ocean (ETNP), one of the most extensive open-ocean oxygen minimum zones (OMZs) in the world, with strong gradients of nutrients, temperature and redox conditions. A wide structural variety in polar lipid head-group composition and core structures exists along physical and geochemical gradients within the water column, from the oxygenated photic zone to the aphotic OMZ. We use this structural diversity in IPLs to evaluate the ecology and ecophysiological adaptations that affect organisms inhabiting the water column, especially the mid-depth OMZ in the context of biogeochemical cycles. Diacylglycerol phospholipids are present at all depths, but exhibit the highest relative abundance and compositional variety (including mixed acyl/ether core structures) in the upper and core OMZ where prokaryotic biomass was enriched. Surface ocean SPM is dominated by diacylglycerol glycolipids that are found in photosynthetic membranes. These and other glycolipids with varying core structures composed of ceramides and hydroxylated fatty acids are also detected with varying relative abundances in the OMZ and deep oxycline, signifying additional non-phototrophic bacterial sources for these lipids. Betaine lipids (with zero or multiple hydroxylations in the core structures) that are typically assigned to microalgae are found throughout the water column down to the deep oxycline but do not show a depth-related trend in relative abundance. Archaeal IPLs comprised of glycosidic and mixed glycosidic-phosphatidic glycerol dibiphytanyl glycerol tetraethers (GDGTs) are most abundant in the upper OMZ, where nitrate maxima point to ammonium oxidation but increase in relative abundance in the core OMZ and deep oxycline. The presence of non-phosphorus substitute lipids within the OMZ suggest that the indigenous microbes might be phosphorus limited (P starved) at ambient phosphate concentrations of 1 to 3.5&thinsp;µM, although specific microbial sources for many of these lipids still remain unknown.</p