Search

Methane is a potent greenhouse gas that enters the marine system in large quantities at seafloor methane seeps. At a newly discovered seep site off the coast of Point Dume, CA, ~ meter‐scale carbonate chimneys host microbial communities that exhibit the highest methane‐oxidizing potential recorded to date. Here, we provide a detailed assessment of chimney geobiology through correlative mineralogical, geochemical, and microbiological studies of seven chimney samples in order to clarify the longevity and heterogeneity of these highly productive systems. U‐Th dating indicated that a methane‐driven carbonate precipitating system at Point Dume has existed for ~20 Kyr, while millimeter‐scale variations in carbon and calcium isotopic values, elemental abundances, and carbonate polymorphs revealed changes in carbon source, precipitation rates, and diagenetic processes throughout the chimneys' lifespan. Microbial community analyses revealed diverse modern communities with prominent anaerobic methanotrophs, sulfate‐reducing bacteria, and Anaerolineaceae; communities were more similar within a given chimney wall transect than in similar horizons of distinct structures. The chimneys represent long‐lived repositories of methane‐oxidizing communities and provide a window into how carbon can be transformed, sequestered, and altered over millennia at the Point Dume methane seep. [ABSTRACT FROM AUTHOR]

Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways. [ABSTRACT FROM AUTHOR]

Summary: Coastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural–functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7‐day in situ incubations with a non‐canonical amino acid that was incorporated into new biomass, samples were resin‐embedded and analysed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence‐activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ~60% in the top centimetre to 9.4%–22.4% between 2 and 10 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to putative sulfate‐reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non‐quartz minerals including rutile, orthoclase and plagioclase. Microbe–mineral relationships appear to be dynamic and context‐dependent arbiters of biogeochemical cycling. [ABSTRACT FROM AUTHOR]

Atmarine methane seeps, vast quantities of methanemove through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated Vmax, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample's methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rockhosted methanotrophy may be an important contributor to marine methane consumption. [ABSTRACT FROM AUTHOR]

Interest 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. [ABSTRACT FROM AUTHOR]

Motivation is a primary determinant of a student's academic success, but in many under-resourced educational contexts around the world, opportunities to develop motivation are lacking. In the City of God neighborhood of Rio de Janeiro, Brazil, we, a group of scientists and science educators, enacted the Ad Astra Academy, a brief, interactive intervention targeting teenage students at risk of dropping out of school. Students participated in an immersive five-day programme, followed by a six-month lecture series, before completing the second, immersive three-day programme. Participants learned how to use the scientific method in real-world settings to generate new knowledge. In order to consolidate these knowledge gains and bolster the inspirational power of the programme, capstone projects empowered participants to speak with NASA mission managers and, in some cases, acquire never-before-seen images of Mars. While longitudinal study and a more robust sample size are required to bolster conclusions about the efficacy of our approach, initial results suggest that Ad Astra programmes significantly enhance self-efficacy and science-oriented career ambitions. [ABSTRACT FROM AUTHOR]

Abstract: Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy‐rich, yet the most efficient methane‐activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by‐products at a comparable rate and in near‐stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost‐effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep‐sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep‐sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full‐scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane‐oxidizing, sulfide‐generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane‐dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth‐based communities were substantially streamlined and were dominated by Desulfotomaculum geothermicum. Fluorescence in situ hybridization microscopy with carbon cloth fibers revealed a novel spatial arrangement of anaerobic methanotrophs and sulfate reducing bacteria suggestive of an electronic coupling enabled by the artificial substrate. This system: 1) enables a more targeted manipulation of methane‐activating microbial communities using a low‐mass and sediment‐free substrate; 2) holds promise for the simultaneous consumption of a strong greenhouse gas and the generation of usable downstream products; and 3) furthers the broader adoption of uncultured, mixed microbial communities for biotechnological use. [ABSTRACT FROM AUTHOR]

The article comments on the importance of the role played by field expeditions in advancing the understanding of the natural world and also talks about telepresence technology in natural systems. Topics discussed include telepresence as the practice of using telecommunications technology, improvement in access to healthcare with the use of telemedicine, and developments in sea-going science.

Biological methane oxidation is a globally relevant process that mediates the flux of an important greenhouse gas through both aerobic and anaerobic metabolic pathways. However, measuring the rates of these metabolisms presents many obstacles, from logistical barriers to regulatory hurdles and poor precision. Here we present a new approach for measuring rates of microbial methane metabolism that is non-toxic, rapid, and relatively high throughput, alleviating some of the current methodological challenges. Specifically, we tested the potential for using monodeuterated methane (CH3D) as a metabolic substrate for measuring the rate of methane activation by quantifying the change in the aqueous D / H ratio over time using a water isotope analyzer. This method represents a non-toxic, comparatively rapid and straightforward approach that is complementary to existing radio (14C)- and stable (13C) carbon isotopic methods; by probing hydrogen atom dynamics, it offers an additional dimension through which to examine the rates and pathways of methane metabolism. We provide direct comparisons between the CH3D procedure and the well-established 14CH4 radiotracer approach for several methanotrophic systems, including type I and type II aerobic methanotroph cultures, and methane seep sediment and carbonate rocks under anoxic and oxic incubation conditions. We also employ this method to investigate the role of pressure on methane oxidation rates in anoxic seep sediment, revealing an 80% increase at the equivalent of ~ 900 m water depth (40 MPa). The monodeuterated methane approach offers a procedurally straightforward, reliable method that advances three specific aims: 1) the direct comparison of methane oxidation rates between different experimental treatments of the same inoculum; 2) the determination of an absolute scaling factor using paired CH3D and 14C-radiocarbon procedures for new systems of interest; and 3) a continued evaluation of C- and H-atom tracking through methanotrophic metabolisms, with specific foci on enzyme reversibility and anabolic/catabolic branch points. The procedural advantages, consistency, and novel research questions enabled by the monodeuterated methane method should prove useful in a wide range of culture-based and environmental microbial systems to further elucidate methane metabolism dynamics. [ABSTRACT FROM AUTHOR]

Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to 15NH4+ and CH4 amended 4 seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were 15N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis--including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)--were all observed to be actively synthesized (15N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of 15N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant conditions. Our work here demonstrates the active synthesis of a metabolically specific minority of enzymes, revealing the surprising longevity of most proteins over the course of an extended incubation experiment in an established, slow-growing, methane-impacted environmental system. [ABSTRACT FROM AUTHOR]

While tensions may lie between science and policy, we argue that dissemination and public engagement are key in alleviating those perceived tensions. Science being valued by society results in fact-based policy-making being demanded by constituents. Constituents' demands will yield representatives who are familiar with the scientific process and research to inform policy decisions. [ABSTRACT FROM AUTHOR]

Although the importance of trophic linkages, including 'top-down forcing', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ13C=−92±4‰; polar lipids −116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as 'archivory'. [ABSTRACT FROM AUTHOR]

Interactions among microorganisms and their mineralogical substrates govern the structure, function and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2 and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities 'as they really are' and explore determinants of metabolic activity across a range of microbiomes. [ABSTRACT FROM AUTHOR]

Exploring Mars would be easier if researchers knew more about the properties and behaviour of martian soils. Jeffrey J Marlow, Zita Martins and Mark A Sephton explain how terrestrial analogues could help – especially if we had more of them. Preparations for missions to Mars are a major concern for scientists. Predicting how equipment and experiments will perform on the planet is difficult because tests are restricted to Earth. Mars soil analogues are being used to solve this problem. These terrestrial materials are chemically and physically similar to martian soils and, because they contain unusual minerals and trace amounts of organic matter, are scientifically interesting in their own right. However, no current analogue is appropriate for all necessary tests. Here we describe Mars soil analogues, identify limitations and suggest the need for new Mars simulants. [ABSTRACT FROM AUTHOR]