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  • 1
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    Autonomous Marine Robotic Technology Reveals an Expansive Benthic Bacterial Community Relevant to Regional Nitrogen Biogeochemistry (2016)
    American Chemistry Society
    In:  Environmental Science & Technology, 50 (20). pp. 11057-11065.
    Details
    Publication Date: 2019-02-01
    Description: Benthic accumulations of filamentous, mat-forming bacteria occur throughout the oceans where bisulfide mingles with oxygen or nitrate, providing key but poorly quantified linkages between elemental cycles of carbon, nitrogen and sulfur. Here we used the autonomous underwater vehicle Sentry to conduct a contiguous, 12.5 km photoimaging survey of sea-floor colonies of filamentous bacteria between 80 and 579 m water depth, spanning the continental shelf to the deep suboxic waters of the Santa Barbara Basin (SBB). The survey provided 〉31 000 images and revealed contiguous, white-colored bacterial colonization coating 〉 ∼80% of the ocean floor and spanning over 1.6 km, between 487 and 523 m water depth. Based on their localization within the stratified waters of the SBB we hypothesize a dynamic and annular biogeochemical zonation by which the bacteria capitalize on periodic flushing events to accumulate and utilize nitrate. Oceanographic time series data bracket the imaging survey and indicate rapid and contemporaneous nitrate loss, while autonomous capture of microbial communities from the benthic boundary layer concurrent with imaging provides possible identities for the responsible bacteria. Based on these observations we explore the ecological context of such mats and their possible importance in the nitrogen cycle of the SBB.
    Type: Article , PeerReviewed
    Format: text
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  • 2
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    The first decade of scientific insights from the Deepwater Horizon oil release (2020)
    Nature Research
    In:  Nature Reviews Earth & Environment, 1 . pp. 237-250.
    Details
    Publication Date: 2021-01-08
    Description: The 2010 Deepwater Horizon disaster remains the largest single accidental release of oil and gas into the ocean. During the 87-day release, scientists used oceanographic tools to collect wellhead oil and gas samples, interrogate microbial community shifts and activities, and track the chemical composition of dissolved oil in the ocean’s interior. In the decade since the disaster, field and laboratory investigations studied the physics and chemistry of irrupted oil and gas at high pressure and low temperature, the role of chemical dispersants in oil composition and microbial hydrocarbon degradation, and the impact of combined oil, gas and dispersants on the flora and fauna of coastal and deep-sea environments. The multi-faceted, multidisciplinary scientific response to the released oil, gas and dispersants culminated in a better understanding of the environmental factors that influence the short-term and long-term fate and transport of oil in marine settings. In this Review, we summarize the unique aspects of the Deepwater Horizon release and highlight the advances in oil chemistry and microbiology that resulted from novel applications of emerging technologies. We end with an outlook on the applicability of these findings to possible oil releases in future deep-sea drilling locations and newly-opened high-latitude shipping lanes.
    Type: Article , PeerReviewed
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  • 3
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    Ideas and perspectives: A strategic assessment of methane and nitrous oxide measurements in the marine environment (2020)
    Copernicus Publications (EGU)
    Details
    Publication Date: 2023-02-08
    Description: In the current era of rapid climate change, accurate characterization of climate-relevant gas dynamics-namely production, consumption, and net emissions-is required for all biomes, especially those ecosystems most susceptible to the impact of change. Marine environments include regions that act as net sources or sinks for numerous climateactive trace gases including methane (CH4) and nitrous oxide (N2O). The temporal and spatial distributions of CH4 and N2O are controlled by the interaction of complex biogeochemical and physical processes. To evaluate and quantify how these mechanisms affect marine CH4 and N2O cycling requires a combination of traditional scientific disciplines including oceanography, microbiology, and numerical modeling. Fundamental to these efforts is ensuring that the datasets produced by independent scientists are comparable and interoperable. Equally critical is transparent communication within the research community about the technical improvements required to increase our collective understanding of marine CH4 and N2O. A workshop sponsored by Ocean Carbon and Biogeochemistry (OCB) was organized to enhance dialogue and collaborations pertaining to marine CH4 and N2O. Here, we summarize the outcomes from the workshop to describe the challenges and opportunities for near-future CH4 and N2O research in the marine environment.
    Type: Article , PeerReviewed
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    Format: video
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  • 4
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    Unraveling the functional dark matter through global metagenomics (2023)
    Nature Research
    Details
    Publication Date: 2024-02-07
    Description: Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
    Type: Article , PeerReviewed
    Format: text
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