ALBERT

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Howell, K. L., Hilario, A., Allcock, A. L., Bailey, D. M., Baker, M., Clark, M. R., Colaco, A., Copley, J., Cordes, E. E., Danovaro, R., Dissanayake, A., Escobar, E., Esquete, P., Gallagher, A. J., Gates, A. R., Gaudron, S. M., German, C. R., Gjerde, K. M., Higgs, N. D., Le Bris, N., Levin, L. A., Manea, E., McClain, C., Menot, L., Mestre, N. C., Metaxas, A., Milligan, R. J., Muthumbi, A. W. N., Narayanaswamy, B. E., Ramalho, S. P., Ramirez-Llodra, E., Robson, L. M., Rogers, A. D., Sellanes, J., Sigwart, J. D., Sink, K., Snelgrove, P. V. R., Stefanoudis, P., V., Sumida, P. Y., Taylor, M. L., Thurber, A. R., Vieira, R. P., Watanabe, H. K., Woodall, L. C., & Xavier, J. R. A blueprint for an inclusive, global deep-sea ocean decade field program. Frontiers in Marine Science, 7, (2020): 584861, doi:10.3389/fmars.2020.584861.

Description: The ocean plays a crucial role in the functioning of the Earth System and in the provision of vital goods and services. The United Nations (UN) declared 2021–2030 as the UN Decade of Ocean Science for Sustainable Development. The Roadmap for the Ocean Decade aims to achieve six critical societal outcomes (SOs) by 2030, through the pursuit of four objectives (Os). It specifically recognizes the scarcity of biological data for deep-sea biomes, and challenges the global scientific community to conduct research to advance understanding of deep-sea ecosystems to inform sustainable management. In this paper, we map four key scientific questions identified by the academic community to the Ocean Decade SOs: (i) What is the diversity of life in the deep ocean? (ii) How are populations and habitats connected? (iii) What is the role of living organisms in ecosystem function and service provision? and (iv) How do species, communities, and ecosystems respond to disturbance? We then consider the design of a global-scale program to address these questions by reviewing key drivers of ecological pattern and process. We recommend using the following criteria to stratify a global survey design: biogeographic region, depth, horizontal distance, substrate type, high and low climate hazard, fished/unfished, near/far from sources of pollution, licensed/protected from industry activities. We consider both spatial and temporal surveys, and emphasize new biological data collection that prioritizes southern and polar latitudes, deeper (〉 2000 m) depths, and midwater environments. We provide guidance on observational, experimental, and monitoring needs for different benthic and pelagic ecosystems. We then review recent efforts to standardize biological data and specimen collection and archiving, making “sampling design to knowledge application” recommendations in the context of a new global program. We also review and comment on needs, and recommend actions, to develop capacity in deep-sea research; and the role of inclusivity - from accessing indigenous and local knowledge to the sharing of technologies - as part of such a global program. We discuss the concept of a new global deep-sea biological research program ‘Challenger 150,’ highlighting what it could deliver for the Ocean Decade and UN Sustainable Development Goal 14.

Description: Development of this paper was supported by funding from the Scientific Committee on Oceanic Research (SCOR) awarded to KH and AH as working group 159 co-chairs. KH, BN, and KS are supported by the UKRI funded One Ocean Hub NE/S008950/1. AH work is supported by the CESAM (UIDP/50017/2020 + 1432 UIDB/50017/2020) that is funded by Fundação para a Ciência e a Tecnologia (FCT)/MCTES through national funds. AA is supported by Science Foundation Ireland and the Marine Institute under the Investigators Program Grant Number SFI/15/IA/3100 co-funded under the European Regional Development Fund 2014–2020. AC is supported through the FunAzores -ACORES 01-0145-FEDER-000123 grant and by FCT through strategic project UID/05634/2020 and FCT and Direção-Geral de Politica do Mar (DGPM) through the project Mining2/2017/005. PE is funded by national funds (OE), through FCT in the scope of the framework contract foreseen in the numbers 4, 5 and 6 of the article 23, of the Decree-Law 57/2016, of August 29, changed by Law 57/2017, of July 19. SG research is supported by CNRS funds. CG is supported by an Independent Study Award and the Investment in Science Fund at WHOI. KG gratefully acknowledges support from Synchronicity Earth. LL is funded by the NOAA Office of Ocean Exploration and Research (NA19OAR0110305) and the US National Science Foundation (OCE 1634172). NM is supported by FCT and DGPM, through the project Mining2/2017/001 and the FCT grants CEECIND/00526/2017, UIDB/00350/2020 + UIDP/00350/2020. SR is funded by the FCTgrant CEECIND/00758/2017. JS is supported by ANID FONDECYT #1181153 and ANID Millennium Science Initiative Program #NC120030. JX research is funded by the European Union’s Horizon 2020 research and innovation program through the SponGES project (grant agreement no. 679849) and further supported by national funds through FCT within the scope of UIDB/04423/2020 and UIDP/04423/2020. The Natural Sciences and Engineering Council of Canada supports AM and PVRS. MB and the Deep-Ocean Stewardship Initiative are supported by Arcadia - A charitable fund of Lisbet Rausing and Peter Baldwin. BN work is supported by the NERC funded Arctic PRIZE NE/P006302/1.

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mayers, K. M. J., Poulton, A. J., Bidle, K., Thamatrakoln, K., Schieler, B., Giering, S. L. C., Wells, S. R., Tarran, G. A., Mayor, D., Johnson, M., Riebesell, U., Larsen, A., Vardi, A., & Harvey, E. L. The possession of coccoliths fails to deter microzooplankton grazers. Frontiers in Marine Science, 7, (2020): 562020, doi:10.3389/fmars.2020.569896.

Description: Phytoplankton play a central role in the regulation of global carbon and nutrient cycles, forming the basis of the marine food webs. A group of biogeochemically important phytoplankton, the coccolithophores, produce calcium carbonate scales that have been hypothesized to deter or reduce grazing by microzooplankton. Here, a meta-analysis of mesocosm-based experiments demonstrates that calcification of the cosmopolitan coccolithophore, Emiliania huxleyi, fails to deter microzooplankton grazing. The median grazing to growth ratio for E. huxleyi (0.56 ± 0.40) was not significantly different among non-calcified nano- or picoeukaryotes (0.71 ± 0.31 and 0.55 ± 0.34, respectively). Additionally, the environmental concentration of E. huxleyi did not drive preferential grazing of non-calcified groups. These results strongly suggest that the possession of coccoliths does not provide E. huxleyi effective protection from microzooplankton grazing. Such indiscriminate consumption has implications for the dissolution and fate of CaCO3 in the ocean, and the evolution of coccoliths.

Description: Mesocosm experiments in 2015 were supported by the Kiel Excellence Cluster “The Future Ocean” (CP1540) and the Leibniz Award to UR, in 2017 the MESOHUX experiment was supported by NSF (OCE-1559179) to KT and KB, NSF (OCE-1537951 and OCE-1459200) to KB, NSF (OCE-1459190, 1657808, and DBI-1624593) to EH, and in 2018 by AQUACOSM (EU H2020-INFRAIA-project No 731065). KM was supported by a NERC Doctoral Training Partnership (DTP) studentship as part of the Southampton Partnership for Innovative Training of Future Investigators Researching the Environment (SPITFIRE, grant number NE/L002531/1) and Research Council of Norway project (#280414) MIXsTRUCT.

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wilson, S. T., Al-Haj, A. N., Bourbonnais, A., Frey, C., Fulweiler, R. W., Kessler, J. D., Marchant, H. K., Milucka, J., Ray, N. E., Suntharalingam, P., Thornton, B. F., Upstill-Goddard, R. C., Weber, T. S., Arevalo-Martinez, D. L., Bange, H. W., Benway, H. M., Bianchi, D., Borges, A., V., Chang, B. X., Crill, P. M., del Valle, D. A., Farias, L., Joye, S. B., Kock, A., Labidi, J., Manning, C. C., Pohlman, J. W., Rehder, G., Sparrow, K. J., Tortell, P. D., Treude, T., Valentine, D. L., Ward, B. B., Yang, S., & Yurganov, L. N. Ideas and perspectives: a strategic assessment of methane and nitrous oxide measurements in the marine environment. Biogeosciences, 17(22), (2020): 5809-5828, https://doi.org/10.5194/bg-17-5809-2020.

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 climate-active 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.

Description: This article was an outcome of a workshop organized by the Ocean Carbon and Biogeochemistry (OCB) project office, which is supported by the US National Science Foundation (grant no. 1558412) and the National Aeronautics and Space Administration (grant no. NNX17AB17G). The workshop received additional funding from the Scientific Committee on Ocean Research (SCOR) which receives funding from the US National Science Foundation (grant no. 1840868) and contributions by additional national SCOR committees. The Chilean COPAS N2O time-series measurements were supported by Agencia Nacional de Investigación y Desarrollo (grant no. 1200861).

Description: While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their in vivo biosynthetic functionality. Using fluorescent in situ enzyme assay targeting carrier proteins common to polyketide (PKS) and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated cell sorting to tunicate microbiome to enrich for microbes with active secondary metabolic capabilities. Single-cell genomics uncovered the genetic basis for a wide biosynthetic diversity in the enzyme-active cells and revealed a member of marine Oceanospirillales harboring a novel NRPS gene cluster with high similarity to phylogenetically distant marine and terrestrial bacteria. Interestingly, this synthase belongs to a larger class of siderophore biosynthetic gene clusters commonly associated with pestilence and disease. This demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Visser, A., Wankel, S. D., Niklaus, P. A., Byrne, J. M., Kappler, A. A., & Lehmann, M. F. Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics. Biogeosciences, 17(16), (2020): 4355-4374, doi:10.5194/bg-17-4355-2020.

Description: Anaerobic nitrate-dependent Fe(II) oxidation (NDFeO) is widespread in various aquatic environments and plays a major role in iron and nitrogen redox dynamics. However, evidence for truly enzymatic, autotrophic NDFeO remains limited, with alternative explanations involving the coupling of heterotrophic denitrification with the abiotic oxidation of structurally bound or aqueous Fe(II) by reactive intermediate nitrogen (N) species (chemodenitrification). The extent to which chemodenitrification is caused (or enhanced) by ex vivo surface catalytic effects has not been directly tested to date. To determine whether the presence of either an Fe(II)-bearing mineral or dead biomass (DB) catalyses chemodenitrification, two different sets of anoxic batch experiments were conducted: 2 mM Fe(II) was added to a low-phosphate medium, resulting in the precipitation of vivianite (Fe3(PO4)2), to which 2 mM nitrite (NO−2) was later added, with or without an autoclaved cell suspension (∼1.96×108 cells mL−1) of Shewanella oneidensis MR-1. Concentrations of nitrite (NO−2), nitrous oxide (N2O), and iron (Fe2+, Fetot) were monitored over time in both set-ups to assess the impact of Fe(II) minerals and/or DB as catalysts of chemodenitrification. In addition, the natural-abundance isotope ratios of NO−2 and N2O (δ15N and δ18O) were analysed to constrain the associated isotope effects. Up to 90 % of the Fe(II) was oxidized in the presence of DB, whereas only ∼65 % of the Fe(II) was oxidized under mineral-only conditions, suggesting an overall lower reactivity of the mineral-only set-up. Similarly, the average NO−2 reduction rate in the mineral-only experiments (0.004±0.003 mmol L−1 d−1) was much lower than in the experiments with both mineral and DB (0.053±0.013 mmol L−1 d−1), as was N2O production (204.02±60.29 nmol L−1 d−1). The N2O yield per mole NO−2 reduced was higher in the mineral-only set-ups (4 %) than in the experiments with DB (1 %), suggesting the catalysis-dependent differential formation of NO. N-NO−2 isotope ratio measurements indicated a clear difference between both experimental conditions: in contrast to the marked 15N isotope enrichment during active NO−2 reduction (15εNO2=+10.3 ‰) observed in the presence of DB, NO−2 loss in the mineral-only experiments exhibited only a small N isotope effect (〈+1 ‰). The NO−2-O isotope effect was very low in both set-ups (18εNO2 〈1 ‰), which was most likely due to substantial O isotope exchange with ambient water. Moreover, under low-turnover conditions (i.e. in the mineral-only experiments as well as initially in experiments with DB), the observed NO−2 isotope systematics suggest, transiently, a small inverse isotope effect (i.e. decreasing NO−2 δ15N and δ18O with decreasing concentrations), which was possibly related to transitory surface complexation mechanisms. Site preference (SP) of the 15N isotopes in the linear N2O molecule for both set-ups ranged between 0 ‰ and 14 ‰, which was notably lower than the values previously reported for chemodenitrification. Our results imply that chemodenitrification is dependent on the available reactive surfaces and that the NO−2 (rather than the N2O) isotope signatures may be useful for distinguishing between chemodenitrification catalysed by minerals, chemodenitrification catalysed by dead microbial biomass, and possibly true enzymatic NDFeO.

Description: This research has been supported by the Deutsche Forschungsgemeinschaft (DFG; grant no. GRK 1708, “Molecular principles of bacterial survival strategies”) and the University of Basel, Switzerland.

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., Onstott, T. C., Woyke, T., & Stepanauskas, R. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology, 11, (2020): 1848, doi:10.3389/fmicb.2020.01848.

Description: Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.

Description: This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548.

Description: Between 2003-2016, the Greenland ice sheet (GrIS) was one of the largest contributors to sea level rise, as it lost about 255 Gt of ice per year. This mass loss slowed in 2017 and 2018 to about 100 Gt yr−1. Here we examine further changes in rate of GrIS mass loss, by analyzing data from the GRACE-FO (Gravity Recovery and Climate Experiment – Follow On) satellite mission, launched in May 2018. Using simulations with regional climate models we show that the mass losses observed in 2017 and 2018 by the GRACE and GRACE-FO missions are lower than in any other two year period between 2003 and 2019, the combined period of the two missions. We find that this reduced ice loss results from two anomalous cold summers in western Greenland, compounded by snow-rich autumn and winter conditions in the east. For 2019, GRACE-FO reveals a return to high melt rates leading to a mass loss of 223 ± 12 Gt month−1 during the month of July alone, and a record annual mass loss of 532 ± 58 Gt yr−1.

Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molino, G. D., Defne, Z., Aretxabaleta, A. L., Ganju, N. K., & Carr, J. A. Quantifying slopes as a driver of forest to marsh conversion using geospatial techniques: application to Chesapeake Bay coastal-plain, United States. Frontiers in Environmental Science, 9, (2021): 616319, https://doi.org/10.3389/fenvs.2021.616319.

Description: Coastal salt marshes, which provide valuable ecosystem services such as flood mitigation and carbon sequestration, are threatened by rising sea level. In response, these ecosystems migrate landward, converting available upland into salt marsh. In the coastal-plain surrounding Chesapeake Bay, United States, conversion of coastal forest to salt marsh is well-documented and may offset salt marsh loss due to sea level rise, sediment deficits, and wave erosion. Land slope at the marsh-forest boundary is an important factor determining migration likelihood, however, the standard method of using field measurements to assess slope across the marsh-forest boundary is impractical on the scale of an estuary. Therefore, we developed a general slope quantification method that uses high resolution elevation data and a repurposed shoreline analysis tool to determine slope along the marsh-forest boundary for the entire Chesapeake Bay coastal-plain and find that less than 3% of transects have a slope value less than 1%; these low slope environments offer more favorable conditions for forest to marsh conversion. Then, we combine the bay-wide slope and elevation data with inundation modeling from Hurricane Isabel to determine likelihood of coastal forest conversion to salt marsh. This method can be applied to local and estuary-scale research to support management decisions regarding which upland forested areas are more critical to preserve as available space for marsh migration.

Description: Funding for this study was provided by the United States Geological Survey’s Coastal/Marine Hazards and Resources Program and Ecosystems Mission Area.

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zang, Z., Xue, Z. G., Xu, K., Bentley, S. J., Chen, Q., D'Sa, E. J., Zhang, L., & Ou, Y. The role of sediment-induced light attenuation on primary production during Hurricane Gustav (2008). Biogeosciences, 17(20), (2020): 5043-5055, doi:10.5194/bg-17-5043-2020.

Description: We introduced a sediment-induced light attenuation algorithm into a biogeochemical model of the Coupled Ocean–Atmosphere–Wave–Sediment Transport (COAWST) modeling system. A fully coupled ocean–atmospheric–sediment–biogeochemical simulation was carried out to assess the impact of sediment-induced light attenuation on primary production in the northern Gulf of Mexico during the passage of Hurricane Gustav in 2008. When compared with model results without sediment-induced light attenuation, our new model showed a better agreement with satellite data on both the magnitude of nearshore chlorophyll concentration and the spatial distribution of offshore bloom. When Hurricane Gustav approached, resuspended sediment shifted the inner shelf ecosystem from a nutrient-limited one to a light-limited one. Only 1 week after Hurricane Gustav's landfall, accumulated nutrients and a favorable optical environment induced a posthurricane algal bloom in the top 20 m of the water column, while the productivity in the lower water column was still light-limited due to slow-settling sediment. Corresponding with the elevated offshore NO3 flux (38.71 mmol N m−1 s−1) and decreased chlorophyll flux (43.10 mg m−1 s−1), the outer shelf posthurricane bloom should have resulted from the cross-shelf nutrient supply instead of the lateral dispersed chlorophyll. Sensitivity tests indicated that sediment light attenuation efficiency affected primary production when sediment concentration was moderately high. Model uncertainties due to colored dissolved organic matter and parameterization of sediment-induced light attenuation are also discussed.

Description: This research has been supported by the National Science Foundation (grant nos. CCF-1856359, EnvS-1903340, OCE-1635837 and EAR-1427389), NASA (grant no. NNH17ZHA002C), the Louisiana Board of Regents (grant no. NASA/LEQSF(2018-20)-Phase3-11) and the LSU Foundation Billy and Ann Harrison Endowment for Sedimentary Geology.

Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Muenzer, P., Negro, R., Fukui, S., di Meglio, L., Aymonnier, K., Chu, L., Cherpokova, D., Gutch, S., Sorvillo, N., Shi, L., Magupalli, V. G., Weber, A. N. R., Scharf, R. E., Waterman, C. M., Wu, H., & Wagner, D. D. NLRP3 inflammasome assembly in neutrophils is supported by PAD4 and promotes NETosis under sterile conditions. Frontiers in Immunology, 12, (2021): 683803, https://doi.org/10.3389/fimmu.2021.683803.

Description: Neutrophil extracellular trap formation (NETosis) and the NLR family pyrin domain containing 3 (NLRP3) inflammasome assembly are associated with a similar spectrum of human disorders. While NETosis is known to be regulated by peptidylarginine deiminase 4 (PAD4), the role of the NLRP3 inflammasome in NETosis was not addressed. Here, we establish that under sterile conditions the cannonical NLRP3 inflammasome participates in NETosis. We show apoptosis-associated speck-like protein containing a CARD (ASC) speck assembly and caspase-1 cleavage in stimulated mouse neutrophils without LPS priming. PAD4 was needed for optimal NLRP3 inflammasome assembly by regulating NLRP3 and ASC protein levels post-transcriptionally. Genetic ablation of NLRP3 signaling resulted in impaired NET formation, because NLRP3 supported both nuclear envelope and plasma membrane rupture. Pharmacological inhibition of NLRP3 in either mouse or human neutrophils also diminished NETosis. Finally, NLRP3 deficiency resulted in a lower density of NETs in thrombi produced by a stenosis-induced mouse model of deep vein thrombosis. Altogether, our results indicate a PAD4-dependent formation of the NLRP3 inflammasome in neutrophils and implicate NLRP3 in NETosis under noninfectious conditions in vitro and in vivo.

Description: This work was supported by a grant from National Heart, Lung, and Blood Institute of the National Institutes of Health (grant R35 HL135765) and a Steven Berzin family support to DDW, an Individual Erwin Deutsch fellowship by the German, Austrian and Swiss Society of Thrombosis and Hemostasis Research to RES, a Whitman fellowship (MBL) to DDW, and an Individual Marie Skłodowska-Curie Actions fellowship by the European Commission (796365 - COAGULANT) to PM. ANRW was funded by the Deutsche Forschungsgemeinschaft (TRR156/2 –246807620) and a research grant (We-4195/15-19). CMW was supported by the Division of Intramural Research, NHLBI, NIH.