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  • 1
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    Microbial sources of exocellular DNA in the ocean (2022)
    American Society for Microbiology
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Linney, M. D., Eppley, J. M., Romano, A. E., Luo, E., DeLong, E. F., & Karl, D. M. Microbial sources of exocellular DNA in the ocean. Applied and Environmental Microbiology, 88(7), (2022): e02093-21, https://doi.org/10.1128/aem.02093-21.
    Description: Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism.
    Description: This work was supported by the Simons Collaboration on Ocean Processes and Ecology (awards 329108 to D.M.K. and E.F.D., 721252 to D.M.K., and 721223 to E.F.D.).
    Keywords: Bbacteriophage ; Bacterioplankton ; EDNA ; Exocellular DNA ; Free DNA ; Metagenomics ; Microbial ecology ; Microbial oceanography ; Open ocean ; Vesicle
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Open ocean particle flux variability from surface to seafloor (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cael, B. B., Bisson, K., Conte, M., Duret, M. T., Follett, C. L., Henson, S. A., Honda, M. C., Iversen, M. H., Karl, D. M., Lampitt, R. S., Mouw, C. B., Muller-Karger, F., Pebody, C. A., Smith, K. L., & Talmy, D. Open ocean particle flux variability from surface to seafloor. Geophysical Research Letters, 48(9), (2021): e2021GL092895, https://doi.org/10.1029/2021GL092895.
    Description: The sinking of carbon fixed via net primary production (NPP) into the ocean interior is an important part of marine biogeochemical cycles. NPP measurements follow a log-normal probability distribution, meaning NPP variations can be simply described by two parameters despite NPP's complexity. By analyzing a global database of open ocean particle fluxes, we show that this log-normal probability distribution propagates into the variations of near-seafloor fluxes of particulate organic carbon (POC), calcium carbonate, and opal. Deep-sea particle fluxes at subtropical and temperate time-series sites follow the same log-normal probability distribution, strongly suggesting the log-normal description is robust and applies on multiple scales. This log-normality implies that 29% of the highest measurements are responsible for 71% of the total near-seafloor POC flux. We discuss possible causes for the dampening of variability from NPP to deep-sea POC flux, and present an updated relationship predicting POC flux from mineral flux and depth.
    Description: B. B. Cael and S. A. Henson acknowledge support from the National Environmental Research Council (NE/R015953/1) and the Horizon 2020 Framework Programme (820989, project COMFORT). The work reflects only the authors' views; the European Commission and their executive agency are not responsible for any use that may be made of the information the work contains. S. A. Henson also acknowledges support from a European Research Council Consolidator grant (GOCART, agreement number 724416). C. L. Follett acknowledges support from the Simons Foundation (grants #827829 and #553242). M. H. Iversen acknowledges support from the DFG-Research Center/Cluster of Excellence “The Ocean Floor – Earth's Uncharted Interface”: EXC-2077-390741603 and the HGF Young Investigator Group SeaPump “Seasonal and regional food web interactions with the biological pump”: VH-NG-1000. M. C. Honda acknowledges financial support from the Ministry of Education, Culture, Sports, Science, and Technology – Japan (grants #: KAKENHI JP18H04144 and JP19H05667). M. Conte acknowledges support from the US National Science Foundation, Division of Ocean Sciences for support for the Oceanic Flux Program time-series since inception, most recently by NSF OCE grant 1829885. D. M. Karl acknowledges support from the Gordon and Betty Moore Foundation (#3794) and the Simons Foundation (SCOPE #329108).
    Keywords: Ballast ; bathypelagic ; biogeochemistry ; log-normal ; particle flux ; variability
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Open ocean particle flux variability from surface to seafloor (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48(9), pp. e2021GL092895, ISSN: 0094-8276
    Details
    Publication Date: 2022-08-15
    Description: The sinking of carbon fixed via net primary production (NPP) into the ocean interior is an important part of marine biogeochemical cycles. NPP measurements follow a log-normal probability distribution, meaning NPP variations can be simply described by two parameters despite NPP's complexity. By analyzing a global database of open ocean particle fluxes, we show that this log-normal probability distribution propagates into the variations of near-seafloor fluxes of particulate organic carbon (POC), calcium carbonate, and opal. Deep-sea particle fluxes at subtropical and temperate time-series sites follow the same log-normal probability distribution, strongly suggesting the log-normal description is robust and applies on multiple scales. This log-normality implies that 29% of the highest measurements are responsible for 71% of the total near-seafloor POC flux. We discuss possible causes for the dampening of variability from NPP to deep-sea POC flux, and present an updated relationship predicting POC flux from mineral flux and depth.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 4
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    Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean (2022)
    Springer Nature
    Details
    Publication Date: 2022-06-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Luo, E., Leu, A. O., Eppley, J. M., Karl, D. M., & DeLong, E. F. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME Journal, 16, : 1627–1635, https://doi.org/10.1038/s41396-022-01202-1.
    Description: Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
    Description: This project is funded by grants from the Simons Foundation (#329108 to EFD and DMK, #721223 to EFD, and #721252 to DMK) and the Gordon and Betty Moore Foundation (GBMF3777 to EFD and GBMF3794 to DMK). Partial support for EL was provided by the Natural Sciences and Engineering Research Council of Canada (PGSD3-487490-2016).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    Phosphonate cycling supports methane and ethylene supersaturation in the phosphate-depleted western North Atlantic Ocean (2020)
    Wiley
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sosa, O. A., Burrell, T. J., Wilson, S. T., Foreman, R. K., Karl, D. M., & Repeta, D. J. Phosphonate cycling supports methane and ethylene supersaturation in the phosphate-depleted western North Atlantic Ocean. Limnology and Oceanography, (2020), doi:10.1002/lno.11463.
    Description: In oligotrophic ocean regions, dissolved organic phosphorus (DOP) plays a prominent role as a source of phosphorus (P) to microorganisms. An important bioavailable component of DOP is phosphonates, organophosphorus compounds with a carbon‐phosphorus (C‐P) bond, which are ubiquitous in high molecular weight dissolved organic matter (HMWDOM). In addition to being a source of P, the degradation of phosphonates by the bacterial C‐P lyase enzymatic pathway causes the release of trace hydrocarbon gases relevant to climate and atmospheric chemistry. In this study, we investigated the roles of phosphate and phosphonate cycling in the production of methane (CH4) and ethylene (C2H4) in the western North Atlantic Ocean, a region that features a transition in phosphate concentrations from coastal to open ocean waters. We observed an inverse relationship between phosphate and the saturation state of CH4 and C2H4 in the water column, and between phosphate and the relative abundance of the C‐P lyase marker gene phnJ . In phosphate‐depleted waters, methylphosphonate and 2‐hydroxyethylphosphonate, the C‐P lyase substrates that yield CH4 and C2H4, respectively, were readily degraded in proportions consistent with their abundance and bioavailability in HMWDOM and with the concentrations of CH4 and C2H4 in the water column. We conclude that phosphonate degradation through the C‐P lyase pathway is an important source and a common production pathway of CH4 and C2H4 in the phosphate‐depleted surface waters of the western North Atlantic Ocean and that phosphate concentration can be an important control on the saturation state of these gases in the upper ocean.
    Description: We thank the captain and crew of the R/V Neil Armstrong and chief scientist Benjamin Van Mooy for supporting and leading research at sea. Chiara Santinelli and Eric Grabowski provided analyses of dissolved organic carbon. This research was funded by NSF Chemical Oceanography award OCE‐1634080 to D.J.R. Additional support was provided by the Gordon and Betty Moore Foundation grant 3794 to D.M.K. and grant 6000 to D.J.R., and the Simons Collaboration on Ocean Processes and Ecology (SCOPE) program grant 329108 to D.M.K., E.F.D., and D.J.R.
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Autonomous tracking and sampling of the deep chlorophyll maximum layer in an open-ocean eddy by a long-range autonomous underwater vehicle (2020)
    Institute of Electrical and Electronics Engineers
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, Y., Kieft, B., Hobson, B. W., Ryan, J. P., Barone, B., Preston, C. M., Roman, B., Raanan, B., Marin,Roman,,III, O'Reilly, T. C., Rueda, C. A., Pargett, D., Yamahara, K. M., Poulos, S., Romano, A., Foreman, G., Ramm, H., Wilson, S. T., DeLong, E. F., Karl, D. M., Birch, J. M., Bellingham, J. G., & Scholin, C. A. Autonomous tracking and sampling of the deep chlorophyll maximum layer in an open-ocean eddy by a long-range autonomous underwater vehicle. IEEE Journal of Oceanic Engineering, 45(4), (2020): 1308-1321, doi:10.1109/JOE.2019.2920217.
    Description: Phytoplankton communities residing in the open ocean, the largest habitat on Earth, play a key role in global primary production. Through their influence on nutrient supply to the euphotic zone, open-ocean eddies impact the magnitude of primary production and its spatial and temporal distributions. It is important to gain a deeper understanding of the microbial ecology of marine ecosystems under the influence of eddy physics with the aid of advanced technologies. In March and April 2018, we deployed autonomous underwater and surface vehicles in a cyclonic eddy in the North Pacific Subtropical Gyre to investigate the variability of the microbial community in the deep chlorophyll maximum (DCM) layer. One long-range autonomous underwater vehicle (LRAUV) carrying a third-generation Environmental Sample Processor (3G-ESP) autonomously tracked and sampled the DCM layer for four days without surfacing. The sampling LRAUV's vertical position in the DCM layer was maintained by locking onto the isotherm corresponding to the chlorophyll peak. The vehicle ran on tight circles while drifting with the eddy current. This mode of operation enabled a quasi-Lagrangian time series focused on sampling the temporal variation of the DCM population. A companion LRAUV surveyed a cylindrical volume around the sampling LRAUV to monitor spatial and temporal variation in contextual water column properties. The simultaneous sampling and mapping enabled observation of DCM microbial community in its natural frame of reference.
    Description: 10.13039/501100008982 - National Science Foundation 10.13039/100000936 - Gordon and Betty Moore Foundation 10.13039/100000008 - David and Lucile Packard Foundation 10.13039/100016377 - Schmidt Ocean Institute 10.13039/100000893 - Simons Foundation
    Keywords: Autonomous underwater vehicle (AUV) ; eddy ; Environmental Sample Processor (ESP) ; phytoplankton ; sampling ; tracking
    Repository Name: Woods Hole Open Access Server
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  • 7
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    The estimation of gross oxygen production and community respiration from autonomous time-series measurements in the oligotrophic ocean (2020)
    Wiley
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Barone, B., Nicholson, D., Ferron, S., Firing, E., & Karl, D. The estimation of gross oxygen production and community respiration from autonomous time-series measurements in the oligotrophic ocean. Limnology and Oceanography-Methods, 17, (2019): 650-664, doi: 10.1002/lom3.10340.
    Description: Diel variations in oxygen concentration have been extensively used to estimate rates of photosynthesis and respiration in productive freshwater and marine ecosystems. Recent improvements in optical oxygen sensors now enable us to use the same approach to estimate metabolic rates in the oligotrophic waters that cover most of the global ocean and for measurements collected by autonomous underwater vehicles. By building on previous methods, we propose a procedure to estimate photosynthesis and respiration from vertically resolved diel measurements of oxygen concentration. This procedure involves isolating the oxygen variation due to biological processes from the variation due to physical processes, and calculating metabolic rates from biogenic oxygen changes using linear least squares analysis. We tested our method on underwater glider observations from the surface layer of the North Pacific Subtropical Gyre where we estimated rates of gross oxygen production and community respiration both averaging 1.0 mmol O2 m−3 d−1, consistent with previous estimates from the same environment. Method uncertainty was computed as the standard deviation of the fitted parameters and averaged 0.6 and 0.5 mmol O2 m−3 d−1 for oxygen production and respiration, respectively. The variability of metabolic rates was larger than this uncertainty and we were able to discern covariation in the biological production and consumption of oxygen. The proposed method resolved variability on time scales of approximately 1 week. This resolution can be improved in several ways including by measuring turbulent mixing, increasing the number of measurements in the surface ocean, and adopting a Lagrangian approach during data collection.
    Description: This study would not have been possible without the skilled contribution of Steve Poulos (University of Hawaii) who directed glider operations including deployments, recoveries, and piloting. We thank Steve and all the other people involved in these activities including Sarah Searson, Gabe Foreman, Jim Burkitt, and Blake Watkins (University of Hawaii). We thank Henry Bittig (Laboratoire d'Océanographie de Villefranche) for his advice on the inverse filtering correction. We thank Saulo Soares, Andrei Natarov, and Kelvin Richards (University of Hawaii) for their comments on an early draft of this manuscript. We also thank Sam Wilson, Tara Clemente, Dan Sadler, Susan Curless, and Walt Deppe (University of Hawaii) for leading the oceanographic cruises used for glider deployments and recoveries. We thank the HOT‐SCOPE team for measuring the Winkler O2 concentration used for optode calibration. We thank Jesse M. Wilson for providing us the period of the CR measurements reported in Wilson et al. (2014). Finally, we thank captains and crews of R/V Kilo Moana and R/V Ka'imikai‐O‐Kanaloa, and the Ocean Technology Group of the University of Hawaii for their assistance at sea. Glider data used in this article are available on the ftp server of the School of Ocean and Earth Science and Technology of the University of Hawaii (ftp://ftp.soest.hawaii.edu/pilot/). Blended Sea Winds are distributed by NOAA‐NCDC and are available at https://www.ncdc.noaa.gov. Sea‐level pressure from the NCEP/NCAR reanalysis is available at https://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis.surface.html. Satellite PAR is distributed by NASA and available at https://oceandata.sci.gsfc.nasa.gov. This research was supported by the 2015 Balzan Prize to D.M.K., the Simons Foundation (SCOPE award 329108 to D.M.K. and E.F. DeLong), the Gordon and Betty Moore Foundation (grant #3794 to D.M.K.), and the National Science Foundation through grants to C‐MORE (EF‐0424599 to D.M.K.) and HOT (OCE‐1260164 to D.M.K). D.N. was supported by NSF (OCE‐1129644) and an Independent Study Award from the Woods Hole Oceanographic Institution.
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Iron depletion in the deep chlorophyll maximum: mesoscale eddies as natural iron fertilization experiments (2022)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hawco, N. J., Barone, B., Church, M. J., Babcock-Adams, L., Repeta, D. J., Wear, E. K., Foreman, R. K., Bjorkman, K. M., Bent, S., Van Mooy, B. A. S., Sheyn, U., DeLong, E. F., Acker, M., Kelly, R. L., Nelson, A., Ranieri, J., Clemente, T. M., Karl, D. M., & John, S. G. Iron depletion in the deep chlorophyll maximum: mesoscale eddies as natural iron fertilization experiments. Global Biogeochemical Cycles, 35(12), (2021): e2021GB007112, https://doi.org/10.1029/2021GB007112.
    Description: In stratified oligotrophic waters, phytoplankton communities forming the deep chlorophyll maximum (DCM) are isolated from atmospheric iron sources above and remineralized iron sources below. Reduced supply leads to a minimum in dissolved iron (dFe) near 100 m, but it is unclear if iron limits growth at the DCM. Here, we propose that natural iron addition events occur regularly with the passage of mesoscale eddies, which alter the supply of dFe and other nutrients relative to the availability of light, and can be used to test for iron limitation at the DCM. This framework is applied to two eddies sampled in the North Pacific Subtropical Gyre. Observations in an anticyclonic eddy center indicated downwelling of iron-rich surface waters, leading to increased dFe at the DCM but no increase in productivity. In contrast, uplift of isopycnals within a cyclonic eddy center increased supply of both nitrate and dFe to the DCM, and led to dominance of picoeukaryotic phytoplankton. Iron addition experiments did not increase productivity in either eddy, but significant enhancement of leucine incorporation in the light was observed in the cyclonic eddy, a potential indicator of iron stress among Prochlorococcus. Rapid cycling of siderophores and low dFe:nitrate uptake ratios also indicate that a portion of the microbial community was stressed by low iron. However, near-complete nitrate drawdown in this eddy, which represents an extreme case in nutrient supply compared to nearby Hawaii Ocean Time-series observations, suggests that recycling of dFe in oligotrophic ecosystems is sufficient to avoid iron limitation in the DCM under typical conditions.
    Description: The expedition and analyses were supported by the Simons Foundation SCOPE Grant 329108 to S. G. John, M. J. Church, D. J. Repeta, B. Van Mooy, E. F. DeLong, and D. M. Karl. N. J. Hawco was supported by a Simons Foundation Marine Microbial Ecology and Evolution postdoctoral fellowship (602538) and Simons Foundation grant 823167.
    Keywords: Chlorophyll ; Photosynthesis ; Iron limitation ; Oligotrophic ; Prochlorococcus ; Eddies
    Repository Name: Woods Hole Open Access Server
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