Karl
David M.
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David M.
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ArticlePhosphonate cycling supports methane and ethylene supersaturation in the phosphate-depleted western North Atlantic Ocean(Wiley, 2020-05-20) Sosa, Oscar A. ; Burrell, Timothy J. ; Wilson, Samuel T. ; Foreman, Rhea K. ; Karl, David M. ; Repeta, Daniel J.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.
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ArticleAutonomous tracking and sampling of the deep chlorophyll maximum layer in an open-ocean eddy by a long-range autonomous underwater vehicle(Institute of Electrical and Electronics Engineers, 2020-10-13) Zhang, Yanwu ; Kieft, Brian ; Hobson, Brett W. ; Ryan, John P. ; Barone, Benedetto ; Preston, Christina M. ; Roman, Brent ; Raanan, Ben-Yair ; Marin, Roman ; O’Reilly, Thomas C. ; Rueda, Carlos A. ; Pargett, Douglas ; Yamahara, Kevan M. ; Poulos, Steve ; Romano, Anna ; Foreman, Gabe ; Ramm, Hans ; Wilson, Samuel T. ; DeLong, Edward F. ; Karl, David M. ; Birch, James M. ; Bellingham, James G. ; Scholin, Christopher A.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.
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PreprintParticle export from the upper ocean over the continental shelf of the west Antarctic Peninsula: A long-term record, 1992–2007( 2008-03) Ducklow, Hugh W. ; Erickson, Matthew ; Kelly, Joann ; Montes-Hugo, Martin ; Ribic, Christine A. ; Smith, Raymond C. ; Stammerjohn, Sharon E. ; Karl, David M.We report on results of a long-term (1993-2007) time series sediment trap moored at 170 m to the west of the Antarctic Peninsula in the mid-continental shelf region (350 m depth; 64º30’ S, 66º00’ W). This is a region characterized by late spring-summer diatom blooms, moderately high seasonal primary productivity (50-150 mmol C m-2 d-1 in December-February) and high phytoplankton and krill biomass in the seasonal sea ice zone. The mass flux ranged from near 0 to over 1 g m-2 d-1 and was near 0 to >30% organic carbon (mean 8%). Sedimentation from the upper ocean as estimated by the trap collections at 170 m exhibited strong seasonality with high fluxes (1-10 mmol C m-2 d-1) in November-March following ice retreat and very low fluxes (<0.001 mmol C m-2 d-1) during the Austral winter and under sea ice cover. An average of 85% of the annual export of 212 mmol C m-2 occurred during the seasonal peak flux episodes. Over the trap record, the annual peak flux episode has tended to occur later in the Austral summer, advancing by about 40 days since 1993. The time-integrated sedimentation during the peak flux episode was <1 – 50% of the SeaWiFS-estimated primary production (mean 4%) at the trap site over the period 1998-2006. The elemental composition of material captured in the traps had an average C:N:P of 212:28:1, greater than the canonical Redfield values. High C:P ratios (400- 600) corresponded with the annual flux peak, indicating preferential loss of P from the sinking particles in the summer, ice-free period. The composition of the exported material more closely approximated the Redfield composition during the low-flux, winter period.
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ArticleInterannual variability of primary production and dissolved organic nitrogen storage in the North Pacific Subtropical Gyre(American Geophysical Union, 2012-08-10) Luo, Ya-Wei ; Ducklow, Hugh W. ; Friedrichs, Marjorie A. M. ; Church, Matthew J. ; Karl, David M. ; Doney, Scott C.The upper ocean primary production measurements from the Hawaii Ocean Time series (HOT) at Station ALOHA in the North Pacific Subtropical Gyre showed substantial variability over the last two decades. The annual average primary production varied within a limited range over 1991–1998, significantly increased in 1999–2000 and then gradually decreased afterwards. This variability was investigated using a one-dimensional ecosystem model. The long-term HOT observations were used to constrain the model by prescribing physical forcings and lower boundary conditions and optimizing the model parameters against data using data assimilation. The model reproduced the general interannual pattern in the observed primary production, and mesoscale variability in vertical velocity was identified as a major contributing factor to the interannual variability in the simulation. Several strong upwelling events occurred in 1999, which brought up nitrate at rates several times higher than other years and elevated the model primary production. Our model results suggested a hypothesis for the observed interannual variability pattern of primary production at Station ALOHA: Part of the upwelled nitrate input in 1999 was converted to and accumulated as semilabile dissolved organic nitrogen (DON), and subsequent recycling of this semilabile DON supported enhanced primary productivity for the next several years as the semilabile DON perturbation was gradually removed via export.
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ArticlePolyphosphate dynamics at Station ALOHA, North Pacific subtropical gyre(John Wiley & Sons, 2015-10-27) Diaz, Julia M. ; Björkman, Karin M. ; Haley, Sheean T. ; Ingall, Ellery ; Karl, David M. ; Longo, Amelia ; Dyhrman, Sonya T.Polyphosphate (polyP) was examined within the upper water column (≤ 150 m) of Station ALOHA (22° 45′N, 158° 00′W) during two cruises conducted in May–June 2013 and September 2013. Phosphorus molar ratios of particulate polyP to total particulate phosphorus (TPP) were relatively low, similar to previously reported values from the temperate western North Atlantic, and did not exhibit strong vertical gradients, reflecting a lack of polyP recycling relative to other forms of TPP with depth. Furthermore, relationships among polyP:TPP, soluble reactive phosphorus (SRP), and alkaline phosphatase activity (APA) were also consistent with previous observations from the Atlantic Ocean. To ascertain potential mechanisms of biological polyP production and utilization, surface seawater was incubated following nutrient additions. Results were consistent with polyP:TPP enrichment under opposite extremes of APA, suggesting diverse polyP accumulation/retention mechanisms. Addition of exogenous polyP (45 ± 5 P atoms) to field incubations did not increase chlorophyll content relative to controls, suggesting that polyP was not bioavailable to phytoplankton at Station ALOHA. To clarify this result, phytoplankton cultures were screened for the ability to utilize exogenous polyP. PolyP bioavailability was variable among model diatoms of the genus Thalassiosira, yet chain length did not influence polyP bioavailability. Thus, microbial community composition may influence polyP dynamics in the ocean, and vice versa.
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PreprintWill ocean acidification affect marine microbes?( 2010-05) Joint, Ian ; Doney, Scott C. ; Karl, David M.The pH of the surface ocean is changing as a result of increases in atmospheric carbon dioxide (CO2) and there are concerns about potential impacts of lower pH and associated alterations in seawater carbonate chemistry on the biogeochemical processes in the ocean. However, it is important to place these changes within the context of pH in the present day ocean, which is not constant; it varies systematically with season, depth and along productivity gradients. Yet this natural variability in pH has rarely been considered in assessments of the effect of ocean acidification on marine microbes. Surface pH can change as a consequence of microbial utilisation and production of carbon dioxide, and to a lesser extent other microbiallymediated processes such as nitrification. Useful comparisons can be made with microbes in other aquatic environments that readily accommodate very large and rapid pH change. For example, in many freshwater lakes, pH changes that are orders of magnitude greater than those projected for the 22nd century oceans can occur over periods of hours. Marine and freshwater assemblages have always experienced variable pH conditions. Therefore, an appropriate null hypothesis may be, until evidence is obtained to the contrary, that major biogeochemical processes in the oceans other than calcification will not be fundamentally different under future higher CO2 / lower pH conditions.
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DatasetPrimary productivity measurements from the Hawaii Ocean Time-Series (HOT) project from 1989-09-22 to 2016-10-15 at station ALOHA.(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-12-10) Karl, David M.Primary productivity measurements from the Hawaii Ocean Time-Series (HOT). Photosynthetic production of organic matter was measured by the 14C tracer method. All incubations from 1990 through mid-2000 were conducted in situ at eight depths (5, 25, 45, 75, 100, 125, 150 and 175m) over one daylight period using a free-drifting array as described by Winn et al. (1991). Starting HOT-119 (October 2000), we collected samples from only the upper six depths & modeled the lower two depths based on the monthly climatology. During 2015, all incubations were conducted in situ on a free floating, surface tethered array. Integrated carbon assimilation rates were calculated using the trapezoid rule with the shallowest value extended to 0 meters and the deepest extrapolated to a value of zero at 200 meters. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/737163
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DatasetConcentration measurements of water column phosphate, nitrate and nitrite, dissolved organic phosphorus, methane, and ethylene from samples collected during the R/V Neil Armstrong cruise AR16 in the western North Atlantic Ocean in May 2017(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-07-22) Repeta, Daniel J. ; Karl, David M.Concentration measurements of water column phosphate, nitrate and nitrite, dissolved organic phosphorus, methane, and ethylene from samples collected during the R/V Niel Armstrong cruise AR16 in the western North Atlantic Ocean in May 2017. Seawater was collected from Niskin bottles deployed on a rosette with a CTD. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/769203
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DatasetSediment trap flux measurements from the Hawaii Ocean Time-Series (HOT) project at station ALOHA.(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-12-11) Karl, David M.Particle flux measurements from the Hawaii Ocean Time-Series (HOT). Particle flux was measured at a standard reference depth of 150 m using multiple cylindrical particle interceptor traps deployed on a free-floating array for approximately 60 h during each cruise. Sediment trap design and collection methods are described in Winn et al. (1991). Samples were analyzed for particulate C, N, P & Si. Typically six traps are analyzed for PC and PN, three for PP, and another three traps for PSi. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/737393
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ArticleIsolation and characterization of bacteria that degrade phosphonates in marine dissolved organic matter(Frontiers Media, 2017-09-26) Sosa, Oscar A. ; Repeta, Daniel J. ; Ferrón, Sara ; Bryant, Jessica A. ; Mende, Daniel R. ; Karl, David M. ; DeLong, Edward F.Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.
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ArticleDiversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean(Springer Nature, 2022-03-02) Luo, Elaine ; Leu, Andy O. ; Eppley, John ; Karl, David M. ; DeLong, Edward F.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.
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ArticleThe estimation of gross oxygen production and community respiration from autonomous time-series measurements in the oligotrophic ocean(Wiley, 2019-11-20) Barone, Benedetto ; Nicholson, David P. ; Ferrón, Sara ; Firing, Eric ; Karl, David M.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.
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ArticleData-based assessment of environmental controls on global marine nitrogen fixation(Copernicus Publications on behalf of the European Geosciences Union, 2014-02-06) Luo, Ya-Wei ; Lima, Ivan D. ; Karl, David M. ; Deutsch, Curtis A. ; Doney, Scott C.There are a number of hypotheses concerning the environmental controls on marine nitrogen fixation (NF). Most of these hypotheses have not been assessed against direct measurements on the global scale. In this study, we use ~ 500 depth-integrated field measurements of NF covering the Pacific and Atlantic oceans to test whether the spatial variance of these measurements can be explained by the commonly hypothesized environmental controls, including measurement-based surface solar radiation, mixed layer depth, average solar radiation in the mixed layer, sea surface temperature, wind speed, surface nitrate and phosphate concentrations, surface excess phosphate (P*) concentration and subsurface minimum dissolved oxygen (in upper 500 m), as well as model-based P* convergence and atmospheric dust deposition. By conducting simple linear regression and stepwise multiple linear regression (MLR) analyses, surface solar radiation (or sea surface temperature) and subsurface minimum dissolved oxygen are identified as the predictors that explain the most spatial variance in the observed NF data, although it is unclear why the observed NF decreases when the level of subsurface minimum dissolved oxygen is higher than ~ 150 μM. Dust deposition and wind speed do not appear to influence the spatial patterns of NF on global scale. The weak correlation between the observed NF and the P* convergence and concentrations suggests that the available data currently remain insufficient to fully support the hypothesis that spatial variability in denitrification is the principal control on spatial variability in marine NF. By applying the MLR-derived equation, we estimate the global-integrated NF at 74 (error range 51–110) Tg N yr−1 in the open ocean, acknowledging that it could be substantially higher as the 15N2-assimilation method used by most of the field samples underestimates NF. More field NF samples in the Pacific and Indian oceans, particularly in the oxygen minimum zones, are needed to reduce uncertainties in our conclusion.
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ArticleChallenges of modeling depth-integrated marine primary productivity over multiple decades : a case study at BATS and HOT(American Geophysical Union, 2010-09-15) Saba, Vincent S. ; Friedrichs, Marjorie A. M. ; Carr, Mary-Elena ; Antoine, David ; Armstrong, Robert A. ; Asanuma, Ichio ; Aumont, Olivier ; Bates, Nicholas R. ; Behrenfeld, Michael J. ; Bennington, Val ; Bopp, Laurent ; Bruggeman, Jorn ; Buitenhuis, Erik T. ; Church, Matthew J. ; Ciotti, Aurea M. ; Doney, Scott C. ; Dowell, Mark ; Dunne, John P. ; Dutkiewicz, Stephanie ; Gregg, Watson ; Hoepffner, Nicolas ; Hyde, Kimberly J. W. ; Ishizaka, Joji ; Kameda, Takahiko ; Karl, David M. ; Lima, Ivan D. ; Lomas, Michael W. ; Marra, John F. ; McKinley, Galen A. ; Melin, Frederic ; Moore, J. Keith ; Morel, Andre ; O'Reilly, John ; Salihoglu, Baris ; Scardi, Michele ; Smyth, Tim J. ; Tang, Shilin ; Tjiputra, Jerry ; Uitz, Julia ; Vichi, Marcello ; Waters, Kirk ; Westberry, Toby K. ; Yool, AndrewThe performance of 36 models (22 ocean color models and 14 biogeochemical ocean circulation models (BOGCMs)) that estimate depth-integrated marine net primary productivity (NPP) was assessed by comparing their output to in situ 14C data at the Bermuda Atlantic Time series Study (BATS) and the Hawaii Ocean Time series (HOT) over nearly two decades. Specifically, skill was assessed based on the models' ability to estimate the observed mean, variability, and trends of NPP. At both sites, more than 90% of the models underestimated mean NPP, with the average bias of the BOGCMs being nearly twice that of the ocean color models. However, the difference in overall skill between the best BOGCM and the best ocean color model at each site was not significant. Between 1989 and 2007, in situ NPP at BATS and HOT increased by an average of nearly 2% per year and was positively correlated to the North Pacific Gyre Oscillation index. The majority of ocean color models produced in situ NPP trends that were closer to the observed trends when chlorophyll-a was derived from high-performance liquid chromatography (HPLC), rather than fluorometric or SeaWiFS data. However, this was a function of time such that average trend magnitude was more accurately estimated over longer time periods. Among BOGCMs, only two individual models successfully produced an increasing NPP trend (one model at each site). We caution against the use of models to assess multiannual changes in NPP over short time periods. Ocean color model estimates of NPP trends could improve if more high quality HPLC chlorophyll-a time series were available.
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ArticleEvaluating triple oxygen isotope estimates of gross primary production at the Hawaii Ocean Time-series and Bermuda Atlantic Time-series Study sites(American Geophysical Union, 2012-05-08) Nicholson, David P. ; Stanley, Rachel H. R. ; Barkan, Eugeni ; Karl, David M. ; Luz, Boaz ; Quay, Paul D. ; Doney, Scott C.The triple oxygen isotopic composition of dissolved oxygen (17Δ) is a promising tracer of gross oxygen productivity (P) in the ocean. Recent studies have inferred a high and variable ratio of P to 14C net primary productivity (12–24 h incubations) (e.g., P:NPP(14C) of 5–10) using the 17Δ tracer method, which implies a very low efficiency of phytoplankton growth rates relative to gross photosynthetic rates. We added oxygen isotopes to a one-dimensional mixed layer model to assess the role of physical dynamics in potentially biasing estimates of P using the 17Δ tracer method at the Bermuda Atlantic Time-series Study (BATS) and Hawaii Ocean Time-series (HOT). Model results were compared to multiyear observations at each site. Entrainment of high 17Δ thermocline water into the mixed layer was the largest source of error in estimating P from mixed layer 17Δ. At both BATS and HOT, entrainment bias was significant throughout the year and resulted in an annually averaged overestimate of mixed layer P of 60 to 80%. When the entrainment bias is corrected for, P calculated from observed 17Δ and 14C productivity incubations results in a gross:net productivity ratio of 2.6 (+0.9 −0.8) at BATS. At HOT a gross:net ratio decreasing linearly from 3.0 (+1.0 −0.8) at the surface to 1.4 (+0.6 −0.6) at depth best reproduced observations. In the seasonal thermocline at BATS, however, a significantly higher gross:net ratio or large lateral fluxes of 17Δ must be invoked to explain 17Δ field observations.
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ArticleDraft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome(Genomic Standards Consortium, 2014) Durham, Bryndan P. ; Grote, Jana ; Whittaker, Kerry A. ; Bender, Sara J. ; Luo, Haiwei ; Grim, Sharon L. ; Brown, Julia M. ; Casey, John F. ; Dron, Antony ; Florez-Leiva, Lennis ; Krupke, Andreas ; Luria, Catherine M. ; Mine, Aric ; Nigro, Olivia D. ; Pather, Santhiska ; Talarmin, Agathe ; Wear, Emma K. ; Weber, Thomas S. ; Wilson, Jesse M. ; Church, Matthew J. ; DeLong, Edward F. ; Karl, David M. ; Steward, Grieg F. ; Eppley, John ; Kyrpides, Nikos C. ; Schuster, Stephan ; Rappe, Michael S.Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.
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ArticleIron depletion in the deep chlorophyll maximum: mesoscale eddies as natural iron fertilization experiments(American Geophysical Union, 2021-11-17) Hawco, Nicholas J. ; Barone, Benedetto ; Church, Matthew J. ; Babcock-Adams, Lydia ; Repeta, Daniel J. ; Wear, Emma K. ; Foreman, Rhea K. ; Björkman, Karin M. ; Bent, Shavonna M. ; Van Mooy, Benjamin A. S. ; Sheyn, Uri ; DeLong, Edward F. ; Acker, Marianne ; Kelly, Rachel L. ; Nelson, Alexa ; Ranieri, John ; Clemente, Tara M. ; Karl, David M. ; John, Seth G.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.
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ArticleMicrobial group specific uptake kinetics of inorganic phosphate and adenosine-5′-triphosphate (ATP) in the North Pacific Subtropical Gyre(Frontiers Media, 2012-06-11) Björkman, Karin M. ; Duhamel, Solange ; Karl, David M.We investigated the concentration dependent uptake of inorganic phosphate (Pi) and adenosine-5′-triphosphate (ATP) in microbial populations in the North Pacific Subtropical Gyre (NPSG). We used radiotracers to measure substrate uptake into whole water communities, differentiated microbial size classes, and two flow sorted groups; Prochlorococcus (PRO) and non-pigmented bacteria (NPB). The Pi concentrations, uptake rates, and Pi pool turnover times (Tt) were (mean, ±SD); 54.9 ± 35.0 nmol L−1 (n = 22), 4.8 ± 1.9 nmol L−1 day−1 (n = 19), and 14.7 ± 10.2 days (n = 19), respectively. Pi uptake into >2 μm cells was on average 12 ± 7% (n = 15) of the total uptake. The kinetic response to Pi (10–500 nmol L−1) was small, indicating that the microorganisms were close to their maximum uptake velocity (Vmax). Vmax averaged 8.0 ± 3.6 nmol L−1 day−1 (n = 19) in the >0.2 μm group, with half saturation constants (Km) of 40 ± 28 nmol L−1 (n = 19). PRO had three times the cell specific Pi uptake rate of NPB, at ambient concentrations, but when adjusted to cells L−1 the rates were similar, and these two groups were equally competitive for Pi. The Tt of γ-P-ATP in the >0.2 μm group were shorter than for the Pi pool (4.4 ± 1.0 days; n = 6), but this difference diminished in the larger size classes. The kinetic response to ATP was large in the >0.2 μm class with Vmax exceeding the rates at ambient concentrations (mean 62 ± 27 times; n = 6) with a mean Vmax for γ-P-ATP of 2.8 ± 1.0 nmol L−1 day−1, and Km at 11.5 ± 5.4 nmol L−1 (n = 6). The NPB contribution to γ-P-ATP uptake was high (95 ± 3%, n = 4) at ambient concentrations but decreased to ∼50% at the highest ATP amendment. PRO had Km values 5–10 times greater than NPB. The above indicates that PRO and NPB were in close competition in terms of Pi acquisition, whereas P uptake from ATP could be attributed to NPB. This apparent resource partitioning may be a niche separating strategy and an important factor in the successful co-existence within the oligotrophic upper ocean of the NPSG.
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ArticleQuantifying subtropical North Pacific gyre mixed layer primary productivity from Seaglider observations of diel oxygen cycles(John Wiley & Sons, 2015-05-22) Nicholson, David P. ; Wilson, Samuel T. ; Doney, Scott C. ; Karl, David M.Using autonomous underwater gliders, we quantified diurnal periodicity in dissolved oxygen, chlorophyll, and temperature in the subtropical North Pacific near the Hawaii Ocean Time-series (HOT) Station ALOHA during summer 2012. Oxygen optodes provided sufficient stability and precision to quantify diel cycles of average amplitude of 0.6 µmol kg−1. A theoretical diel curve was fit to daily observations to infer an average mixed layer gross primary productivity (GPP) of 1.8 mmol O2 m−3 d−1. Cumulative net community production (NCP) over 110 days was 500 mmol O2 m−2 for the mixed layer, which averaged 57 m in depth. Both GPP and NCP estimates indicated a significant period of below-average productivity at Station ALOHA in 2012, an observation confirmed by 14C productivity incubations and O2/Ar ratios. Given our success in an oligotrophic gyre where biological signals are small, our diel GPP approach holds promise for remote characterization of productivity across the spectrum of marine environments.
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ArticleOpen ocean particle flux variability from surface to seafloor(American Geophysical Union, 2021-04-18) Cael, B. Barry ; Bisson, Kelsey ; Conte, Maureen H. ; Duret, Manon T. ; Follett, Christopher L. ; Henson, Stephanie A. ; Honda, Makio C. ; Iversen, Morten H. ; Karl, David M. ; Lampitt, Richard S. ; Mouw, Colleen B. ; Muller-Karger, Frank E. ; Pebody, Corinne ; Smith, Kenneth L., Jr. ; Talmy, DavidThe 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.