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  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1786, doi:10.3389/fmicb.2017.01786.
    Description: 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.
    Description: Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599 to DK and ED), the National Science Foundation HOT program (OCE-1260164 to M. J. Church and DK), the Gordon and Betty Moore Foundation (grants #492.01 and #3777 to ED, #3298 to DR, and #3794 to DK), and the Simons Foundation (award ID 329108 to DK, DR, and ED). Additional support was provided by the Agouron Institute through a fellowship to OS.
    Keywords: Bacterial degradation ; Dissolved organic matter (DOM) ; Phosphonate metabolism ; C-P lyase ; Methane ; Ethylene ; Oligotrophic conditions
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 3 (2012): 189, doi:10.3389/fmicb.2012.00189.
    Description: 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.
    Description: This work was supported by grants from the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative and The National Science Foundation OCE 0326616 and EF 04-24599, awarded to D. M. Karl.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 3
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Benway, H. M., Lorenzoni, L., White, A. E., Fiedler, B., Levine, N. M., Nicholson, D. P., DeGrandpre, M. D., Sosik, H. M., Church, M. J., O'Brien, T. D., Leinen, M., Weller, R. A., Karl, D. M., Henson, S. A., & Letelier, R. M. Ocean time series observations of changing marine ecosystems: An era of integration, synthesis, and societal applications. Frontiers in Marine Science, 6, (2019): 393, doi:10.3389/fmars.2019.00393.
    Description: Sustained ocean time series are critical for characterizing marine ecosystem shifts in a time of accelerating, and at times unpredictable, changes. They represent the only means to distinguish between natural and anthropogenic forcings, and are the best tools to explore causal links and implications for human communities that depend on ocean resources. Since the inception of sustained ocean observations, ocean time series have withstood many challenges, most prominently availability of uninterrupted funding and retention of trained personnel. This OceanObs’19 review article provides an overarching vision for sustained ocean time series observations for the next decade, focusing on the growing challenges of maintaining sustained ocean time series, including ship-based and autonomous coastal and open-ocean platforms, as well as remote sensing. In addition to increased diversification of funding sources to include the private sector, NGOs, and other groups, more effective engagement of stakeholders and other end-users will be critical to ensure the sustainability of ocean time series programs. Building a cohesive international time series network will require dedicated capacity to coordinate across observing programs and leverage existing infrastructure and platforms of opportunity. This review article outlines near-term observing priorities and technology needs; explores potential mechanisms to broaden ocean time series data applications and end-user communities; and describes current tools and future requirements for managing increasingly complex multi-platform data streams and developing synthesis products that support science and society. The actionable recommendations outlined herein ultimately form the basis for a robust, sustainable, fit-for-purpose time series network that will foster a predictive understanding of changing ocean systems for the benefit of society.
    Description: This work was led by HB in the Ocean Carbon and Biogeochemistry (OCB) Project Office, which is supported by the NSF OCE (1558412) and the NASA (NNX17AB17G).
    Keywords: Ocean time series ; Marine ecosystems ; Climate ; End-users ; Synthesis ; Sustained observations
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2017-09-07
    Description: The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea1,2. Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain3,4,5,6,7. Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift. Across a narrow range of increasing depth of just tens of metres, diverse microbial clades trend towards larger genome size, higher genomic GC content, and proteins with higher nitrogen but lower carbon content. These community-wide changes in genome features appear to be driven by gradients in the surrounding environmental energy and nutrient fields. Collectively, our data support hypotheses invoking nutrient limitation as a central driver in the evolution of core bacterial and archaeal genomic and proteomic properties.
    Type: Article , PeerReviewed
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  • 5
    Publication Date: 2021-02-08
    Description: Large-scale climatic forcing is impacting oceanic biogeochemical cycles and is expected to influence the water-column distribution of trace gases, including methane and nitrous oxide. Our ability as a scientific community to evaluate changes in the water-column inventories of methane and nitrous oxide depends largely on our capacity to obtain robust and accurate concentration measurements that can be validated across different laboratory groups. This study represents the first formal international intercomparison of oceanic methane and nitrous oxide measurements whereby participating laboratories received batches of seawater samples from the subtropical Pacific Ocean and the Baltic Sea. Additionally, compressed gas standards from the same calibration scale were distributed to the majority of participating laboratories to improve the analytical accuracy of the gas measurements. The computations used by each laboratory to derive the dissolved gas concentrations were also evaluated for inconsistencies (e.g., pressure and temperature corrections, solubility constants). The results from the intercomparison and intercalibration provided invaluable insights into methane and nitrous oxide measurements. It was observed that analyses of seawater samples with the lowest concentrations of methane and nitrous oxide had the lowest precisions. In comparison, while the analytical precision for samples with the highest concentrations of trace gases was better, the variability between the different laboratories was higher: 36% for methane and 27% for nitrous oxide. In addition, the comparison of different batches of seawater samples with methane and nitrous oxide concentrations that ranged over an order of magnitude revealed the ramifications of different calibration procedures for each trace gas. Finally, this study builds upon the intercomparison results to develop recommendations for improving oceanic methane and nitrous oxide measurements, with the aim of precluding future analytical discrepancies between laboratories.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Format: archive
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  • 6
    Publication Date: 2024-02-07
    Description: Complex assemblages of microbes in the surface ocean are responsible for approximately half of global carbon fixation. The persistence of high taxonomic diversity despite competition for a small suite of relatively homogeneously distributed nutrients, that is, 'the paradox of the plankton', represents a long-standing challenge for ecological theory. Here we find evidence consistent with temporal niche partitioning of nitrogen assimilation processes over a diel cycle in the North Pacific Subtropical Gyre. We jointly analysed transcript abundances, lipids and metabolites and discovered that a small number of diel archetypes can explain pervasive periodic dynamics. Metabolic pathway analysis of identified diel signals revealed asynchronous timing in the transcription of nitrogen uptake and assimilation genes among different microbial groups-cyanobacteria, heterotrophic bacteria and eukaryotes. This temporal niche partitioning of nitrogen uptake emerged despite synchronous transcription of photosynthesis and central carbon metabolism genes and associated macromolecular abundances. Temporal niche partitioning may be a mechanism by which microorganisms in the open ocean mitigate competition for scarce resources, supporting community coexistence.
    Type: Article , PeerReviewed
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  • 7
    Publication Date: 2024-02-07
    Description: Marine diazotrophs convert dinitrogen (N-2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N-2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N-2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N-2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43-57 versus 45-63 TgNyr (-1); ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223 +/- 30 TgNyr (-1) (mean +/- standard error; same hereafter) compared to version 1 (74 +/- 7 TgNyr (-1)). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88 +/- 23 versus 20 +/- 2 TgNyr 1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40 +/- 9 versus 10 +/- 2 TgNyr (-1)). Moreover, version 2 estimates the N-2 fixation rate in the Indian Ocean to be 35 +/- 14 TgNyr (-1), which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N-2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional N-15(2) bubble method yields lower rates in 69% cases compared to the new N-15(2) dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022).
    Type: Article , PeerReviewed
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