Saito Mak A.

Last Name

Saito

First Name

Mak A.

ORCID

0000-0001-6040-9295

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What role should a domain-specific repository play in treating code as a first class research product? [poster]

( 2018-12-13) Biddle, Matt ; Ake, Hannah ; Copley, Nancy ; Kinkade, Danie ; Rauch, Shannon ; Saito, Mak A. ; Shepherd, Adam ; Wiebe, Peter ; York, Amber

The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. The BCO-DMO repository works closely with investigators funded through the NSF OCE Division’s Biological and Chemical Sections and Antarctic Organisms & Ecosystems. The office provides services that span the full data life cycle, from data management planning support and DOI creation, to archiving with appropriate national facilities. Recently, more and more of the projects submitted to BCO-DMO represent modeling efforts which further increase our knowledge of the chemical and biological properties within the ocean ecosystem. But, as a repository traditionally focused on observational data as a primary research output, what roles should domain-specific data repositories play in this field? Recognizing code as a first class research product, how should repositories support the discovery, access and reuse of code and software used in hypothesis driven research? We feel the time is at hand for the community to begin a concerted and holistic approach to the curation of code and software. Such strategy development should begin with asking what is the appropriate output to curate? What is the minimum metadata required for re-use? How should code be stored and accessed? Should repositories support or facilitate peer reviewing code? The answers to these questions will better inform domain-specific repositories on how to better manage code as a first class research asset in order to support the scientific community. This presentation will explore these topics, inviting discussion from the audience to advance a collective strategy.
Share Your Thoughts [poster]

(Woods Hole Oceanographic Institution, 2020-02-21) Haskins, Christina ; Biddle, Matt ; Copley, Nancy J. ; Rauch, Shannon ; Soenen, Karen ; York, Amber ; Kinkade, Danie ; Saito, Mak A. ; Shepherd, Adam ; Wiebe, Peter

Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO, and presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input can help BCO-DMO improve its service to the research community.
Needles in the blue sea : sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome

( 2015-03-27) Saito, Mak A. ; Dorsk, Alexander ; Post, Anton F. ; McIlvin, Matthew R. ; Rappe, Michael S. ; DiTullio, Giacomo R. ; Moran, Dawn M.

Proteomics has great potential for studies of marine microbial biogeochemistry, yet high microbial diversity in many locales presents us with unique challenges. We addressed this challenge with a targeted metaproteomics workflow for NtcA and P-II, two nitrogen regulatory proteins, and demonstrated its application for cyanobacterial taxa within microbial samples from the Central Pacific Ocean. Using METATRYP, an open-source Python toolkit, we examined the number of shared (redundant) tryptic peptides in representative marine microbes, with the number of tryptic peptides shared between different species typically being 1% or less. The related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8+1.9% of their tryptic peptides, while shared intraspecies peptides were higher, 13+15% shared peptides between 12 Prochlorococcus genomes. An NtcA peptide was found to target multiple cyanobacteria species, whereas a P-II peptide showed specificity to the high-light Prochlorococcus ecotype. Distributions of NtcA and P-II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ~4x107, 1000-fold larger than an individual microbial proteome and 27-fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples.
Dissolved and particulate trace metal micronutrients under the McMurdo Sound seasonal sea ice : basal sea ice communities as a capacitor for iron

(Frontiers Media, 2013-10-30) Noble, Abigail E. ; Moran, Dawn M. ; Allen, Andrew E. ; Saito, Mak A.

Dissolved and particulate metal concentrations are reported from three sites beneath and at the base of the McMurdo Sound seasonal sea ice in the Ross Sea of Antarctica. This dataset provided insight into Co and Mn biogeochemistry, supporting a previous hypothesis for water column mixing occurring faster than scavenging. Three observations support this: first, Mn-containing particles with Mn/Al ratios in excess of the sediment were present in the water column, implying the presence of bacterial Mn-oxidation processes. Second, dissolved and labile Co were uniform with depth beneath the sea ice after the winter season. Third, dissolved Co:PO3−4 ratios were consistent with previously observed Ross Sea stoichiometry, implying that over-winter scavenging was slow relative to mixing. Abundant dissolved Fe and Mn were consistent with a winter reserve concept, and particulate Al, Fe, Mn, and Co covaried, implying that these metals behaved similarly. Elevated particulate metals were observed in proximity to the nearby Islands, with particulate Fe/Al ratios similar to that of nearby sediment, consistent with a sediment resuspension source. Dissolved and particulate metals were elevated at the shallowest depths (particularly Fe) with elevated particulate P/Al and Fe/Al ratios in excess of sediments, demonstrating a sea ice biomass source. The sea ice biomass was extremely dense (chl a >9500 μg/L) and contained high abundances of particulate metals with elevated metal/Al ratios. A hypothesis for seasonal accumulation of bioactive metals at the base of the McMurdo Sound sea ice by the basal algal community is presented, analogous to a capacitor that accumulates iron during the spring and early summer. The release and transport of particulate metals accumulated at the base of the sea ice by sloughing is discussed as a potentially important mechanism in providing iron nutrition during polynya phytoplankton bloom formation and could be examined in future oceanographic expeditions.
Rare earth elements (REEs) in the tropical South Atlantic and quantitative deconvolution of their non-conservative behavior

( 2016-01-24) Zheng, Xin-Yuan ; Plancherel, Yves ; Saito, Mak A. ; Scott, Peter M. ; Henderson, Gideon M.

This study presents new concentration measurements of dissolved REEs (dREEs) along a full-depth east-west section across the tropical South Atlantic (~12°S), and uses these data to investigate the oceanic cycling of the REEs. Enrichment of dREEs, associated with the redox cycling of Fe-Mn oxides, is observed in the oxygen minimum zone (OMZ) off the African shelf. For deeper-waters, a multi-parameter mixing model was developed to deconvolve the relative importance of physical transport (i.e. water mass mixing) from biogeochemical controls on the dREE distribution in the deep Atlantic. This approach enables chemical processes involved in REE cycling, not apparent from the measurements alone, to be distinguished and quantified. Results show that the measured dREE concentrations below ~1000 m are dominantly controlled (>75%) by preformed REE concentrations resulting from water mass mixing. This result indicates that the linear correlation between dREEs and dissolved Si observed in Atlantic deep waters results from the dominantly conservative behaviour of these tracers, rather than from similar chemical processes influencing both dREEs and Si. Minor addition of dREEs (~10% of dNd and ~5% of dYb) is observed in the deep (>~4000 m) Brazil Basin, resulting from either remineralization of particles in-situ or along the flow path. Greater addition of dREEs (up to 25% for dNd and 20% for dYb) is found at ~1500 m and below ~4000 m in the Angola Basin near the African continental margin. Cerium anomalies suggest that different sources are responsible for these dREE addition plumes. The 1500 m excess is most likely attributed to dREE release from Fe oxides, whereas the 4000 m excess may be due to remineralization of calcite. Higher particulate fluxes and a more sluggish ocean circulation in the Angola Basin may explain why the dREE excesses in this basin are significantly higher 45 than that observed in the Brazil Basin. Hydrothermal venting over the mid-Atlantic ridge acts as a regional net sink for light REEs, but has little influence on the net budget of heavy REEs. The combination of dense REE measurements with water mass deconvolution is shown to provide quantitative assessment of the relative roles of physical and biogeochemical processes in the oceanic cycling of REEs.
The Biological and Chemical Oceanography Data Management Office: Accelerating Scientific Discovery Through Responsive Management of Observational Oceanographic Data [poster]

(Woods Hole Oceanographic Institution, 2019-09-16) Kinkade, Danie ; Shepherd, Adam ; Biddle, Matt ; Copley, Nancy ; Haskins, Christina ; Soenen, Karen ; Rauch, Shannon ; York, Amber ; Saito, Mak A. ; Wiebe, Peter

Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO.
Capturing Provenance of Data Curation at BCO-DMO

(Woods Hole Oceanographic Institution, 2020-05-15) Shepherd, Adam ; York, Amber ; Schloer, Conrad ; Kinkade, Danie ; Rauch, Shannon ; Biddle, Matt ; Copley, Nancy ; Haskins, Christina ; Soenen, Karen ; Saito, Mak A. ; Wiebe, Peter

At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easer for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.
Capturing Provenance of Data Curation at BCO-DMO

(Woods Hole Oceanographic Institution, 2020-11-09) Shepherd, Adam ; York, Amber ; Schloer, Conrad ; Kinkade, Danie ; Rauch, Shannon ; Copley, Nancy ; Gerlach, Dana ; Haskins, Christina ; Soenen, Karen ; Saito, Mak A. ; Wiebe, Peter

At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easier for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.
Biological & Chemical Oceanography Data Management Office : a domain-specific repository for oceanographic data from around the world [poster]

( 2018-02-14) Ake, Hannah ; Biddle, Matt ; Copley, Nancy ; Kinkade, Danie ; Rauch, Shannon ; Saito, Mak A. ; Shepherd, Adam ; Switzer, Megan ; Wiebe, Peter ; York, Amber

The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a domain-specific digital data repository that works with investigators funded under the National Science Foundation’s Division of Ocean Sciences and Office of Polar Programs to manage their data free of charge. Data managers work closely with investigators to satisfy their data sharing requirements and to develop comprehensive Data Management Plans, as well as to ensure that their data will be well described with extensive metadata creation. Additionally, BCO-DMO offers tools to find and reuse these high-quality data and metadata packages, and services such as DOI generation for publication and attribution. These resources are free for all to discover, access, and utilize. As a repository embedded in our research community, BCO-DMO is well positioned to offer knowledge and expertise from both domain trained data managers and the scientific community at large. BCO-DMO is currently home to more than 9000 datasets and 900 projects, all of which are or will be submitted for archive at the National Centers for Environmental Information (NCEI). Our data holdings continue to grow, and encompass a wide range of oceanographic research areas, including biological, chemical, physical, and ecological. These data represent cruises and experiments from around the world, and are managed using community best practices, standards, and technologies to ensure accuracy and promote re-use. BCO-DMO is a repository and tool for investigators, offering both ocean science data and resources for data dissemination and publication.
Does sea spray aerosol contribute significantly to aerosol trace element loading? a case study from the US GEOTRACES Pacific Meridional Transect (GP15)

(American Geophysical Union, 2022-07-21) Marsay, Christopher M. ; Landing, William M. ; Umstead, Devon ; Till, Claire P. ; Freiberger, Robert ; Fitzsimmons, Jessica N. ; Lanning, Nathan ; Shiller, Alan M. ; Hatta, Mariko ; Chmiel, Rebecca ; Saito, Mak A. ; Buck, Clifton S.

Atmospheric deposition represents a major input for micronutrient trace elements (TEs) to the surface ocean and is often quantified indirectly through measurements of aerosol TE concentrations. Sea spray aerosol (SSA) dominates aerosol mass concentration over much of the global ocean, but few studies have assessed its contribution to aerosol TE loading, which could result in overestimates of “new” TE inputs. Low-mineral aerosol concentrations measured during the U.S. GEOTRACES Pacific Meridional Transect (GP15; 152°W, 56°N to 20°S), along with concurrent towfish sampling of surface seawater, provided an opportunity to investigate this aspect of TE biogeochemical cycling. Central Pacific Ocean surface seawater Al, V, Mn, Fe, Co, Ni, Cu, Zn, and Pb concentrations were combined with aerosol Na data to calculate a “recycled” SSA contribution to aerosol TE loading. Only vanadium was calculated to have a SSA contribution averaging >1% along the transect (mean of 1.5%). We derive scaling factors from previous studies on TE enrichments in the sea surface microlayer and in freshly produced SSA to assess the broader potential for SSA contributions to aerosol TE loading. Maximum applied scaling factors suggest that SSA could contribute significantly to the aerosol loading of some elements (notably V, Cu, and Pb), while for others (e.g., Fe and Al), SSA contributions largely remained <1%. Our study highlights that a lack of focused measurements of TEs in SSA limits our ability to quantify this component of marine aerosol loading and the associated potential for overestimating new TE inputs from atmospheric deposition.
Cobalt, manganese, and iron near the Hawaiian Islands : a potential concentrating mechanism for cobalt within a cyclonic eddy and implications for the hybrid-type trace metals

( 2007-09-26) Noble, Abigail E. ; Saito, Mak A. ; Maiti, Kanchan ; Benitez-Nelson, Claudia R.

The vertical distributions of cobalt, iron, and manganese in the water column were studied during the E-Flux Program (E-Flux II and III), which focused on the biogeochemistry of cold-core cyclonic eddies that form in the lee of the Hawaiian Islands. During E-Flux II (January 2005) and E-Flux III (March 2005), 17 stations were sampled for cobalt (n =147), all of which demonstrated nutrient-like depletion in surface waters. During E-Flux III, two depth profiles collected from within a mesoscale coldcore eddy, Cyclone Opal, revealed small distinct maxima in cobalt at ~100m depth and a larger inventory of cobalt within the eddy. We hypothesize that this was due to a cobalt concentrating effect within the eddy, where upwelled cobalt was subsequently associated with sinking particulate organic carbon (POC) via biological activity and was released at a depth coincident with nearly complete POC remineralization (Benitez-Nelson et al. 2007). There is also evidence for the formation of a correlation between cobalt and soluble reactive phosphorus during E-Flux III relative to the E-Flux II cruise that we suggest is due to increased productivity, implying a minimum threshold of primary production below which cobalt-phosphate coupling does not occur. Dissolved iron was measured in E-Flux II and found in somewhat elevated concentrations (~0.5nM) in surface waters relative to the iron depleted waters of the surrounding Pacific (Fitzwater et al. 1996), possibly due to island effects associated with the iron-rich volcanic soil from the Hawaiian Islands and/or anthropogenic inputs. Distinct depth maxima in total dissolved cobalt were observed at 400 to 600m depth, suggestive of the release of metals from the shelf area of comparable depth that surrounds these islands.
Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide

(Nature Publishing Group, 2015-09-01) Hutchins, David A. ; Walworth, Nathan G. ; Webb, Eric A. ; Saito, Mak A. ; Moran, Dawn M. ; McIlvin, Matthew R. ; Gale, Jasmine ; Fu, Fei-Xue

Nitrogen fixation rates of the globally distributed, biogeochemically important marine cyanobacterium Trichodesmium increase under high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity. However, its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. Here we show that experimental evolution under extended selection at projected future elevated CO2 levels results in irreversible, large increases in nitrogen fixation and growth rates, even after being moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained after returning to the ancestral environment. Constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, and increased activity of a potentially regulatory DNA methyltransferase enzyme. High CO2-selected cell lines also exhibit increased phosphorus-limited growth rates, suggesting a potential advantage for this keystone organism in a more nutrient-limited, acidified future ocean.
Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

(John Wiley & Sons, 2017-04-05) Santoro, Alyson E. ; Saito, Mak A. ; Goepfert, Tyler J. ; Lamborg, Carl H. ; Dupont, Christopher L. ; DiTullio, Giacomo R.

Thaumarchaea are among the most abundant microbial groups in the ocean, but controls on their abundance and the distribution and metabolic potential of different subpopulations are poorly constrained. Here, two ecotypes of ammonia-oxidizing thaumarchaea were quantified using ammonia monooxygenase (amoA) genes across the equatorial Pacific Ocean. The shallow, or water column “A” (WCA), ecotype was the most abundant ecotype at the depths of maximum nitrification rates, and its abundance correlated with other biogeochemical indicators of remineralization such as NO3 : Si and total Hg. Metagenomes contained thaumarchaeal genes encoding for the catalytic subunit of the urease enzyme (ureC) at all depths, suggesting that members of both WCA and the deep, water column “B” (WCB) ecotypes may contain ureC. Coupled urea hydrolysis-ammonia oxidation rates were similar to ammonia oxidation rates alone, suggesting that urea could be an important source of ammonia for mesopelagic ammonia oxidizers. Potential inducement of metal limitation of both ammonia oxidation and urea hydrolysis was demonstrated via additions of a strong metal chelator. The water column inventory of WCA was correlated with the depth-integrated abundance of WCB, with both likely controlled by the flux of sinking particulate organic matter, providing strong evidence of vertical connectivity between the ecotypes. Further, depth-integrated amoA gene abundance and nitrification rates were correlated with particulate organic nitrogen flux measured by contemporaneously deployed sediment traps. Together, the results refine our understanding of the controls on thaumarchaeal distributions in the ocean, and provide new insights on the relationship between material flux and microbial communities in the mesopelagic.
The role of external inputs and internal cycling in shaping the global ocean cobalt distribution : insights from the first cobalt biogeochemical model

(John Wiley & Sons, 2018-04-16) Tagliabue, Alessandro ; Hawco, Nicholas J. ; Bundy, Randelle M. ; Landing, William M. ; Milne, Angela ; Morton, Peter L. ; Saito, Mak A.

Cobalt is an important micronutrient for ocean microbes as it is present in vitamin B12 and is a co‐factor in various metalloenzymes that catalyze cellular processes. Moreover, when seawater availability of cobalt is compared to biological demands, cobalt emerges as being depleted in seawater, pointing to a potentially important limiting role. To properly account for the potential biological role for cobalt, there is therefore a need to understand the processes driving the biogeochemical cycling of cobalt and, in particular, the balance between external inputs and internal cycling. To do so, we developed the first cobalt model within a state‐of‐the‐art three‐dimensional global ocean biogeochemical model. Overall, our model does a good job in reproducing measurements with a correlation coefficient of >0.7 in the surface and >0.5 at depth. We find that continental margins are the dominant source of cobalt, with a crucial role played by supply under low bottom‐water oxygen conditions. The basin‐scale distribution of cobalt supplied from margins is facilitated by the activity of manganese‐oxidizing bacteria being suppressed under low oxygen and low temperatures, which extends the residence time of cobalt. Overall, we find a residence time of 7 and 250 years in the upper 250 m and global ocean, respectively. Importantly, we find that the dominant internal resupply process switches from regeneration and recycling of particulate cobalt to dissolution of scavenged cobalt between the upper ocean and the ocean interior. Our model highlights key regions of the ocean where biological activity may be most sensitive to cobalt availability.
A dissolved cobalt plume in the oxygen minimum zone of the eastern tropical South Pacific

(Copernicus Publications on behalf of the European Geosciences Union, 2016-10-17) Hawco, Nicholas J. ; Ohnemus, Daniel C. ; Resing, Joseph A. ; Twining, Benjamin S. ; Saito, Mak A.

Cobalt is a nutrient to phytoplankton, but knowledge about its biogeochemical cycling is limited, especially in the Pacific Ocean. Here, we report sections of dissolved cobalt and labile dissolved cobalt from the US GEOTRACES GP16 transect in the South Pacific. The cobalt distribution is closely tied to the extent and intensity of the oxygen minimum zone in the eastern South Pacific with highest concentrations measured at the oxycline near the Peru margin. Below 200 m, remineralization and circulation produce an inverse relationship between cobalt and dissolved oxygen that extends throughout the basin. Within the oxygen minimum zone, elevated concentrations of labile cobalt are generated by input from coastal sources and reduced scavenging at low O2. As these high cobalt waters are upwelled and advected offshore, phytoplankton export returns cobalt to low-oxygen water masses underneath. West of the Peru upwelling region, dissolved cobalt is less than 10 pM in the euphotic zone and strongly bound by organic ligands. Because the cobalt nutricline within the South Pacific gyre is deeper than in oligotrophic regions in the North and South Atlantic, cobalt involved in sustaining phytoplankton productivity in the gyre is heavily recycled and ultimately arrives from lateral transport of upwelled waters from the eastern margin. In contrast to large coastal inputs, atmospheric deposition and hydrothermal vents along the East Pacific Rise appear to be minor sources of cobalt. Overall, these results demonstrate that oxygen biogeochemistry exerts a strong influence on cobalt cycling.
Overexpression and characterization of an iron storage and DNA-binding Dps protein from Trichodesmium erythraeum

(American Society for Microbiology, 2006-04) Castruita, M. ; Saito, Mak A. ; Schottel, P. C. ; Elmegreen, L. A. ; Myneni, Satish C. B. ; Stiefel, E. I. ; Morel, Francois M. M.

Although the role of iron in marine productivity has received a great deal of attention, no iron storage protein has been isolated from a marine microorganism previously. We describe an Fe-binding protein belonging to the Dps family (DNA binding protein from starved cells) in the N2-fixing marine cyanobacterium Trichodesmium erythraeum. A dps gene encoding a protein with significant levels of identity to members of the Dps family was identified in the genome of T. erythraeum. This gene codes for a putative DpsT. erythraeurm protein (Dpstery) with 69% primary amino acid sequence similarity to Synechococcus DpsA. We expressed and purified Dpstery, and we found that Dpstery, like other Dps proteins, is able to bind Fe and DNA and protect DNA from degradation by DNase. We also found that Dpstery binds phosphate, like other ferritin family proteins. Fe K near-edge X-ray absorption of Dpstery indicated that it has an iron core that resembles that of horse spleen ferritin.
Iron limitation of a springtime bacterial and phytoplankton community in the Ross Sea : implications for vitamin B12 nutrition

(Frontiers Media, 2011-08-15) Bertrand, Erin M. ; Saito, Mak A. ; Lee, Peter A. ; Dunbar, Robert B. ; Sedwick, Peter N. ; DiTullio, Giacomo R.

The Ross Sea is home to some of the largest phytoplankton blooms in the Southern Ocean. Primary production in this system has previously been shown to be iron limited in the summer and periodically iron and vitamin B12 colimited. In this study, we examined trace metal limitation of biological activity in the Ross Sea in the austral spring and considered possible implications for vitamin B12 nutrition. Bottle incubation experiments demonstrated that iron limited phytoplankton growth in the austral spring while B12, cobalt, and zinc did not. This is the first demonstration of iron limitation in a Phaeocystis antarctica-dominated, early season Ross Sea phytoplankton community. The lack of B12 limitation in this location is consistent with previous Ross Sea studies in the austral summer, wherein vitamin additions did not stimulate P. antarctica growth and B12 was limiting only when bacterial abundance was low. Bottle incubation experiments and a bacterial regrowth experiment also revealed that iron addition directly enhanced bacterial growth. B12 uptake measurements in natural water samples and in an iron fertilized bottle incubation demonstrated that bacteria serve not only as a source for vitamin B12, but also as a significant sink, and that iron additions enhanced B12 uptake rates in phytoplankton but not bacteria. Additionally, vitamin uptake rates did not become saturated upon the addition of up to 95 pM B12. A rapid B12 uptake rate was observed after 13 min, which then decreased to a slower constant uptake rate over the next 52 h. Results from this study highlight the importance of iron availability in limiting early season Ross Sea phytoplankton growth and suggest that rates of vitamin B12 production and consumption may be impacted by iron availability.
Cobalt and nickel in the Peru upwelling region : a major flux of labile cobalt utilized as a micronutrient

(American Geophysical Union, 2004-12-28) Saito, Mak A. ; Moffett, James W. ; DiTullio, Giacomo R.

The geochemistry of cobalt in the Peru upwelling region is dominated by its importance as a micronutrient. A large and previously undocumented flux of labile cobalt behaved as a micronutrient with correlations with major nutrients (nitrate, phosphate; r 2 = 0.90, 0.96) until depleted to ≤50 pM of strongly complexed cobalt. Co:P utilization ratios were an order of magnitude higher than in the North Pacific, comparable to utilization rates of zinc in other oceanic regions. Cobalt speciation measurements showed that available cobalt decreased over 4 orders of magnitude in this region, with shifts in phytoplankton assemblages occurring at transitions between labile and nonlabile cobalt. Only small changes in total dissolved nickel were observed, and nickel was present in a labile chemical form throughout the region. In the Peru upwelling region, cobalt uptake was highest at the surface and decreased with depth, suggesting phytoplankton uptake was a more important removal mechanism than co-oxidation with microbial manganese oxidation. These findings show the importance of cobalt as a micronutrient and that cobalt scarcity and speciation may be important in influencing phytoplankton species composition in this economically important environment.
Trace elements at the intersection of marine biological and geochemical evolution

( 2016-10) Robbins, Leslie J. ; Lalonde, Stefan V. ; Planavsky, Noah J. ; Partin, Camille A. ; Reinhard, Christopher T. ; Kendall, Brian ; Scott, Clint ; Hardisty, Dalton S. ; Gill, Benjamin C. ; Alessi, Daniel S. ; Dupont, Christopher L. ; Saito, Mak A. ; Crowe, Sean A. ; Poulton, Simon W. ; Bekker, Andrey ; Lyons, Timothy W. ; Konhauser, Kurt O.

Life requires a wide variety of bioessential trace elements to act as structural components and reactive centers in metalloenzymes. These requirements differ between organisms and have evolved over geological time, likely guided in some part by environmental conditions. Until recently, most of what was understood regarding trace element concentrations in the Precambrian oceans was inferred by extrapolation, geochemical modeling, and/or genomic studies. However, in the past decade, the increasing availability of trace element and isotopic data for sedimentary rocks of all ages have yielded new, and potentially more direct, insights into secular changes in seawater composition – and ultimately the evolution of the marine biosphere. Compiled records of many bioessential trace elements (including Ni, Mo, P, Zn, Co, Cr, Se, and I) provide new insight into how trace element abundance in Earth’s ancient oceans may have been linked to biological evolution. Several of these trace elements display redox-sensitive behavior, while others are redox-sensitive but not bioessential (e.g., Cr, U). Their temporal trends in sedimentary archives provide useful constraints on changes in atmosphere-ocean redox conditions that are linked to biological evolution, for example, the activity of oxygen-producing, photosynthetic cyanobacteria. In this review, we summarize available Precambrian trace element proxy data, and discuss how temporal trends in the seawater concentrations of specific trace elements may be linked to the evolution of both simple and complex life. We also examine several biologically relevant and/or redox-sensitive trace elements that have yet to be fully examined in the sedimentary rock record (e.g., Cu, Cd, W) and suggest several directions for future studies.
A manganese-rich environment supports superoxide dismutase activity in a lyme disease pathogen, Borrelia burgdorferi

( 2013-01-28) Aguirre, J. Dafhne ; Clark, Hillary M. ; McIlvin, Matthew R. ; Vazquez, Christine ; Palmere, Shaina L. ; Grab, Dennis J. ; Seshu, J. ; Hart, P. John ; Saito, Mak A. ; Culotta, Valeria C.

The Lyme disease pathogen Borrelia burgdorferi represents a novel organism in which to study metalloprotein biology in that this spirochete has uniquely evolved with no requirement for iron. Not only is iron low, but we show here that B. burgdorferi has the capacity to accumulate remarkably high levels of manganese. This high manganese is necessary to activate the SodA superoxide dismutase (SOD) essential for virulence. Using a metalloproteomic approach, we demonstrate that a bulk of B. burgdorferi SodA directly associates with manganese and a smaller pool of inactive enzyme accumulates as apoprotein. Other metalloproteins may have similarly adapted to using manganese as co-factor including the BB0366 amino-peptidase. While B. burgdorferi SodA has evolved in a manganese-rich, iron-poor environment, the opposite is true for Mn-SODs of organisms such as E. coli and bakers’ yeast. These Mn-SODs still capture manganese in an iron-rich cell, and we tested whether the same is true for Borrelia SodA. When expressed in the iron-rich mitochondria of S. cerevisiae, B. burgdorferi SodA was inactive. Activity was only possible when cells accumulated extremely high levels of manganese that exceeded cellular iron. Moreover, there was no evidence for iron inactivation of the SOD. B. burgdorferi SodA shows strong overall homology with other members of the Mn-SOD family, but computer assisted modeling revealed some unusual features of the hydrogen bonding network near the enzyme’s active site. The unique properties of B. burgdorferi SodA may represent adaptation to expression in the manganese-rich and iron-poor environment of the spirochete.

Saito Mak A.

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