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  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 387, doi:10.3389/fmicb.2013.00387.
    Description: Synechococcus sp. WH 8102 is a motile marine cyanobacterium isolated originally from the Sargasso Sea. To test the response of this organism to cadmium (Cd), generally considered a toxin, cultures were grown in a matrix of high and low zinc (Zn) and phosphate (PO43−) and were then exposed to an addition of 4.4 pM free Cd2+ at mid-log phase and harvested after 24 h. Whereas Zn and PO43− had little effect on overall growth rates, in the final 24 h of the experiment three growth effects were noticed: (i) low PO43− treatments showed increased growth rates relative to high PO43− treatments, (ii) the Zn/high PO43− treatment appeared to enter stationary phase, and (iii) Cd increased growth rates further in both the low PO43− and Zn treatments. Global proteomic analysis revealed that: (i) Zn appeared to be critical to the PO43− response in this organism, (ii) bacterial metallothionein (SmtA) appears correlated with PO43− stress-associated proteins, (iii) Cd has the greatest influence on the proteome at low PO43− and Zn, (iv) Zn buffered the effects of Cd, and (v) in the presence of both replete PO43− and added Cd the proteome showed little response to the presence of Zn. Similar trends in alkaline phosphate (ALP) and SmtA suggest the possibility of a Zn supply system to provide Zn to ALP that involves SmtA. In addition, proteome results were consistent with a previous transcriptome study of PO43− stress (with replete Zn) in this organism, including the greater relative abundance of ALP (PhoA), ABC phosphate binding protein (PstS) and other proteins. Yet with no Zn in this proteome experiment the PO43− response was quite different including the greater relative abundance of five hypothetical proteins with no increase in PhoA or PstS, suggesting that Zn nutritional levels are connected to the PO43− response in this cyanobacterium. Alternate ALP PhoX (Ca) was found to be a low abundance protein, suggesting that PhoA (Zn, Mg) may be more environmentally relevant than PhoX.
    Description: We would like to thank the Gordon and Betty Moore Foundation (#2724), C-MORE, the Office of Naval Research, and NSF Chemical Oceanography (OCE-1031271, OCE-1233261, OCE-1220484) for support.
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 61, doi:10.3389/fmars.2018.00061.
    Description: The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in the mesopelagic.
    Description: This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747).
    Keywords: Iron ; Siderophores ; Station ALOHA ; Organic ligands ; Iron limitation
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2015): 794, doi:10.3389/fmicb.2014.00794.
    Description: Atmospheric deposition is a major source of trace metals in marine surface waters and supplies vital micronutrients to phytoplankton, yet measured aerosol trace metal solubility values are operationally defined, and there are relatively few multi-element studies on aerosol-metal solubility in seawater. Here we measure the solubility of aluminum (Al), cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) from natural aerosol samples in seawater over a 7 days period to (1) evaluate the role of extraction time in trace metal dissolution behavior and (2) explore how the individual dissolution patterns could influence biota. Dissolution behavior occurs over a continuum ranging from rapid dissolution, in which the majority of soluble metal dissolved immediately upon seawater exposure (Cd and Co in our samples), to gradual dissolution, where metals dissolved slowly over time (Zn, Mn, Cu, and Al in our samples). Additionally, dissolution affected by interactions with particles was observed in which a decline in soluble metal concentration over time occurred (Fe and Pb in our samples). Natural variability in aerosol chemistry between samples can cause metals to display different dissolution kinetics in different samples, and this was particularly evident for Ni, for which samples showed a broad range of dissolution rates. The elemental molar ratio of metals in the bulk aerosols was 23,189Fe: 22,651Al: 445Mn: 348Zn: 71Cu: 48Ni: 23Pb: 9Co: 1Cd, whereas the seawater soluble molar ratio after 7 days of leaching was 11Fe: 620Al: 205Mn: 240Zn: 20Cu: 14Ni: 9Pb: 2Co: 1Cd. The different kinetics and ratios of aerosol metal dissolution have implications for phytoplankton nutrition, and highlight the need for unified extraction protocols that simulate aerosol metal dissolution in the surface ocean.
    Description: This work was supported by NSF-OCE grant 0850467 to Adina Paytan, NSF-OCE grant 1233261 to Mak A. Saito, and NATO Science for Peace Grant to Adina Paytan and Anton F. Post (SfP 982161). Katherine R. M. Mackey was supported by a National Science Foundation Postdoctoral Research Fellowship in Biology (Grant No. NSF 1103575) and Chia-Te Chien by an international graduate student fellowship from the ministry of education, Taiwan.
    Keywords: Aerosols ; Atmospheric deposition ; Phytoplankton ; Trace metals ; Ligands
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2019-02-19
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bundy, R. M., Boiteau, R. M., McLean, C., Turk-Kubo, K. A., Mcllvin, M. R., Saito, M. A., Van Mooy, B. A. S., & Repeta, D. J.. Distinct siderophores contribute to iron cycling in the mesopelagic at station ALOHA. Frontiers in Marine Science, 5, (2018): 61. doi:10.3389/fmars.2018.00061.
    Description: The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in the mesopelagic.
    Description: We thank Chief Scientists Tara Clemente and Sam Wilson for leading the SCOPE Diel cruises. We also thank the Captain and crew of the R/V Ka'imikai-O-Kanaloa, as well as Paul Henderson in the Woods Hole Oceanographic Nutrient Analytical Facility for nutrient analyses. This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747). We also thank two reviewers for helpful comments on the manuscript.
    Keywords: iron ; siderophores ; Station ALOHA ; organic ligands ; iron limitation
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Chemistry 1 (2013): 25, doi:10.3389/fchem.2013.00025.
    Description: 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.
    Description: This research was funded by NSF OPP grant 0732665, NSF-OCE grant numbers 1031271, 0928414, 0752291, 1233261, and the Gordon and Betty Moore Foundation.
    Repository Name: Woods Hole Open Access Server
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  • 6
    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): 385, doi:10.3389/fmicb.2012.00385.
    Description: Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and analysis of sequence counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. k-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes, but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability 〈 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes.
    Description: This research was funded by the National Science Foundation grant #OCE-0723667 (to Sonya T. Dyhrman, Mak A. Saito, Bethany D. Jenkins, and Tatiana A. Rynearson). Harriet Alexander is funded under a National Defense Science and Engineering Graduate (NDSEG) Fellowship.
    Keywords: Thalassiosira pseudonana ; Diatom ; Phytoplankton ; Housekeeping genes ; RT-qPCR ; Transcriptome ; Relative gene expression ; Reference gene
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 189, doi:10.3389/fmicb.2018.00189.
    Description: Only select prokaryotes can biosynthesize vitamin B12 (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that 〉95% of cyanobacteria can only produce a cobalamin analog, pseudo-B12, due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B12 is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB, is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B12 biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B12 inputs by Trichodesmium. These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.
    Description: This work was funded by NSF research grants OCE-1260233, OCE-1260490, OCE-1657757, and OCE-143566.
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  • 8
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 243, doi:10.3389/fmars.2016.00243.
    Description: Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poorly constrained, which has hindered progress in modeling marine metal speciation. In this study, we detected and characterized natural ligands that bind copper (Cu) and nickel (Ni) in the eastern South Pacific Ocean with liquid chromatography tandem inductively coupled plasma mass spectrometry (LC-ICPMS), and high-resolution electrospray ionization mass spectrometry (ESIMS). Dissolved Cu, Ni, and ligand concentrations were highest near the coast. Chromatographically unresolved polar compounds dominated ligands isolated near the coast by solid phase extraction. Offshore, metal and ligand concentrations decreased, but several new ligands appeared. One major ligand was detected that bound both Cu2+ and Ni2+. Based on accurate mass and fragmentation measurements, this compound has a molecular formula of [C20H21N4O8S2+M]+ (M = metal isotope) and contains several azole-like metal binding groups. Additional lipophilic Ni complexes were also present only in oligotrophic waters, with masses of 649, 698, and 712 m/z (corresponding to the 58Ni metal complex). Molecular formulae of [C32H54N3O6S2Ni]+ and [C33H56N3O6S2Ni]+ were determined for two of these compounds. Addition of Cu and Ni to the samples also revealed the presence of additional compounds that can bind both Ni and Cu. Although these specific compounds represent a small fraction of the total dissolved Cu and Ni pool, they highlight the compositional diversity and spatial heterogeneity of marine Ni and Cu ligands, as well as variability in the extent to which different metals in the same environment compete for ligand binding.
    Description: Support was provided by the National Science Foundation (NSF) program in Chemical Oceanography (OCE-1356747, OCE-1233261, OCE-1233733, OCE-1233502, and OCE-1237034), the NSF Science and Technology Center for Microbial Oceanography Research and Education (C-MORE; DBI-0424599), the Gordon and Betty Moore Foundation (#3298 and 3934), and the Simons Foundation (#329108, DR).
    Keywords: Copper ; Nickel ; Marine ligands ; Metal competition ; GEOTRACES ; Eastern Pacific
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums. The definitive version was published in Frontiers in Microbiology 2 (2011): 160, doi:10.3389/fmicb.2011.00160.
    Description: 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.
    Description: This research was supported by NSF grants OCE-0752291, OPP-0440840, OPP-0338097, OPP-0338164, ANT-0732665, OCE-0452883, and OCE-1031271, the Center for Microbial Oceanography Research and Education (CMORE) and a National Science Foundation (NSF) Graduate Research Fellowship (2007037200) and an Environmental Protection Agency STAR Fellowship to EMB (F6E20324).
    Keywords: Iron limitation ; Vitamin B12 ; Ross Sea ; Colimitation ; Bacteria ; Phytoplankton ; Iron fertilization
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited. The definitive version was published in Frontiers in Microbiology 2 (2011): 215, doi:10.3389/fmicb.2011.00215.
    Description: Improvements in temporal and spatial sampling frequency have the potential to open new windows into the understanding of marine microbial dynamics. In recent years, efforts have been made to allow automated samplers to collect microbial biomass for DNA/RNA analyses from moored observatories and autonomous underwater vehicles. Measurements of microbial proteins are also of significant interest given their biogeochemical importance as enzymes that catalyze reactions and transporters that interface with the environment. We examined the influence of five preservatives solutions (SDS-extraction buffer, ethanol, trichloroacetic acid, B-PER, and RNAlater) on the proteome integrity of the marine cyanobacterium Synechococcus WH8102 after 4 weeks of storage at room temperature. Four approaches were used to assess degradation: total protein recovery, band integrity on an SDS detergent polyacrylamide electrophoresis (SDS-PAGE) gel, and number of protein identifications and relative abundances by 1-dimensional LC–MS/MS proteomic analyses. Total protein recoveries from the preserved samples were lower than the frozen control due to processing losses, which could be corrected for with internal standardization. The trichloroacetic acid preserved sample showed significant loss of protein band integrity on the SDS-PAGE gel. The RNAlater preserved sample showed the highest number of protein identifications (103% relative to the control; 520 ± 31 identifications in RNAlater versus 504 ± 4 in the control), equivalent to the frozen control. Relative abundances of individual proteins in the RNAlater treatment were quite similar to that of the frozen control (average ratio of 1.01 ± 0.27 for the 50 most abundant proteins), while the SDS-extraction buffer, ethanol, and B-PER all showed significant decreases in both number of identifications and relative abundances of individual proteins. Based on these findings, RNAlater was an effective proteome preservative, although further study is warranted on additional marine microbes.
    Description: This work was funded by the National Science Foundation Chemical and Biological Oceanography, Center for Microbial Oceanography Research and Education (C-MORE), and the Gordon and Betty Moore Foundation.
    Keywords: Proteome ; Preservation ; Autonomous sampling ; Cyanobacteria ; Alkaline phosphatase ; Proteomics ; Synechococcus WH8102
    Repository Name: Woods Hole Open Access Server
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