Rocap Gabrielle

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Rocap
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Gabrielle
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  • Article
    Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones.
    (National Academy of Sciences, 2019-04-29) Saunders, Jaclyn K. ; Fuchsman, Clara A. ; McKay, Cedar ; Rocap, Gabrielle
    Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (>30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.
  • Dataset
    Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-08-25) Rocap, Gabrielle
    This dataset describes assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278. 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/733748
  • Dataset
    CTD hydrography and nutrients from casts conducted on R/V Kilo Moana cruises KM1919 and KM1920 from September to October 2019
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-04-22) Devol, Allan ; Keil, Richard ; Rocap, Gabrielle
    The dataset contains the processed bottle files, i.e., depths and associated data collected electronically by the CTD, for all CTD casts during cruises KM1919 and KM1920, along with all nutrient data on casts from which it was collected. The nutrients include nitrate, nitrite, silicate, phosphate, and ammonium. The concentrations for all nutrients are in micromoles per kg as is the CTD oxygen concentration. These two cruises took place on the R/V Kilo Moana from September to October 2019 in the Eastern Tropical North Pacific, off the coast of Mexico and Southern California. The data were collected as part of NSF grant numbers 1542240 to Gabrielle Rocap, Rick Keil, Allan Devol, and Curtis Deutsch along with NSF-1657958 to Allan Devol. 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/849710
  • Article
    Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences
    (American Society for Microbiology, 2002-03) Rocap, Gabrielle ; Distel, Daniel L. ; Waterbury, John B. ; Chisholm, Sallie W.
    Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world's oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.
  • Preprint
    Production of cobalt binding ligands in a Synechococcus feature at the Costa Rica upwelling dome
    ( 2005) Saito, Mak A. ; Rocap, Gabrielle ; Moffett, James W.
    The Costa Rica upwelling dome (CRD; ~8.67ºN and 90.6ºW) was characterized chemically for cobalt and nickel abundances and speciation, and biologically using cyanobacterial abundances and phylogeny. Total dissolved cobalt was 93 pmol L-1at 90 m depth and decreased in surface waters to 45 pmol L-1 at 10 m. Cobalt was 40% labile at 90 m, but was completely complexed by strong ligands at 10 m. A surface transect out of the dome showed decreasing total dissolved cobalt from 57 pmol L-1 to 12 pmol L-1. Detection window studies showed that natural cobalt ligand complexes have conditional stability constants greater than 1016.8, and that competition with nickel did not release cobalt bound to organic complexes, consistent with natural cobalt ligands being Co(III)-complexes. Synechococcus cell densities at the CRD are among the highest reported in nature, varying between 1.2 x 106 to 3.7 x 106 cells ml-1. Phylogenetic analysis using the 16S-23S rDNA internally transcribed spacer showed the majority of clones were related to Synechococcus strain MIT S9220, while the remaining subset form a novel group within the marine Synechococcus lineage. In a bottle incubation experiment chlorophyll increased with cobalt and iron additions relative to each element alone and the unamended control treatment. Cobalt speciation analysis of incubation experiments revealed large quantities of strong cobalt ligand complexes in the cobalt addition treatments (401 pmol L-1), whereas cobalt added to a 0.2 mm filtered control remained predominantly labile (387 pmol L-1), demonstrating that the Synechococcus-dominated community is a source of strong cobalt ligands.