Rao Deepa

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Rao
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Deepa
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  • Thesis
    Characterizing cobalamin cycling by Antarctic marine microbes across multiple scales
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2020-05) Rao, Deepa
    Highly productive marine microbial communities in the coastal Southern Ocean sustain the broader Antarctic ecosystem and play a key role in Earth’s climate via the biological pump. Regional phytoplankton growth is primarily limited by iron and co-limited by cobalamin (vitamin B12), a trace cobalt-containing organometallic compound only synthesized by some bacteria and archaea. These micronutrients impact primary production and the microbial ecology of the two keystone phytoplankton types: diatoms and Phaeocystis antarctica. This thesis investigates microbe-driven cobalamin cycling in Antarctic seas across multiple spatiotemporal scales. I conducted laboratory culture experiments with complementary proteomics and transcriptomics to investigate the B12-ecophysiology of P. antarctica strain CCMP 1871 morphotypes under iron-B12 co-limitation. We observed colony formation under higher iron treatments, and a facultative use of B12-dependent (MetH) and B12-independent (MetE) methionine synthase isoforms in response to vitamin availability, demonstrating that this strain is not B12-auxotrophic. Through comparative ’omics, we identified a putative MetE protein in P. antarctica abundant under low B12, which is also found in other marine microbes. Across Antarctic seas, community-scale cobalt and B12 uptake rates were measured by 57Co radiotracer incubation experiments and integrated with hydrographic and phytoplankton pigment data. I observed significant correlations between uptake fluxes and environmental variables, providing evidence for predominantly diatom-driven uptake of these micronutrients in warmer, fresher surface waters with notable regional differences. To date, this work is the most comprehensive attempt to elucidate the processes governing the co-cycling of cobalt and B12 in any marine system. At the ecosystem-scale, I developed and tested a hypothesis of micronutrient-driven community dynamics through a trait-based model with cross-feeding interactions. The model demonstrates how the observed seasonal succession of springtime P. antarctica from solitary to colonial cells, bacterioplankton, and summertime diatoms may be explained by the microbial cycling of iron, dissolved organic carbon, and B12. Overall, this dissertation provides new information about the micronutrient-driven ecology of Antarctic marine microbes and adds to our understanding of the interconnections between organismal life cycle, trace metals, and trace organics in marine environments.
  • Article
    Inhibited manganese oxide formation hinders cobalt scavenging in the Ross Sea
    (American Geophysical Union, 2021-04-30) Oldham, Véronique E. ; Chmiel, Rebecca ; Hansel, Colleen M. ; DiTullio, Giacomo R. ; Rao, Deepa ; Saito, Mak A.
    The Southern Ocean plays a critical role in regulating global uptake of atmospheric CO2. Trace elements like iron (Fe), cobalt (Co), and manganese (Mn) have been shown to modulate this primary productivity. Despite limited data, the vertical profiles for Mn, Fe, and Co in the Ross Sea show no evidence of scavenging, as typically observed in oceanic sites. This was previously attributed to low-particle abundance and/or by mixing rates exceeding scavenging rates. Scavenging of some trace metals such as cobalt (Co) is thought to be largely governed by Mn (oxyhydr)oxides, assumed to be the main component of particulate Mn (pMn). However, our data show that pMn has an average oxidation state below 3 and with nondetectable Mn oxides. In addition, soluble Co profiles show no evidence of scavenging and Co uptake measurements show little Co uptake in the euphotic zone and low/no scavenging at depth. Instead, high concentrations of dissolved Mn (dMn, up to 90 nM), which is primarily complexed as Mn(III)-L (up to 100%), are observed. Average dMn concentrations (10 ± 14 nM) are highest in bottom and surface waters. Manganese sources may include sediments and sea-ice melt, as elevated dMn was measured in sea ice (12 nM) compared to its surrounding waters (3 nM), and sea ice dMn was 97% Mn(III)-L. We contend that the lack of Co scavenging in the Ross Sea is due to a unique Mn redox cycle that favors the stabilization of Mn(III)-complexes at the expense of Mn oxide particle formation.
  • Preprint
    Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria
    ( 2013-10) Meredith, Laura K. ; Rao, Deepa ; Bosak, Tanja ; Klepac-Ceraj, Vanja ; Tada, Kendall R. ; Hansel, Colleen M. ; Ono, Shuhei ; Prinn, Ronald G.
    Microbe-mediated soil uptake is the largest and most uncertain variable in the budget of atmospheric hydrogen (H2). The diversity and ecophysiological role of soil microorganisms that can consume low atmospheric abundances of H2 with high-affinity [NiFe]-hydrogenases is unknown. We expanded the library of atmospheric H2-consuming strains to include four soil Harvard Forest Isolate (HFI) Streptomyces spp., Streptomyces cattleya, and Rhodococcus equi by assaying for high-affinity hydrogenase (hhyL) genes and quantifying H2 uptake rates. We find that aerial structures (hyphae and spores) are important for Streptomyces H2 consumption; uptake was not observed in Streptomyces griseoflavus Tu4000 (deficient in aerial structures) and was reduced by physical disruption of Streptomyces sp. HFI8 aerial structures. H2 consumption depended on the life cycle stage in developmentally distinct actinobacteria: Streptomyces sp. HFI8 (sporulating) and R. equi (non-sporulating, non-filamentous). Strain HFI8 took up H2 only after forming aerial hyphae and sporulating, while R. equi only consumed H2 in the late exponential and stationary phase. These observations suggest that conditions favoring H2 uptake by actinobacteria are associated with energy and nutrient limitation. Thus, H2 may be an important energy source for soil microorganisms inhabiting systems in which nutrients are frequently limited.