Biology subjects

Rocap, G.

Publications and source records attributed to Rocap, G..

3 recordsLinked to original sources

bioRxiv2025

Marine community metabolomes in the eastern tropical North Pacific Oxygen Deficient Zone reveal glycine betaine as a metabolic link between Prochlorococcus and SAR11

Oxygen deficient zones (ODZs) are subsurface marine systems that harbor distinct microbial communities, including populations of the picocyanobacteria Prochlorococcus that can form a secondary chlorophyll maximum (SCM), and low-oxygen tolerant strains of the globally abundant heterotroph Pelagibacter (SAR11). Yet, the small labile molecules (metabolites) responsible for maintaining these ODZ communities are unknown. Here, we compared the metabolome of an ODZ to that of an oxygenated site by quantifying 87 metabolites across depth profiles in the eastern tropical North Pacific ODZ and the oxygenated waters of the North Pacific Gyre. Metabolomes were largely consistent between anoxic and oxic water columns. However, the osmolyte glycine betaine (GBT) was enriched in the oxycline and SCM of the ETNP, comprising as much as 1.2% of particulate organic carbon. Transcriptomes revealed two active GBT production pathways, glycine methylation (SDMT/bsmB) expressed by Prochlorococcus and choline oxidation (betB) expressed by Gammaproteobacteria. GBT consumption through demethylation involved diverse microbial taxa, with SAR11 contributing nearly half of the transcripts for the initial step of GBT demethylation (BHMT), which is predicted to convert GBT and homocysteine into dimethylglycine and methionine, a compound SAR11 cannot otherwise produce. Thus, GBT connects the metabolisms of the dominant phototroph and heterotroph in the oceans.

systems biology↗

bioRxiv2024

Cyanobacteria from marine oxygen deficient zones encode both form I and form II rubiscos

Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon to biomass. To date, all studied Cyanobacterial lineages encode carbon fixation machinery hinged upon form I rubisco enzymes within a CO2-concentrating carboxysome. Here, we report that the AMZ IB lineage of Prochlorococcus from global oxygen deficient zones (ODZs) harbor both form I and form II rubisco enzymes, the latter of which are typically non-carboxysomal and possess biochemical properties tuned towards low oxygen environments. Our analyses reveal that these cyanobacterial form II enzymes are functional in vitro and were likely acquired via lateral gene transfer from proteobacteria. Global metagenomic read recruitment demonstrates that Prochlorococcus with form II rubisco are essentially restricted to ODZs in the Eastern Tropical Pacific, suggesting that acquisition may confer an advantage specifically under low-O2 conditions. Populations of AMZ IB Prochlorococcus express both forms of rubisco in situ, with the highest form II rubisco expression at depths where both oxygen and light are particularly low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for the overall capacity of ODZs to sequester carbon.

microbiology↗

bioRxiv2023

Hi-C assembled genomes of estuarine populations reveal virus-microbe associations and a broad interaction range of a cyanophage

Aquatic microbes play key roles in global biogeochemical cycles and their viral-induced mortality influences the flow of carbon and nutrients between the dissolved and particulate pools. However, many microbes remain uncultivated, hindering understanding of their metabolic capabilities and preventing isolation of viruses that infect them. Here we augment metagenomic sequencing with Hi-C, a proximity-linkage method whereby DNA within a cell is physically bound and then sequenced to link contigs within a metagenome that originated from the same cell. In a size-fractioned water sample from beneath the euphotic zone in a hypoxic estuarine fjord in Puget Sound, WA we resolved 49 proximity-linked bins above 50% complete, including 21 Hi-C Assembled Genomes (HAGs) over 90% complete and a nearly complete genome of the eukaryotic green alga Picochlorum. Viral and microbial sequence within the same HAG identified 18 virus-microbe interactions. A myovirus and a siphovirus were associated with 2 different genera within the Saltatorellus clade of Planctomycetes, a phylum for which no virus has been identified. A partial Phycodnaviridae genome linked to Haptophyte sequence is consistent with contemporaneous observations of a dissipating coccolithophore bloom. A cyanophage S-CAM7-like sequence had a broad interaction range. It was associated with a partial Synechococcus genome in the >3.0 {micro}m size fraction and with a Gammaproteobacteria related to Alcanivorax in the 0.2{micro}m-3.0{micro}m fraction. We suggest that viruses produced in surface waters that are shuttled to depth on sinking aggregates may interact with different hosts in deeper waters, providing an important avenue for gene transfer across broad taxonomic ranges. ImportanceAquatic microbes are important in global elemental cycling. Knowing which viruses infect them in the environment remains a challenge. Using Hi-C, a molecular technique to physically link DNA within a cell, we assembled nearly complete genomes of both prokaryotes and eukaryotes from a hypoxic estuary. Hi-C links captured virus-host interactions for known virus-host pairs and for hosts with no previously known viruses. The same virus was linked to two distinct microbes in different size fractions of water, suggesting it has a broad host range. Viral lysis in surface waters generates sinking particles that deliver newly produced viruses to deeper waters where they interact with different potential hosts, providing an opportunity for gene exchange between unrelated microbes.

microbiology↗