Gabrielle Rocap
· OceanographyVerifiedUniversity of Washington · Program on the Environment
Active 1991–2026
About
Gabrielle Rocap is a biological oceanographer who studies the evolution and ecology of marine bacteria. She works in diverse environments—everywhere from Puget Sound to the South Atlantic Ocean—and uses physiological, molecular, and computational techniques to work with the different species of phytoplankton that drive the bulk of global primary production. She is also working to understand the role that viruses might play in the outbreak or suppression of toxic algal blooms. The questions at the root of her many projects are: How does genetic diversity arise in marine microbial populations? How is it maintained? And how does it influence ecological success?
Research topics
- Biology
- Ecology
- Computer Science
- Genetics
- Environmental chemistry
- Geology
- Botany
- Environmental science
- Oceanography
- Evolutionary biology
- Computational biology
- Chemistry
Selected publications
Environmental Microbiology · 2026-03-30
articleOpen accessSenior authorOxygen-deficient zones (ODZs) influence global nitrogen cycling as key sites for the removal of bioavailable nitrogen through denitrification and anammox. Despite their importance, many microbes and viruses in ODZs remain uncultivated, limiting our understanding of their ecological roles. This study employed Hi-C proximity linkages, combined with long and short read metagenomic sequencing to characterise active viral interactions in the prokaryotic community at a secondary chlorophyll maximum in the Eastern Tropical North Pacific ODZ. Among the identified 861 assembled viral contigs over 10 kb, 75 showed significant links to microbial genomes. Virus-host linkages indicated 19 novel virus-microbe pairs that were likely infectious, and which conventional in silico host prediction methods largely missed. The virus-host relationships involved nine distinct microbial phyla, with previously unrecorded viral infections of Planctomycetes, Chloroflexota, Alphaproteobacteria, Gammaproteobactera, Myxococcota and Verrucomicrobia. Most hosts carried the genomic potential for denitrification. Phylogenetic analysis of the terminase large subunit (terL) genes from linked viruses suggested that many active phages resemble known temperate phages, indicating that lysogeny may be an ecological strategy in ODZs. Our comprehensive metagenomic approach offers new insights into viral-host interactions in this ecosystem, highlighting the importance of including proximity methods in viral ecology studies of uncultivated microbial populations.
The Plant Journal · 2025-06-01 · 8 citations
articleOpen accessPlastids of diatoms and related algae with complex plastids of red algal origin are surrounded by four membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes. Metabolic reactions as well as cell biological processes take place in the PPC; however, genome-wide predictions of the proteins targeted to this compartment were so far based on manual annotation work. Using published experimental protein localizations as reference data, we developed the first automatic prediction method for PPC proteins, which we included as a new feature in an updated version of the plastid protein predictor ASAFind. With our method, at least a subset of the PPC proteins can be predicted with high specificity, with an estimate of at least 81 proteins (0.7% of the predicted proteome) targeted to the PPC in the model diatom Phaeodactylum tricornutum. The proportion of PPC proteins varies, since 180 PPC proteins (1.3% of the predicted proteome) were predicted in the genome of the diatom Thalassiosira pseudonana. The new ASAFind version can also generate a newly designed graphical output that visualizes the contribution of each position in the sequence to the score and accepts the output of the recent versions of SignalP (5.0) and TargetP (2.0) as input data. Furthermore, we release a script to calculate custom scoring matrices that can be used for predictions in a simplified score cut-off mode. This allows for adjustments of the method to other groups of algae.
bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-12
preprintOpen accessSenior authorOxygen 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.
Environmental Microbiology · 2025-08-01 · 2 citations
articleOpen accessSenior authorCorrespondingOxygen deficient zones (ODZs) are subsurface marine systems that harbour 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.
Cyanobacteria from marine oxygen deficient zones encode both form I and form II rubiscos
bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-07
preprintOpen accessAbstract 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 CO 2 -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-O 2 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.
Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos
Proceedings of the National Academy of Sciences · 2024-11-25 · 6 citations
articleOpen accessCyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all studied cyanobacterial lineages encode carbon fixation machinery relying upon form I Rubiscos within a CO 2 -concentrating carboxysome. Here, we report that the uncultivated anoxic marine zone (AMZ) IB lineage of Prochlorococcus from pelagic oxygen-deficient zones (ODZs) harbors both form I and form II Rubiscos, the latter of which are typically noncarboxysomal and possess biochemical properties tuned toward low-oxygen environments. We demonstrate that these cyanobacterial form II enzymes are functional in vitro and were likely acquired from proteobacteria. Metagenomic analysis reveals that AMZ IB are essentially restricted to ODZs in the Eastern Pacific, suggesting that form II acquisition may confer an advantage under low-O 2 conditions. AMZ IB populations express both forms of Rubisco in situ, with the highest form II expression at depths where oxygen and light are 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 carbon sequestration in natural and engineered systems.
arXiv (Cornell University) · 2023-03-04 · 2 citations
preprintOpen accessSenior authorCells of diatoms and related algae with complex plastids of red algal origin are highly compartmentalized. These plastids are surrounded by four envelope membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes. The PPC corresponds to the cytosol of the eukaryotic alga that was the ancestor of the complex plastid. Metabolic reactions as well as cell biological processes take place in this compartment; however, its exact function remains elusive. Automated predictions of protein locations proved useful for genome wide explorations of metabolism in the case of plastid proteins, but until now, no automated method for the prediction of PPC proteins was available. Here, we present an updated version of the plastid protein predictor ASAFind, which includes optional prediction of PPC proteins. The new ASAFind version also accepts the output of the most recent versions of SignalP (5.0) and TargetP (2.0) input data. Furthermore, we release a Python script to calculate custom scoring matrices for adjustment of the ASAFind method to other groups of algae, and included the option to run the predictions with custom scoring matrices in a simplified score cut-off mode.
bioRxiv (Cold Spring Harbor Laboratory) · 2023-12-06 · 1 citations
preprintOpen accessSenior authorCorrespondingAbstract 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 µm size fraction and with a Gammaproteobacteria related to Alcanivorax in the 0.2µm-3.0µm 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. Importance Aquatic 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.
arXiv (Cornell University) · 2023-03-04 · 4 citations
preprintOpen accessPlastid targeted proteins of diatoms and related algae can be predicted with\nhigh sensitivity and specificity using the ASAFind method published in 2015.\nASAFind predictions rely on SignalP predictions of endoplasmic reticulum (ER)\ntargeting signal peptides. Recently (in 2019), a new version of SignalP was\nreleased, SignalP 5.0. We tested the ability of SignalP 5.0 to recognize signal\npeptides of nucleus-encoded, plastid-targeted diatom pre-proteins, and to\nidentify the signal peptide cleavage site. The results were compared to manual\npredictions of the characteristic cleavage site motif, and to previous versions\nof SignalP. SignalP 5.0 is less sensitive than the previous versions of SignalP\nin this specific task, and also in the detection of signal peptides of\nnon-plastid proteins in diatoms. However, in combination with ASAFind, the\nresulting prediction performance for plastid proteins is high. In addition, we\ntested the multi-location prediction tool TargetP for its suitability to\nprovide signal peptide information to ASAFind. The newest version, TargetP 2.0,\nhad the highest prediction performances for diatom signal peptides and\nmitochondrial transit peptides compared to other versions of SignalP and\nTargetP, thus it provides a good basis for ASAFind predictions.\n
Matters · 2023 · 2 citations
- Computer Science
- Biology
- Computational biology
Plastid targeted proteins of diatoms and related algae can be predicted with high sensitivity and specificity using the ASAFind method published in 2015. ASAFind predictions rely on SignalP predictions of endoplasmic reticulum (ER) targeting signal peptides. Recently (in 2019), a new version of SignalP was released, SignalP 5.0. We tested the ability of SignalP 5.0 to recognize signal peptides of nucleus-encoded, plastid-targeted diatom pre-proteins, and to identify the signal peptide cleavage site. The results were compared to manual predictions of the characteristic cleavage site motif, and to previous versions of SignalP. SignalP 5.0 is less sensitive than the previous versions of SignalP in this specific task, and also in the detection of signal peptides of non-plastid proteins in diatoms. However, in combination with ASAFind, the resulting prediction performance for plastid proteins is high. In addition, we tested the multi-location prediction tool TargetP for its suitability to provide signal peptide information to ASAFind. The newest version, TargetP 2.0, had the highest prediction performances for diatom signal peptides and mitochondrial transit peptides compared to other versions of SignalP and TargetP, thus it provides a good basis for ASAFind predictions.
Recent grants
NSF · $2.0M · 2015–2021
NSF · $597k · 2007–2011
Microbial Genome Sequencing: Stramenopile Genomics: Comparative Chloroplast Sequencing
NSF · $360k · 2005–2008
NSF · $173k · 2004–2007
NSF · $321k · 2005–2009
Frequent coauthors
- 16 shared
Clara A. Fuchsman
University of Maryland Center for Environmental Science
- 15 shared
Sallie W. Chisholm
Massachusetts Institute of Technology
- 14 shared
Lisa R. Moore
Menlo School
- 13 shared
Nathan A. Ahlgren
Clark University
- 11 shared
Cedar McKay
University of Washington
- 10 shared
Miroslav Obornı́k
Czech Academy of Sciences, Biology Centre
- 10 shared
Ansgar Gruber
- 9 shared
K. Roache-Johnson
Heart Imaging Technologies (United States)
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