Bio

I am a Staff Scientist at the Stanford Center for Ocean Solutions. My research focuses on optimizing molecular and computational tools to address ecological and evolutionary questions. I have published in the areas of environmental change, ocean health, biodiversity, disease, eDNA, -omics, and aquaculture. I hold a B.S. in Biology from the University of Georgia, began my doctoral studies at the University of California, Merced, and earned my Ph.D. at Penn State. I completed two postdoctoral appointments, first as a joint-postdoctoral researcher at University of Washington's School of Aquatic and Fishery Sciences and University of Maryland's Institute for Marine and Environmental Technology. Second, I completed advanced collaborative training as a postdoctoral scholar at Stanford University’s Woods Institute for the Environment in conjunction with the Department of Civil and Environmental Engineering. I enjoy exploring and teaching about the natural world, its diversity, complexities, and the challenges faced by our environment.

Academic Appointments

Professional Education

  • B.S., University of Georgia, Athens, Biology (2005)
  • Ph.D., The Pennsylvania State University, University Park, Biology (2014)

Contact

  • Academic
    closek@stanford.edu
    University - Academic staff Department: Center for Ocean Solutions Position: Basic Life Scientist

Additional Info

  • Mail Code: 4205

Links

All Publications

  • Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nature communications Djurhuus, A., Closek, C. J., Kelly, R. P., Pitz, K. J., Michisaki, R. P., Starks, H. A., Walz, K. R., Andruszkiewicz, E. A., Olesin, E., Hubbard, K., Montes, E., Otis, D., Muller-Karger, F. E., Chavez, F. P., Boehm, A. B., Breitbart, M. 2020; 11 (1): 254

    Abstract

    Environmental DNA (eDNA) analysis allowsthe simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015-2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence of expected predator-prey relationships, trophic linkages, and seasonal shifts across all domains of life. We conclude that eDNA-based analyses can provide detailed information about marine ecosystem dynamics and identify sensitive biological indicators that can suggest ecosystem changes and inform conservation strategies.

    View details for DOI 10.1038/s41467-019-14105-1

    View details for PubMedID 31937756

  • Quantitative PCR assays to detect whales, rockfish, and common murre environmental DNA in marine water samples of the Northeastern Pacific. PloS one Andruszkiewicz, E. A., Yamahara, K. M., Closek, C. J., Boehm, A. B. 2020; 15 (12): e0242689

    Abstract

    Monitoring aquatic species by identification of environmental DNA (eDNA) is becoming more common. To obtain quantitative eDNA datasets for individual species, organism-specific quantitative PCR (qPCR) assays are required. Here, we present detailed methodology of qPCR assay design and testing, including in silico, in vitro, and in vivo testing, and comment on the challenges associated with assay design and performance. We use the presented methodology to design assays for three important marine organisms common in the California Current Ecosystem (CCE): humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge). All three assays have excellent sensitivity and high efficiencies ranging from 92% to 99%. However, specificities of the assays varied from species-specific in the case of common murre, genus-specific for the shortbelly rockfish assay, and broadly whale-specific for the humpback whale assay, which cross-amplified with other two other whale species, including one in a different family. All assays detected their associated targets in complex environmental water samples.

    View details for DOI 10.1371/journal.pone.0242689

    View details for PubMedID 33264323

  • Marine Vertebrate Biodiversity and Distribution Within the Central California Current Using Environmental DNA (eDNA) Metabarcoding and Ecosystem Surveys FRONTIERS IN MARINE SCIENCE Closek, C. J., Santora, J. A., Starks, H. A., Schroeder, I. D., Andruszkiewicz, E. A., Sakuma, K. M., Bograd, S. J., Hazenv, E. L., Field, J. C., Boehm, A. B. 2019; 6

    View details for DOI 10.3389/fmars.2019.00732

    View details for Web of Science ID 000502974200001

  • Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding. Ecology and evolution Sawaya, N. A., Djurhuus, A., Closek, C. J., Hepner, M., Olesin, E., Visser, L., Kelble, C., Hubbard, K., Breitbart, M. 2019; 9 (3): 1029–40

    Abstract

    Environmental DNA (eDNA) is the DNA suspended in the environment (e.g., water column), which includes cells, gametes, and other material derived from but not limited to shedding of tissue, scales, mucus, and fecal matter. Amplifying and sequencing marker genes (i.e., metabarcoding) from eDNA can reveal the wide range of taxa present in an ecosystem through analysis of a single water sample. Metabarcoding of eDNA provides higher resolution data than visual surveys, aiding in assessments of ecosystem health. This study conducted eDNA metabarcoding of two molecular markers (cytochrome c oxidase I (COI) and 18S ribosomal RNA (rRNA) genes) to survey eukaryotic diversity across multiple trophic levels in surface water samples collected at three sites along the coral reef tract within the Florida Keys National Marine Sanctuary (FKNMS) during four research cruises in 2015. The 18S rRNA gene sequences recovered 785 genera while the COI gene sequences recovered 115 genera, with only 33 genera shared between the two datasets, emphasizing the complementarity of these marker genes. Community composition for both genetic markers clustered by month of sample collection, suggesting that temporal variation has a larger effect on biodiversity than spatial variability in the FKNMS surface waters. Sequences from both marker genes were dominated by copepods, but each marker recovered distinct phytoplankton groups, with 18S rRNA gene sequences dominated by dinoflagellates and COI sequences dominated by coccolithophores. Although eDNA samples were collected from surface waters, many benthic species such as sponges, crustaceans, and corals were identified. These results show the utility of eDNA metabarcoding for cataloging biodiversity to establish an ecosystem baseline against which future samples can be compared in order to monitor community changes.

    View details for PubMedID 30805138

  • Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host MOLECULAR ECOLOGY Hartmann, A. C., Marhaver, K. L., Klueter, A., Lovci, M. T., Closek, C. J., Diaz, E., Chamberland, V. F., Archer, F. I., Deheyn, D. D., Vermeij, M. A., Medina, M. 2019; 28 (1): 141–55

    Abstract

    Theory suggests that the direct transmission of beneficial endosymbionts (mutualists) from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile's ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae) during the planktonic larval stage was advantageous, as is widely assumed, in the ecologically important and threatened Caribbean reef-building coral Orbicella faveolata. Following larval acquisition, similar changes occurred in host energetic lipid use and gene expression regardless of whether their symbionts were photosynthesizing, suggesting the symbionts did not provide the energetic benefit characteristic of the mutualism in adults. Larvae that acquired photosymbionts isolated from conspecific adults on their natal reef exhibited a reduction in swimming, which may interfere with their ability to find suitable settlement substrate, and also a decrease in survival. Larvae exposed to two cultured algal species did not exhibit differences in survival, but decreased their swimming activity in response to one species. We conclude that acquiring photosymbionts during the larval stage confers no advantages and can in fact be disadvantageous to this coral host. The timing of symbiont acquisition appears to be a critical component of a host's life history strategy and overall reproductive fitness, and this timing itself appears to be under selective pressure.

    View details for DOI 10.1111/mec.14967

    View details for Web of Science ID 000456604600011

    View details for PubMedID 30506836

  • Evaluation of filtration and DNA extraction methods for environmental DNA biodiversity assessments across multiple trophic levels FRONTIERS IN MARINE SCIENCE Djurhuus, A., Port, J., Closek, C. J., Yamahara, K. M., Romero-Maraccini, O., Walz, K. R., Goldsmith, D. B., Michisaki, R., Boehm, A. B., Breitbart, M., Chavez, F. P. 2017: 314

    View details for DOI 10.3389/fmars.2017.00314

  • Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem FRONTIERS IN MARINE SCIENCE Kelly, R. P., Closek, C. J., O'Donnell, J. L., Kralj, J. E., Andrew, S. O., Samhouri, J. F. 2017; 3: 283

    View details for DOI 10.3389/fmars.2016.00283

  • The Use of Filter-feeders to Manage Disease in a Changing World INTEGRATIVE AND COMPARATIVE BIOLOGY Burge, C. A., Closek, C. J., Friedman, C. S., Groner, M. L., Jenkins, C. M., Shore-Maggiok, A., Welsh, J. E. 2016; 56 (4): 573-587

    View details for DOI 10.1093/icb/icw048

    View details for Web of Science ID 000384303700009

  • Up in Arms: Immune and Nervous System Response to Sea Star Wasting Disease PLOS ONE Fuess, L. E., Eisenlord, M. E., Closek, C. J., Tracy, A. M., Mauntz, R., Gignoux-Wolfsohn, S., Moritsch, M. M., Yoshioka, R., Burge, C. A., Harvell, C. D., Friedman, C. S., Hewson, I., Hershberger, P. K., Roberts, S. B. 2015; 10 (7)

    Abstract

    Echinoderms, positioned taxonomically at the base of deuterostomes, provide an important system for the study of the evolution of the immune system. However, there is little known about the cellular components and genes associated with echinoderm immunity. The 2013-2014 sea star wasting disease outbreak is an emergent, rapidly spreading disease, which has led to large population declines of asteroids in the North American Pacific. While evidence suggests that the signs of this disease, twisting arms and lesions, may be attributed to a viral infection, the host response to infection is still poorly understood. In order to examine transcriptional responses of the sea star Pycnopodia helianthoides to sea star wasting disease, we injected a viral sized fraction (0.2 μm) homogenate prepared from symptomatic P. helianthoides into apparently healthy stars. Nine days following injection, when all stars were displaying signs of the disease, specimens were sacrificed and coelomocytes were extracted for RNA-seq analyses. A number of immune genes, including those involved in Toll signaling pathways, complement cascade, melanization response, and arachidonic acid metabolism, were differentially expressed. Furthermore, genes involved in nervous system processes and tissue remodeling were also differentially expressed, pointing to transcriptional changes underlying the signs of sea star wasting disease. The genomic resources presented here not only increase understanding of host response to sea star wasting disease, but also provide greater insight into the mechanisms underlying immune function in echinoderms.

    View details for DOI 10.1371/journal.pone.0133053

    View details for Web of Science ID 000358197600205

    View details for PubMedID 26176852

    View details for PubMedCentralID PMC4503460

  • Microbes in the coral holobiont: partners through evolution, development, and ecological interactions FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY Thompson, J. R., Rivera, H. E., Closek, C. J., Medina, M. 2015; 4

    View details for DOI 10.3389/fcimb.2014.00176

    View details for Web of Science ID 000349155400001

  • Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata ISME JOURNAL Closek, C. J., Sunagawa, S., Desalvo, M. K., Piceno, Y. M., DeSantis, T. Z., Brodie, E. L., Weber, M. X., Voolstra, C. R., Andersen, G. L., Medina, M. 2014; 8 (12): 2411-2422

    Abstract

    Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD.

    View details for DOI 10.1038/ismej.2014.85

    View details for Web of Science ID 000345498200007

    View details for PubMedID 24950107

    View details for PubMedCentralID PMC4260706