Research

My research bridges molecular biology, engineering, and ecology to explore Earth's most challenging marine environments. Through highly collaborative, interdisciplinary research, I combine environmental DNA (eDNA) with RADseq and RNA sequencing to unravel the complex stories of deep-sea ecosystems.

Oceaneering ROV Global Explorer

Cryptic Biodiversity of Mesophotic Reefs

Mesophotic coral reefs (30-150 meters deep) remain largely understudied due to sampling challenges. This "twilight zone" hosts rich communities of cryptobenthic invertebrates that traditional methods fail to capture: scuba diving has limited bottom time, while ROV video cannot detect small organisms hidden within reef structures.

My Ph.D. research pioneers the first-ever Autonomous Reef Monitoring Structures (ARMS) deployment and recovery at mesophotic depths. Working within the Flower Garden Banks National Marine Sanctuary, I integrate these collection devices with environmental DNA (eDNA) metabarcoding to detect species too small, cryptic, or mobile for visual surveys. This approach has documented numerous taxa in the sanctuary for the first time and revealed potentially undescribed species, highlighting the unexplored diversity of these ecosystems. Results from this work also illuminate the environmental drivers of community assembly and the connectivity of patchy reef mosaics.

By expanding the reference barcode database for mesophotic taxa, this NOAA-funded research, conducted in collaboration with the Smithsonian Institution's National Museum of Natural History, enhances our understanding of biodiversity patterns in these vulnerable ecosystems while providing critical data for conservation management.

Octocoral Population Genetics and Reproductive
Biology

As our understanding of mesophotic ecosystems in the Gulf has deepened, my research has evolved to combine multiple molecular approaches, including eDNA, population genomics, and transcriptomics, to examine connectivity and reproductive biology of deep-reef communities comprehensively. Using RADseq-based population genetic analyses, I investigated how Swiftia exserta populations are structured across the Northwestern Gulf of Mexico. This cross-disciplinary work, conducted in collaboration with physical oceanographers, integrates genomic data with oceanographic modeling to reveal how ocean currents create connectivity corridors between seemingly isolated mesophotic habitats.

Complementing this landscape-scale genomic approach, I employ RNA sequencing (long read Iso-Seq) to explore the physiological mechanisms underlying octocoral reproduction. This gene expression analysis helps identify molecular markers for sex determination and reproductive timing in mesophotic octocorals - fundamental processes that remain poorly understood in deep-sea environments. By characterizing these genetic pathways, I aim to develop novel molecular markers that can quickly detect reproductive state and population health.

This multi-omics research framework bridges scales from eDNA detection of communities to individual-level genomic and transcriptomic profiles, providing unprecedented insights into mesophotic coral reef ecology. By integrating these complementary molecular techniques, we can more accurately assess connectivity patterns, population dynamics, and vulnerability to anthropogenic disturbances, ultimately informing science-based management strategies.

WHOI/MISO/NDSF HOV Alvin

Applying eDNA to Hydrothermal Ecosytems

During my first research expedition, we discovered an active off-axis hydrothermal vent field 750m east of the East Pacific Rise Axis at 9º 50'N. This site likely avoided lava flows from the 2005-2006 eruption, potentially serving as a critical larval source for recovering on-axis vents.

My research in this system has applied innovative eDNA approaches to characterize hydrothermal vent biodiversity, where traditional exploration methods are limited by cost and accessibility. I am developing new genetic barcode markers specifically optimized for hydrothermal vent fauna that can detect the presence of vent ecosystems from water samples alone. This eDNA toolkit enables biodiversity monitoring without requiring expensive ROV deployments, democratizing deep-sea exploration and expanding our capacity to discover new vent systems.

Through expeditions to the East Pacific Rise and Western Galápagos Spreading Center, I've deployed Autonomous Reef Monitoring Structures (ARMS) paired with eDNA metabarcoding protocols to test their efficacy in deep-sea environments. This novel integration of ARMS with eDNA represents the first application of this methodology at hydrothermal vents. I'm evaluating how this approach compares with and complements the established Mullineaux sandwich method in characterizing vent communities.

A key component of this work involves expanding the reference barcode library for hydrothermal vent fauna by systematically sampling across diverse benthic habitats. This comprehensive genetic catalog will significantly enhance our ability to interpret eDNA signals from deep-sea environments, enabling rapid biodiversity assessment and ecosystem monitoring in these remote and fragile ecosystems.

Publications

Google Scholar

Peer-Reviewed:

Maloney, R. T.,Ye A. Q., Saint Pre, S-K., Alisch, T., Zimmerman, D.M., Pittoors, N.C., and de Bivort, B.L. 2024. Drift in Individual Behavioral Phenotype as a Strategy for Unpredictable Worlds. eLife. DOI:https://doi.org/10.7554/eLife.103585.

McCartin, L.J., Saso, E., Vohsen, S., Pittoors, N.C., Demetriades, P., McFadden, C., Quattrini, A., and Herrera, S. Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment. 2024. PeerJ ; DOI:https://doi.org/10.7717/peerj.18607.

Herrera, S., Chadwick, W.W., Jackson, M.G., Konter, J., McCartin, L., Pittoors, N., Bushta, E., Merle, S.G. 2023. From basalt to biosphere: Early non-vent community succession on the erupting Vailulu'u deep seamount. Frontiers in Marine Science. 10. DOI: https://doi.org/10.3389/fmars.2023.1110062.

McDermort, J.M., Parnell-Turner, R., Barreyre, T., Herrera, S., Downing, C., Pittoors, N.C., Pehr, K., Vohsen, S.A., Dowd, W.S., Wu, J., Marjanoic, M., Fornari, D. 2022. Discovery of active off-axis vents at 9º 54’N East Pacific Rise. Proceedings of the National Academy of Sciences. 119. DOI: 10.1073/pnas.2205602119.

Maciejewski, M.F., Meyer, K.S., Wheeler, J.D., Anderson, E.J., Pittoors, N.C., Mullineaux, L.S. 2019. Helical swimming as an exploratory behavior in competent larvae of the eastern oyster larvae (Crassostrea virginica). Journal of Experimental Marine Biology and Ecology. 510: 86-94. DOI: 10.1016/j.jembe.2018.10.007.

In Preparation:

McCartin, L.J., Vohsen, S.A., Wood, A. L., Horowitz, J., Oroszco-Juarbe, J.J., Pittoors, N.C., Morrissey, D.,Vaga, C.F., Hansel, C.M., Collins, A.G., Quattrini, A.M., Herrera, S. Accounting for intra and intergenomic sequence variation in reference barcodes improves eDNA metabarcoding biodiversity assessment. Submitted for review in Molecular Ecology.

Pittoors, N.C., Tweedt, S.M., McCartin, L.J., Lopera-Garcia, L.F., Bracco, A., Vohsen, S.A., Durkin, K., Weigt, L., Meyer, C.P., Herrera, S. Benthic assessment of mesophotic reef banks uncovers hidden biodiversity and identifies environmental filtering as the primary driver of benthic community assembly. In preparation. Target Journal: PNAS, target submission date November 2025.

Pittoors, N.C., Lopera-Garcia, L.F., Bracco, A., Quattrini, A.M, Herrera, S. Population connectivity and evidence of clonal structure in the mesophotic octocoral Swiftia exserta. In preparation. Target Journal: Frontiers in Marine Science, target submission date December 2025.

FKt230812-Dive562MissionControl-20230819-Ingle-8291_edited.jpg

Alex Ingle, Schmidt Ocean Institute

Research Expeditions

2024 R/V Atlantis. HOV Alvin. AUV Sentry. AT50-21. Monitoring hydrothermal fluid origin, crustal permeability and seafloor morphology. Leg 3. East Pacific Rise 9º 50’N, Pacific Ocean. Starboard Observer on HOV Alvin dive AL5237, Port Observer on dive AL5241. 34 days.

2023 R/V Falkor (too). ROV SuBastian. FKt230812. Hydrothermal Vents of the Western Galapagos. Galapagos. 30 days. ROV Watch Leader.

2023 R/V Falkor (too). ROV SuBastian. FKt230417. Health Diagnostics of Deep-Sea Corals. Puerto Rico. 19 days.

2023 R/V Atlantis. HOV Alvin. AUV Sentry. AT50-07. Monitoring hydrothermal fluid origin, crustal permeability and seafloor morphology. Leg 2. East Pacific Rise 9º 50’N, Pacific Ocean. Starboard observer on HOV Alvin dive AL5147. 29 days.

2021 R/V Point Sur. ROV Global Explorer. ConnectivitY of CoraL Ecosystems (CYCLE). U.S. Gulf of Mexico. 13 Days.