Applications & Publications
Publications
Phloxine B Staining is Compatible With High-Throughput DNA Barcoding of Meiofauna
Gielings et al. April 30, 2026 Ecol Evol. 2026 Apr 30;16:e73597. doi: 10.1002/ece3.73597
View AbstractPhloxine B Staining is Compatible With High-Throughput DNA Barcoding of Meiofauna
Modern, integrative biodiversity research requires methods capable of bridging the gap between detailed morphological observations and the scalability of DNA sequencing. Integrative approaches like megabarcoding generate DNA sequences, while morphological functional data and abundance data are retained. For small, transparent, and highly abundant animals like meiofauna, the necessity to sort the specimens from organic matter and sediment forms a major bottleneck, as the use of stains required for enhanced manual or automated specimen detection can inhibit downstream molecular workflows. To address this, we tested the compatibility of phloxine B staining with DNA sequencing to facilitate simultaneous morphological and molecular specimen processing. Meiofauna preserved in ethanol, propylene glycol, or a DMSO/EDTA/saturated NaCl solution (DESS) was incubated with phloxine B for 30 min or 24 h. Specimens were manually isolated, the V1-V2 region of the 18S rDNA gene was sequenced, and success was quantified across major meiofaunal phyla. Nematodes, copepods, and annelids consistently showed high sequencing success irrespective of the preservative or staining incubation time. Platyhelminths showed lower success, likely due to misidentification or primer limitations rather than dye inhibition. Overall, these findings demonstrate that phloxine B is compatible with downstream DNA amplification and sequencing, enabling efficient integration of morphological and molecular data. The approach offers high potential for broader application in other microscopic taxa, supporting the way to comprehensive, high-throughput biodiversity assessments or ecological monitoring.
Terry O'Connor on LinkedIn: #embltrec.
August 31, 2023 O’Connor, T. (2023, August 31). Terry O'Connor on LinkedIn: #embltrec. Retrieved September 15, 2023, from https://www.linkedin.com/posts/terry-o-connor-169b8528_embltrec-activity-7102944826588811264-UUlR?utm_source=share&utm_medium=member_android
Terry O'Connor on LinkedIn: #embltrec.
Science on the road: A high-tech tour of EMBL’s Advanced Mobile Laboratory
August 25, 2023 European Molecular Biology Laboratory (EMBL). (2023, August 25). Science on the road: A high-tech tour of EMBL’s Advanced Mobile Laboratory [Video]. YouTube. https://www.youtube.com/watch?v=tSgRkyx-9wM
Science on the road: A high-tech tour of EMBL’s Advanced Mobile Laboratory
Heidelberg/Kristineberg: A High-Tech-Truck on a Research Mission in Sweden.
August 11, 2023 Heidelberg/Kristineberg: A High-Tech-Truck on a Research Mission in Sweden. (2023, August 11). (n.d.). [Video]. RNF.de. https://www.rnf.de/mediathek/video/heidelberg-kristineberg-a-high-tech-truck-on-a-research-mission-in-sweden/
Heidelberg/Kristineberg: A High-Tech-Truck on a Research Mission in Sweden.
Bringing advanced life science technologies to the field
Ghosh, S. August 03, 2023 Ghosh, S. (2023, August 3). Bringing advanced life science technologies to the field | EMBL. EMBL. https://www.embl.org/news/lab-matters/bringing-advanced-life-science-technologies-to-the-field/
Bringing advanced life science technologies to the field
Rapid counting and spectral sorting of live coral larvae using large-particle flow cytometry
Randall et al. July 31, 2020 NATURE Scientific Reports | (2020) 10:12919 | https://doi.org/10.1038/s41598-020-69491-0
Rapid counting and spectral sorting of live coral larvae using large-particle flow cytometry
Characterization of Morphological and Cellular Events Underlying Oral Regeneration in the Sea Anemone, Nematostella vectensis
Amiel et al. December 01, 2015 Int J Mol Sci. 2015 Dec; 16(12): 28449–28471. Published online 2015 Dec 1. doi: 10.3390/ijms161226100
Characterization of Morphological and Cellular Events Underlying Oral Regeneration in the Sea Anemone, Nematostella vectensis
FISH-CS—a rapid method for counting and sorting species of marine zooplankton
Christine M. Henzler¹, ²*, Elizabeth A. Hoaglund¹, ², Steven D. Gaines ¹, ², ³ January 01, 2010 MARINE ECOLOGY PROGRESS SERIES, Vol. 410: 1–11, 2010 1) Marine Science Institute, and 2) Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA 3) Present address: Bren School of Environmental Resource Management, University of California Santa Barbara, Santa Barbara, California 93106, USA
View AbstractFISH-CS—a rapid method for counting and sorting species of marine zooplankton
Understanding population dynamics in marine species has long been hindered by the inherent difficulties of studying species in which all or part of the life cycle is planktonic. Plankton sample processing is laborious and, due to morphological similarity between disparate taxa, often identifies zooplankton only to higher taxonomic levels. As a consequence, many scientific issues that require identification to species level are impossible to explore adequately. Several in situ hybridization protocols show promise for identifying marine larvae by color-coding them with taxon-specific, dye-labeled DNA probes. We adapted these protocols and coupled them with recent cell sorting technology to rapidly and accurately identify bivalve larvae from diverse plankton samples. We developed probes for 2 bivalve taxa: Musculista senhousia and the species complex Mytilus edulis/galloprovincialis/trossulus. Coupled fluorescence in situ hybridization and cell sorting (FISH-CS) separated M. galloprovincialis larvae from both oyster Crassostrea gigas larvae and from a mixed plankton/M. galloprovincialis sample. The number of false positives and false negatives was assessed by a PCR assay. Our FISH-CS method is robust to plankton autofluorescence and can be easily adapted to work with nearly any planktonic species or life stage of appropriate size.
Rapid Identification and Sorting of Marine Larvae
8th Larval Biology Symposium, July 6-11, 2008
Elizabeth A. Hoaglund1, Christine M. Herzler2, Gretcvhen E. Hofmann1, and Steven D. Gaines1, 2.
July 06, 2008
Rapid Identification and Sorting of Marine Larvae
1) Dept. of Ecology, Evolution and Marine Biology, U. of California, Santa Barbara, CA, USA, 2) Marine Science Institute, U. of California, Santa Barbara, CA, USA. Corresponding author email: hoaglund@lifesci.ucsb.edu