Applications & Publications
Technical Notes
Analysis and Sorting of Zooplankton (QTN-008)
Automated Sorting and Quantification of Different Zooplankton Species Compared to Microscopic Analysis (QTN008)
Publications
Mitochondrial Genome Reduction and Accelerated Evolution in Planktonic Foraminiferans
Lai et al. July 30, 2026 Microbiologyopen. 2026 Jul 30;15(4):e70368. doi: 10.1002/mbo3.70368
View AbstractMitochondrial Genome Reduction and Accelerated Evolution in Planktonic Foraminiferans
The evolution of mitochondria provides crucial insights into the diversification of eukaryotes, with complex events of gene losses revealed through comparative analyses of mitochondrial genomes (mitogenomes) across eukaryotic lineages. However, the mitogenomes of many microbial eukaryotes remain underexplored due to challenges in their isolation and cultivation. Particularly understudied are Foraminifera (Rhizaria, SAR), unicellular calcifiers that are widely distributed across global oceans and important paleoenvironmental proxies. Using single-cell genomic sequencing, we report a 22-kb mitogenome from a planktonic foraminiferan in tropical seawater, the smallest known to date among sequenced mitogenomes of Rhizaria, a major lineage of eukaryotes. It contains only six protein-coding genes (including reduced versions of nad1 and cox2) and fragmented ribosomal RNA genes, and has lost most genes in oxidative phosphorylation and all genes encoding mitochondrial ribosomal proteins. Such genome reduction is associated with accelerated evolutionary rates and a lower GC content than that of benthic foraminiferan and other rhizarian mitogenomes. These findings highlight a unique trajectory of mitogenome reduction during rhizarian evolution and the use of single-cell approaches to recover microbial eukaryotic genomes and expand our understanding of mitochondrial evolution.
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.