Technology development to understand microbial diversity and function in the oceans and other ecosystems.

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Microbial diversity in the oceans and other aquatic ecosystems is vast and drives numerous important ecosystem functions and biogeochemical cycles. We hold a long-term interest in understanding the diversity of eukaryotic microbes in aquatic ecosystems and how that diversity fits onto the tree of life. Our work in this area involves developing single cell sampling technologies and new methods to understand microbial diversity and function such as methods to recover deep-sea RNA profiles.

Examples of our work in this area:

  • Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung CM, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR, Mende DR, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W, Worden AZ. 2019. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proceedings of the National Academy of Sciences 116:20574-20583. https://doi.org/10.1073/pnas.1907517116
  • Rodríguez-Martínez R, Leonard G, Milner DS, Sudek S, Conway M, Moore K, Hudson T, Mahé F, Keeling PJ, Santoro AE, Worden AZ, Richards TA. 2020. Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink. The ISME journal 14:984-998. https://doi.org/10.1038/s41396-019-0581-y
  • Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richards TA. 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology 19:21-31. https://doi.org/10.1111/j.1365-294X.2009.04480.x
  • Wideman JG, Monier A, Rodríguez-Martínez R, Leonard G, Cook E, Poirier C, Maguire F, Milner DS, Irwin NA, Moore K, Santoro AE, Keeling PJ, Worden AZ, Richards TA. 2020. Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists. Nature Microbiology 5:154-165. https://doi.org/10.1038/s41564-019-0605-4
  • Záhonová K, Lax G, Sinha SD, Leonard G, Richards TA, Lukeš J, Wideman JG. 2021. Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans. BMC Biology 19:103. https://doi.org/10.1186/s12915-021-01035-y

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