Biology and Ecology of Abundant Protists Lab
Our goal is to isolate, culture and subsequently characterize the cell biology, behavior and ecosystem relevance of the most abundant unknown protists on earth. Protists are single-celled and colonial microbial eukaryotes which, due to their size (generally between a few micrometers and a few hundred micrometers) are a critical part of the food webs in all of earth's principal ecosystems. In addition, protists form the backbone of the eukaryotic tree of life, meaning that studies of protists inform our understanding of the evolution of eukaryotic cell biology, gene content and species diversity. Our work currently consists of four related projects:
1. Biology of Globally Abundant Protists: we aim to isolate and culture the most abundant, and as yet unknown, protists on earth. Once in culture, we will characterize their cell biology, ultrastructure, life history, behavior and interspecies interactions using time-lapse and fluorescence microscopy techniques, accompanied by single-cell sequencing. In this process, we hope to establish these protists as new model systems whose biology and ecosystem relevance can be studied intensively in the lab.
2. Global Gene Expression of Abundant Protists: we begin with hypotheses, based on our lab studies, regarding the potential ecological roles of the abundant protists we study. Armed with the their gene catalogs from genome and transcriptome sequencing, we apply the bioinformatic methods we developed to investigate the patterns in their gene expression in global-scale metatranscriptomic sequencing databases. As examples, these hypotheses may relate to their ecological roles, in terms of species interactions, or their responses to changes in environmental conditions.
3. Eukaryotic Gene Family and Protein Domain Evolution: we develop new computational methods to study the genes and genomes of diverse eukaryotes in order to reconstruct the evolutionary history of gene families, protein domains and the biological processes they drive.
In addition, because only a tiny fraction of protist species are available in culture, we anticipate that the sequence resources we generate for newly isolated protists will be informative for studies of eukaryotic diversity and the evolution of gene content and function.
4. Resources for the Protist Research Community and Beyond: as we work, we design the output of our research projects to be reusable. We make our data, code and wet lab protocols available to the research community. We also lead or participate in projects to collect and organize eukaryotic sequence data and taxonomy, in order to standardize and streamline their use for all researchers.
Web page: https://www.beaplab.org
Zavadska D, Henry N, Auladell A, Berney C, Richter DJ. 2024. Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes. PLoS One, 19(6):e0303697. DOI:10.1371/journal.pone.0303697
Richards TA, Eme L, Archibald JM, Leonard G, Coelho SM, de Mendoza A, Dessimoz C, Dolezal P, Fritz-Laylin LK, Gabaldón T, Hampl V, Kops GJPL, Leger MM, Lopez-Garcia P, McInerney JO, Moreira D, Muñoz-Gómez SA, Richter DJ, Ruiz-Trillo I, Santoro AE, Sebé-Pedrós A, Snel B, Stairs CW, Tromer EC, van Hooff JJE, Wickstead B, Williams TA, Roger AJ, Dacks JB, Wideman JG. 2024. Reconstructing the last common ancestor of all eukaryotes. PLOS Biology, 22(11):e3002917. DOI:10.1371/journal.pbio.3002917
Juéry C, Auladell A, Füssy Z, Chevalier F, Yee DP, Pelletier E, Corre E, Allen AE, Richter DJ, Decelle J. 2024. Transportome remodeling of a symbiotic microalga inside a planktonic host. The ISME Journal, (March):1-18. DOI:10.1093/ismejo/wrae239
Hake KH, West PT, McDonald K, Laundon D, Reyes-Rivera J, Garcia De Las Bayonas A, Feng C, Burkhardt P, Richter DJ, Banfield JF, King N. 2024. A large colonial choanoflagellate from Mono Lake harbors live bacteria. mBio, 1-11 . DOI:10.1128/mbio.01623-24
Gàlvez-Morante A, Guéguen L, Natsidis P, Telford MJ, Richter DJ. 2024. Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions. Genome Biology and Evolution, 16(4). DOI:10.1093/gbe/evae062
Mitsi K, Richter DJ, Arroyo AS, López-Escardó D, Antó M, Oterino AG, Ruiz-Trillo I. 2023. Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding. Scientific Reports, 13(1):3119. DOI:10.1038/s41598-023-30228-4
Del Campo J, Carlos-Oliveira M, Čepička I, Hehenberger E, Horák A, Karnkowska A, Kolisko M, Lara E, Lukeš J, Pánek T, Piwosz K, Richter DJ, Škaloud P, Sutak R, Tachezy J, Hampl V. 2023. The protist cultural renaissance. Trends in Microbiology. DOI:10.1016/j.tim.2023.11.010
Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernàndez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S; Tara Oceans Coordinators, Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcalà M, Iudicone D, Jaillon O. 2022. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife, 11:1-30. DOI:10.7554/eLife.78129
Richter DJ, Levin TC. 2019. The origin and evolution of cell-intrinsic antibacterial defenses in eukaryotes. Current Opinion in Genetics and Development, 58-59:111-122. DOI:10.1016/j.gde.2019.09.002
Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, Del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q. 2019. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology, 66(1):4-119. DOI: 10.1111/jeu.12691