JBPC Publications 2024

Arkhipova, I., Burns, K., & Lesage, P. (2024). Controlling and controlled elements: Highlights of the year in mobile DNA research. Mobile DNA, 15(1). https://doi.org/10.1186/s13100-024-00340-x

Arrington, E., Tarn, J., Kivenson, V., Nunn, B., Liu, R., Paul, B., & Valentine, D. (2024). Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus. The ISME Journal: Multidisciplinary Journal of Microbial Ecology, wrae247. https://doi.org/10.1093/ismejo/wrae247

Attenborough, T., Rawlinson, K. A., Diaz Soria, C. L., Ambridge, K., Sankaranarayanan, G., Graham, J., Cotton, J. A., Doyle, S. R., Rinaldi, G., & Berriman, M. (2024a). A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture. eLife, 13, RP95628. https://doi.org/10.7554/eLife.95628

Attenborough, T., Rawlinson, K., Diaz Soria, C., Ambridge, K., Sankaranarayanan, G., Graham, J., Cotton, J., Doyle, S., Rinaldi, G., & Berriman, M. (2024b). A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture. eLife, 13. https://doi.org/10.7554/elife.95628.3

Brock, M. T., Morrison, H. G., Maignien, L., & Weinig, C. (2024). Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities. FEMS Microbiology Letters, fnae044. https://doi.org/10.1093/femsle/fnae044

Chimileski, S., Borisy, G. G., Dewhirst, F. E., & Mark Welch, J. L. (2024). Tip extension and simultaneous multiple fission in a filamentous bacterium. Proceedings of the National Academy of Sciences, 121(37), e2408654121. https://doi.org/10.1073/pnas.2408654121

Comstock, J., Henderson, L. C., Close, H. G., Liu, S., Vergin, K., Worden, A. Z., Wittmers, F., Halewood, E., Giovannoni, S., & Carlson, C. A. (2024). Marine particle size-fractionation indicates organic matter is processed by differing microbial communities on depth-specific particles. ISME Communications, ycae090. https://doi.org/10.1093/ismeco/ycae090

De Niz, M., Escobedo García, R., Terán Ramirez, C., Pakowski, Y., Abonza, Y., Bialy, N., Orr, V. L., Olivera, A., Abonza, V., Alleva, K., Allodi, S., Almeida, M. F., Becerril Cuevas, A. R., Bonnet, F., Burgos Solorio, A., Chew, T.-L., Chiabrando, G., Cimini, B., Cleret-Buhot, A., Kumar, A., … Guerrero, A. (2024). Building momentum through networks: Bioimaging across the Americas. Journal of Microscopy, 294(3), 420–439. https://doi.org/10.1111/jmi.13318

de Palma, T., Powers, C., Mcpartland, M., Welch, J., & Ramsey, M. (2024). Essential genes for Haemophilus parainfluenzae survival and biofilm growth. mSystems, 9(9). https://doi.org/10.1128/msystems.00674-24

Diaz Soria, C. L., Attenborough, T., Lu, Z., Fontenla, S., Graham, J., Hall, C., Thompson, S., Andrews, T. G. R., Rawlinson, K. A., Berriman, M., & Rinaldi, G. (2024). Single-cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem-cell regulators. Scientific Reports, 14(1), 5974. https://doi.org/10.1038/s41598-024-55790-3

Doré, H., Eisenberg, A., Junkins, E., Leventhal, G., Ganesh, A., Cordero, O., Paul, B., Valentine, D., O’Malley, M., & Wilbanks, E. (2024). Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proceedings of the National Academy of Sciences, 121(9), e2316469121. https://doi.org/10.1073/pnas.2316469121

Eren, A., & Delmont, T. (2024). Bioprospecting marine microbial genomes to improve biotechnology. Nature, 633(8029), 287–288. https://doi.org/10.1038/d41586-024-02661-6

Eren, A., & Banfield, J. F. (2024). Modern microbiology: Embracing complexity through integration across scales. Cell, 187(19), 5151–5170. https://doi.org/10.1016/j.cell.2024.08.028

Fogarty, E. C., Schechter, M. S., Lolans, K., Sheahan, M. L., Veseli, I., Moore, R. M., Kiefl, E., Moody, T., Rice, P. A., Yu, M. K., Mimee, M., Chang, E. B., Ruscheweyh, H.-J., Sunagawa, S., Mclellan, S. L., Willis, A. D., Comstock, L. E., & Eren, A. M. (2024). A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell, 187(5), 1206-1222.e16. https://doi.org/10.1016/j.cell.2024.01.039

Frangieh, C. J., Wilkinson, M. E., Strebinger, D., Strecker, J., Walsh, M. L., Faure, G., Yushenova, I. A., Macrae, R. K., Arkhipova, I. R., & Zhang, F. (2024). Internal initiation of reverse transcription in a Penelope-like retrotransposon. Mobile DNA, 15(1), 12. https://doi.org/10.1186/s13100-024-00322-z

Giacomini, J. J., Torres-Morales, J., Tang, J., Dewhirst, F. E., Borisy, G. G., & Mark Welch, J. L. (2024). Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity. Microbiology Spectrum, 0(0), e04017-23. https://doi.org/10.1128/spectrum.04017-23

Henderson, L. C., Wittmers, F., Carlson, C. A., Worden, A. Z., & Close, H. G. (2024). Variable carbon isotope fractionation of photosynthetic communities over depth in an open-ocean euphotic zone. Proceedings of the National Academy of Sciences, 121(10), e2304613121. https://doi.org/10.1073/pnas.2304613121

Liguori, A., Korm, S., Profetto, A., Richters, E., & Gribble, K. E. (2024). Maternal age effects on offspring lifespan and reproduction vary within a species. Ecology and Evolution, 14(5), e11287. https://doi.org/10.1002/ece3.11287

Majumder, S., Coull, B., Welch, J., La Riviere, P., Dewhirst, F., Starr, J., & Lee, K. (2024). Multivariate Cluster Point Process to Quantify and Explore Multi‐Entity Configurations: Application to Biofilm Image Data. Statistics in Medicine, 43(28), 5446–5460. https://doi.org/10.1002/sim.10261

McMaken, C. M., & Gribble, K. E. (2024). A free and user-friendly software protocol for the quantification of microfauna swimming behavior. BioTechniques. https://doi.org/10.2144/btn-2024-0001

Minařík, M., Modrell, M. S., Gillis, J. A., Campbell, A. S., Fuller, I., Lyne, R., Micklem, G., Gela, D., Pšenička, M., & Baker, C. V. H. (2024). Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs. Frontiers in Cell and Developmental Biology, 12. https://doi.org/10.3389/fcell.2024.1327924

Mullowney, M. W., Fiebig, A., Schnizlein, M. K., McMillin, M., Rose, A. R., Koval, J., Rubin, D., Dalal, S., Sogin, M. L., Chang, E. B., Sidebottom, A. M., & Crosson, S. (2024). Microbially catalyzed conjugation of GABA and tyramine to bile acids. Journal of Bacteriology, 0(0), e00426-23. https://doi.org/10.1128/jb.00426-23

Nowell, R. W., Rodriguez, F., Hecox-Lea, B. J., Mark Welch, D. B., Arkhipova, I. R., Barraclough, T. G., & Wilson, C. G. (2024). Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen. Nature Communications, 15(1), 5787. https://doi.org/10.1038/s41467-024-49919-1

Peña-Montenegro, T., Kleindienst, S., Allen, A., Eren, A., McCrow, J., Arnold, J., & Joye, S. (2024). Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant. Applied and Environmental Microbiology, e0108324. https://doi.org/10.1128/aem.01083-24

Rees, J. M., Kirk, K., Gattoni, G., Hockman, D., Sleight, V. A., Ritter, D. J., Benito-Gutierrez, È., Knapik, E. W., Crump, J. G., Fabian, P., & Gillis, J. A. (2024). A pre-vertebrate endodermal origin of calcitonin-producing neuroendocrine cells. Development, 151(20), dev202821. https://doi.org/10.1242/dev.202821

Ruff, S., de Angelis, I., Mullis, M., Payet, J., Magnabosco, C., Lloyd, K., Sheik, C., Steen, A., Shipunova, A., Morozov, A., Reese, B., Bradley, J., Lemonnier, C., Schrenk, M., Joye, S., Huber, J., Probst, A., Morrison, H., Sogin, M., … Colwell, F. (2024). A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide. Science Advances, 10(51). https://doi.org/10.1126/sciadv.adq0645

Ruff, S. E., Schwab, L., Vidal, E., Hemingway, J., Kraft, B., & Murali, R. (2024). Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments. FEMS Microbiology Ecology, fiae132. https://doi.org/10.1093/femsec/fiae132

Sackville, M. A., Gillis, J. A., & Brauner, C. J. (2024). The origins of gas exchange and ion regulation in fish gills: Evidence from structure and function. Journal of Comparative Physiology B. https://doi.org/10.1007/s00360-024-01545-5

Schaible, G. A., Jay, Z. J., Cliff, J., Schulz, F., Gauvin, C., Goudeau, D., Malmstrom, R. R., Ruff, S. E., Edgcomb, V., & Hatzenpichler, R. (2024). Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells. PLOS Biology, 22(7), e3002638. https://doi.org/10.1371/journal.pbio.3002638

Schiebel, R., Aardema, H. M., Calleja, M. Ll., Dragoneas, A., Heins, L., de Angelis, I. H., Poehlker, C., Slagter, H., Vonhof, H., Walter, D., Arns, A. I., Adolphs, N., Auderset, A., Basic, S., Bieler, A., Bruewer, J. D., Chaabane, S., Cheng, Y., Chilinski, M. T., Ruff, S. E., … Haug, G. H. (2024). Preface: Special Issue on Probing the Open Ocean With the Research Sailing Yacht Eugen Seibold for Climate Geochemistry. Journal of Geophysical Research-atmospheres, 129(17). https://doi.org/10.1029/2023JD040581

Trouche, B., Schrieke, H., Duron, O., Eren, A. M., & Reveillaud, J. (2024). Wolbachia populations across organs of individual Culex pipiens: Highly conserved intra-individual core pangenome with inter-individual polymorphisms. ISME Communications, 4(1), ycae078. https://doi.org/10.1093/ismeco/ycae078

Veseli, I., DeMers, M. A., Cooper, Z. S., Schechter, M. S., Miller, S., Weber, L., Smith, C. B., Rodriguez, L. T., Schroer, W. F., McIlvin, M. R., Lopez, P. Z., Saito, M., Dyhrman, S., Eren, A. M., Moran, M. A., & Braakman, R. (2024). Digital Microbe: A genome-informed data integration framework for team science on emerging model organisms. Scientific Data, 11(1), 967. https://doi.org/10.1038/s41597-024-03778-z

Vineis, J. H., Reznikoff, W. S., Antonopoulos, D. A., Koval, J., Chang, E., Fallon, B. R., Paul, B. G., Morrison, H. G., & Sogin, M. L. (2024). A novel conjugative transposon carrying an autonomously amplified plasmid. mBio, 0(0), e02787-23. https://doi.org/10.1128/mbio.02787-23

Yu, M., Fogarty, E., & Eren, A. (2024). Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess. Nature Microbiology, 9(3), 830–847. https://doi.org/10.1038/s41564-024-01610-3

Zhang, Y., McCarthy, L., Ruff, S. E., & Elhaik, E. (2024). Microbiome Geographic Population Structure (mGPS) Detects Fine-Scale Geography. Genome Biology and Evolution, 16(11). https://doi.org/10.1093/gbe/evae209