JBPC Publications 2025 | Marine Biological Laboratory

Aparicio, N. L., Dryburgh, M., McMaken, C. M., Liguori, A., & Gribble, K. E. (2025). Impact of histone post-translational modification inhibitors on lifespan, reproduction, and stress response in the rotifer Brachionus manjavacas. PLOS ONE, 20(10), e0324769. https://doi.org/10.1371/journal.pone.0324769

Bergauer, K., Suffridge, C. P., Wittmers, F., Sudek, S., Giovannoni, S. J., & Worden, A. Z. (2025). Dark ocean archaeal and bacterial chemoautotrophs drive vitamin B1 production in oxygen minimum zones. ISME Communications, ycaf077. https://doi.org/10.1093/ismeco/ycaf077

Brock, M. T., Nozue, K., Kliebenstein, D. J., Ewers, B. E., Mackay, D. S., Maignien, L., Wang, D. R., Weinig, C., & Maloof, J. N. (2025). Characterization of transcriptional and metabolic responses to a complex plant growth-promoting soil inoculum. Plant Biology, 27(6), 990-1005. https://doi.org/10.1111/plb.70034

Chandler, T., Guo, M., Su, Y., Chen, J., Wu, Y., Liu, J., Agashe, A., Fischer, R. S., Mehta, S. B., Kumar, A., Baskin, T. I., Jaumouille, V., Liu, H., Swaminathan, V., Nain, A. S., Oldenbourg, R., La Riviere, P. J., & Shroff, H. (2025). Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope. Proceedings of the National Academy of Sciences of the United States of America, 122(8), e2406679122. https://doi.org/10.1073/pnas.2406679122

DiSalvo, B., Paul, B. G., & Cardon, Z. G. (2025). Complete genome sequence of Thioclava strain BDS19, isolated from coastal marsh sediment. Microbiology Resource Announcements, e00855-25. https://doi.org/10.1128/mra.00855-25

Elkassas, S. M., Fortunato, C. S., Grim, S. L., Butterfield, D. A., Holden, J. F., Vallino, J. J., Algar, C. K., Zeigler Allen, L., Larson, B. T., Proskurowski, G., Reddington, E., Stewart, L. C., Topcuoglu, B., & Huber, J. A. (2025). Metabolic and population profiles of active subseafloor autotrophs in young oceanic crust at deep-sea hydrothermal vents. Applied and Environmental Microbiology, 91(11). https://doi.org/10.1128/aem.01868-25

Eren, A. M. (2025). Gifting future scientists the past through well-preserved specimens of modern microbial ecosystems. Nature Communications, 16, 6669. https://doi.org/10.1038/s41467-025-62138-6

Freel, K. C., Tucker, S. J., Freel, E. B., Stingl, U., Giovannoni, S. J., Eren, A. M., & Rappé, M. S. (2025). New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales. Nature Communications, 17, 328. https://doi.org/10.1038/s41467-025-67043-6

Gattoni, G., Lin, C.-Y., York, J. R., Shew, C., Keitley, D., LaBonne, C., Yu, J.-K., Gillis, J. A., & Benito-Gutiérrez, E. (2025). Evolutionary dynamics of FoxQ2 transcription factors across metazoans reveals three ancient paralogs. Communications Biology, 9, 98. https://doi.org/10.1038/s42003-025-09368-y

Giacomini, J. J., Torres-Morales, J., Dewhirst, F. E., Borisy, G. G., & Mark Welch, J. L. (2025). Spatial ecology of the Neisseriaceae family in the human oral cavity. Microbiology Spectrum, 13(5), e03275-24. https://doi.org/10.1128/spectrum.03275-24

Gillis, J. A., Criswell, K. E., Palmer, M. A., & Baker, C. V. H. (2025). The skate spiracular organ develops from a unique neurogenic placode, distinct from lateral line placodes. Development, dev.204767. https://doi.org/10.1242/dev.204767

Handa, S., Biswas, T., Chakraborty, J., Ghosh, G., Paul, B. G., & Ghosh, P. (2025). RNA control of reverse transcription in a diversity-generating retroelement. Nature, 638, 1122-1129. https://doi.org/10.1038/s41586-024-08405-w

Hinkle, J., Chanton, J., Moynihan, M., Ruff, S., & Teske, A. (2025). Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq). Frontiers in Microbiology, 15, 1491488. https://doi.org/10.3389/fmicb.2024.1491488

Jiang, Q., Cao, L., Han, Y., Li, S., Zhao, R., Zhang, X., Ruff, S. E., Zhao, Z., Peng, J., Liao, J., Zhu, B., Wang, M., Lin, X., & Dong, X. (2025). Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla. Nature Communications, 16, 1646. https://doi.org/10.1038/s41467-025-56774-1

Jimenez, V., Sudek, S., Eckmann, C., Bachy, C., Poirier, C., Wittmers, F., Santoro, A. E., Follows, M. J., Chavez, F. P., Shilova, I., & Worden, A. Z. (2025). Distinct phytoplankton assemblages underlie hotspots of primary production in the eastern North Pacific Ocean. Limnology and Oceanography, 70(2), 477-492. https://doi.org/10.1002/lno.12771

Kananen, K., Veseli, I., Quiles Pérez, C., Miller, S., Eren, A. M., & Bradley, P. (2025). Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes. Bioinformatics Advances, 5(1), vbaf039. https://doi.org/10.1093/bioadv/vbaf039

Kennedy, S. J., Risser, D. D., & Paul, B. G. (2025). Diel expression dynamics in filamentous cyanobacteria. mBio, 16(12), e03779-24. https://doi.org/10.1128/mbio.03779-24

Liu, S., Longnecker, K., Vergin, K., Bolaños, L. M., Giovannoni, S., Opalk, K., Halewood, E., Kido Soule, M. C., Swarr, G. J., Parsons, R., Maas, A. E., Gossner, H., Blanco-Bercial, L., Wittmers, F., Worden, A. Z., Kujawinski, E. B., Curry, R., Johnson, R., & Carlson, C. A. (2025). Diel study reveals increased nighttime bacterial activity and its connection to organic compounds in the ocean. Communications Biology, 8, 1688. https://doi.org/10.1038/s42003-025-09085-6

Middleton, L., Wu, W., Johnston, T., Tarry, D., Farrar, J., Poulain, P.-M., Özgökmen, T., Shcherbina, A., Pascual, A., McNeill, C., Belgacem, M., Berta, M., Abbott, K., Worden, A., Wittmers, F., Kinsella, A., Centurioni, L., Hormann, V., Cutolo, E., Tintore, J., Ruiz, S., Casas, B., Cheslack, H., CALYPSO Collaboration, D’Asaro, E. A., & Mahadevan, A. (2025). Observations of a splitting ocean cyclone resulting in subduction of surface waters. Sci Adv, 11(30), eadu3221. https://doi.org/10.1126/sciadv.adu3221

Morgan, K., Moynihan, M., Nugraha, A. M. S., & Switzer, A. D. (2025). Sediment fluxes on turbid coral reefs are modulated by monsoon variability in equatorial Southeast Asia. Science of The Total Environment, 1002, 180563. https://doi.org/10.1016/j.scitotenv.2025.180563

Paul, B. G., & DiSalvo, B. (2025). Retracing a tangled tree of archaeal evolution. Nature Microbiology, 10, 1566-1567. https://doi.org/10.1038/s41564-025-02040-5

Paul, B. G., & Mekalanos, J. J. (2025). Natural directed evolution in gut microbiota. Science, 390(6769), 129–130. https://doi.org/10.1126/science.aeb8597

Schoenle, A., Francis, O., Archibald, J. M., Burki, F., de Vries, J., Dumack, K., Eme, L., Florent, I., Hehenberger, E., Hoffmeyer, T. T., Irisarri, I., Lara, E., Leger, M. M., Lukeš, J., Massana, R., Mathur, V., Nitsche, F., Strassert, J. F. H., Worden, A. Z., Yurchenko, V., del Campo, J. & Waldvogel, A.-M. (2025). Protist genomics: Key to understanding eukaryotic evolution. Trends in Genetics, 41(10), P868-882. https://doi.org/10.1016/j.tig.2025.05.004

Schön, I., Chimileski, S., Mark Welch, J., & Martens, K. (2025). Vertical transmission of Cardinium bacteria in parthenogenetic non-marine ostracods (Crustacea). Proceedings of the Royal Society B: Biological Sciences, 292(2058), 20251193. https://doi.org/10.1098/rspb.2025.1193

Scott, W., Ivorra-Molla, E., Akhuli, D., Massam-Wu, T., Lysyganicz, P. K., Walsh, R., Parent, M., Cook, J., Song, L., Kumar, A., Schneider, F., Mishima, M., Crow, A., & Balasubramanian, M. K. (2025). StayRose: A photostable StayGold derivative redshifted by genetic code expansion. Journal of Biological Chemistry, 301(12), 110832. https://doi.org/10.1016/j.jbc.2025.110832

Simon, S., Soares, A., Bornemann, T., Lange, A., Griesdorn, L., Fuentes, A., Dieckmann, M., Krok, B., Ruff, S. E., Hügler, M., Moraru, C., & Probst, A. (2025). Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing. ISME Communications, 5(1), ycaf041. https://doi.org/10.1093/ismeco/ycaf041

Smith, N. F., Rawlinson, K. A., von Dassow, G., Kuris, A. M., Johnson, K. B., & Boyle, M. J. (2025). Chapter 14—Phylum Platyhelminthes. In M. J. Boyle & C. M. Young (Eds.), Atlas of Marine Invertebrate Larvae (Second Edition) (pp. 357–380). Academic Press. https://doi.org/10.1016/B978-0-08-102871-1.00012-9

Sow, S. L. S., van de Poll, W. H., Eveleth, R., Rich, J. J., Ducklow, H. W., Rozema, P. D., Luria, C. M., Bolhuis, H., Meredith, M. P., Amaral-Zettler, L. A., & Engelmann, J. C. (2025). Spatial and temporal variation of Antarctic microbial interactions: A study around the west Antarctic Peninsula. Environmental Microbiome, 20, 21. https://doi.org/10.1186/s40793-025-00663-z

Sures, K., Esser, S. P., Bornemann, T. L. V., Moore, C. J., Soares, A. R., Plewka, J., Figueroa-Gonzalez, P. A., Ruff, S. E., Moraru, C., & Probst, A. J. (2025). Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments. Genome Biology and Evolution, 17(11), evaf201. https://doi.org/10.1093/gbe/evaf201

Thiruppathy, M., Teubner, L., Roberts, R. R., Lasser, M., Moscatello, A., Chen, Y.-W., Hochstim, C., Ruffins, S., Sarkar, A., Tassey, J., Evseenko, D., Lozito, T. P., Willsey, H. R., Gillis, J. A., & Crump, J. G. (2025). Repurposing of a gill gene regulatory program for outer ear evolution. Nature, 639, 682-690. https://doi.org/10.1038/s41586-024-08577-5

Tucker, S. J., Freel, K. C., Eren, A. M., & Rappé, M. S. (2025). Habitat-specificity in SAR11 is associated with a few genes under high selection. The ISME Journal 19(1), wraf216. https://doi.org/10.1093/ismejo/wraf216

Tucker, S. J., Füssel, J., Freel, K. C., Kiefl, E., Freel, E. B., Ramfelt, O., Sullivan, C. E. S., Gajigan, A. P., Mochimaru, H., de Souza, M. R., Quinn, M., Ratum, C., Tran, L. L., Sobczyk, M., Miller, S. E., Trigodet, F., Lolans, K., Morrison, H. G., Fallon, B., Huettel, B., Pan, T., Rappe, M. S., & Eren, A. M. (2025). A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts. Scientific Data, 12, 1913. https://doi.org/10.1038/s41597-025-06166-3

Tucker, S. J., Rii, Y. M., Freel, K. C., Kotubetey, K., Kawelo, A. H., Winter, K. B., & Rappe, M. S. (2025). Seasonal and spatial transitions in phytoplankton assemblages spanning estuarine to open ocean waters of the tropical Pacific. Limnology and Oceanography, 70(6), 1693-1708. https://doi.org/10.1002/lno.70075

Vidal, E., Lindsay, M. R., Bradley, J. A., Osburn, M. R., & Ruff, S. E. (2025). Subsurface Life on Earth as a Key to Unlock Extraterrestrial Mysteries. Microbial Biotechnology, 18(12), e70286. https://doi.org/10.1111/1751-7915.70286

Woods, P. H., Speth, D. R., Laso-Pérez, R., Utter, D. R., Ruff, S. E., & Orphan, V. J. (2025). Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea. Science Advances, 11(25), eadq5232. https://doi.org/10.1126/sciadv.adq5232

Zhao, Y., Zhou, R., Xie, B., Liu, C., Kalski, M., Cham, C., Jiang, Z., Koval, J., Weber, C., Rubin, D., Sogin, M., Crosson, S., Chen, M., Huang, J., Fiebig, A., Dalal, S., Chang, E., Basu, A., & Pott, S. (2025). Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients. Nature Communications, 16, 904. https://doi.org/10.1038/s41467-025-56212-2

Adjuncts or otherwise who do not list JBPC as an affiliation:

Gu, S., Berthelot, H., Lin, Y., Tang, W., Robidart, J., Eren, A., Ducklow, H., & Cassar, N. (2025). Evidence of limited N₂ fixation in the Southern Ocean. Communications Earth & Environment, 6(1). https://doi.org/10.1038/s43247-025-02225-0

Manral, D., Gomez-Navarro, L., Denes, M., Iovino, D., Fogli, P., Masina, S., Hernandez-Carrasco, I., Amaral-Zettler, L., Vichi, M., & van Sebille, E. (2025). Separation Timescales of Vertically Migrating Zooplankton and Other (a)Biotic Materials in the Benguela System. Journal of Geophysical Research-Oceans, 130(4), e2024JC021701. https://doi.org/10.1029/2024JC021701

Theirlynck, T., Staat, L., Servania, D., Engelen, A., van Tussenbroek, B., Muyzer, G., Visser, P., & Amaral-Zettler, L. (2025). Nutrient-driven growth and microbiome shifts in the brown alga Sargassum fluitans III. Journal of Phycology, 61(4), 933-950. https://doi.org/10.1111/jpy.70045

Veseli, I., Chen, Y., Schechter, M., Vanni, C., Fogarty, E., Watson, A., Jabri, B., Blekhman, R., Willis, A., Yu, M., Fernàndez-Guerra, A., Füssel, J., & Eren, A. M. (2025). Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. eLife, 12, rp89862. https://doi.org/10.7554/elife.89862

Welch, J., & Borisy, G. (2025a). Dental plaque Who is in the neighborhood and why it matters. JADA Foundational Science, 4, 100051. https://doi.org/10.1016/j.jfscie.2025.100051

Welch, J., & Borisy, G. (2025b). Dental plaque Who is in the neighborhood and why it matters. Journal of the American Dental Association, 156(8). https://doi.org/10.1016/j.adaj.2025.05.005

Zhao, S., Kvale, K., Zhu, L., Zettler, E., Egger, M., Mincer, T., Amaral-Zettler, L., Lebreton, L., Niemann, H., Nakajima, R., Thiel, M., Bos, R., Galgani, L., & Stubbins, A. (2025). The distribution of subsurface microplastics in the ocean. NATURE, 641(8061). https://doi.org/10.1038/s41586-025-08818-1