JBPC Publications 2023 | Marine Biological Laboratory

Amaral-Zettler, L. (2023a). Algae. In M. Gargaud, W. M. Irvine, R. Amils, P. Claeys, H. J. Cleaves, M. Gerin, D. Rouan, T. Spohn, S. Tirard, & M. Viso (Eds.), Encyclopedia of Astrobiology (pp. 81–83). Springer. https://doi.org/10.1007/978-3-662-65093-6_48

Amaral-Zettler, L. (2023b). Eukarya. In M. Gargaud, W. M. Irvine, R. Amils, P. Claeys, H. J. Cleaves, M. Gerin, D. Rouan, T. Spohn, S. Tirard, & M. Viso (Eds.), Encyclopedia of Astrobiology (pp. 931–934). Springer Nature. https://doi.org/10.1007/978-3-662-65093-6_537

Arkhipova, I. R., Burns, K. H., Chiappinelli, K. B., Chuong, E. B., Goubert, C., Guarné, A., Larracuente, A. M., Lee, E. A., & Levin, H. L. (2023). Meeting report: Transposable elements at the crossroads of evolution, health and disease 2023. Mobile DNA, 14(1), 19. https://doi.org/10.1186/s13100-023-00307-4

Arkhipova, I., & Yushenova, I. (2023a). To be mobile or not: The variety of reverse transcriptases and their recruitment by host genomes. Biokhimiya, 88(11), 2127–2137. https://doi.org/10.31857/s0320972523110088

Arkhipova, I., & Yushenova, I. (2023b). To be mobile or not: The variety of reverse transcriptases and their recruitment by host genomes. Biokhimiya, 88(11), 1754–1762. https://doi.org/10.1134/s000629792311007x

Arkhipova, I., Yushenova, I., & Rodriguez, F. (2023). Shaping eukaryotic epigenetic systems by horizontal gene transfer. Bioessays, 45(7), e2200232. https://doi.org/10.1002/bies.202200232

Baker, J. L., Mark Welch, J. L., Kauffman, K. M., McLean, J. S., & He, X. (2023). The oral microbiome: Diversity, biogeography and human health. Nature Reviews Microbiology, 1–16. https://doi.org/10.1038/s41579-023-00963-6

Bos, R. P., Kaul, D., Zettler, E. R., Hoffman, J. M., Dupont, C. L., Amaral-Zettler, L. A., & Mincer, T. J. (2023). Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients. Environmental Microbiology. https://doi.org/10.1111/1462-2920.16391

Chaouni, B., Idrissi Azami, A., Raoui, S., Amzazi, S., Nejjari, C., Bakkali, F., Zaid, E. H., Hamamouch, N., Amaral-Zettler, L., & Ghazal, H. (2023). Spatio-temporal patterns of Synechococcus oligotypes in Moroccan lagoonal environments. Scientific Reports, 13(1), 110. https://doi.org/10.1038/s41598-022-27263-y

DeWolf, E., Brock, M., Calder, W., Kliebenstein, D., Katz, E., Li, B., Morrison, H., Maïgnien, L., & Weinig, C. (2023). The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa. Molecular Ecology, 32(3), 741–751. https://doi.org/10.1111/mec.16782

Eckmann, C. A., Eberle, J. S., Wittmers, F., Wilken, S., Bergauer, K., Poirier, C., Blum, M., Makareviciute-Fichtner, K., Jimenez, V., Bachy, C., Vermeij, M. J. A., & Worden, A. Z. (2023). Eukaryotic algal community composition in tropical environments from solar salterns to the open sea. Frontiers in Marine Science, 10. https://doi.org/10.3389/fmars.2023.1131351

Feng, H., Bavister, G., Gribble, K. E., & Welch, D. B. M. (2023). Highly efficient CRISPR-mediated gene editing in a rotifer. PLoS Biology, 21(7), e3001888. https://doi.org/10.1371/journal.pbio.3001888

Fiebig, A., Schnizlein, M. K., Pena-Rivera, S., Trigodet, F., Dubey, A. A., Hennessy, M. K., Basu, A., Pott, S., Dalal, S., Rubin, D., Sogin, M. L., Eren, A. M., Chang, E. B., & Crosson, S. (2023). Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. mBio, 0(0), e02830-23. https://doi.org/10.1128/mbio.02830-23

Ghousein, A., Tutagata, J., Schrieke, H., Etienne, M., Chaumeau, V., Boyer, S., Pages, N., Roiz, D., Eren, A. M., Cambray, G., & Reveillaud, J. (2023). pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex pipiens and Culex quinquefasciatus mosquitoes worldwide. ISME Communications, 3(1), 1–5. https://doi.org/10.1038/s43705-023-00248-2

Giacomini, J. J., Torres-Morales, J., Dewhirst, F. E., Borisy, G. G., & Mark Welch, J. L. (2023). Site Specialization of Human Oral Veillonella Species. Microbiology Spectrum, 0(0), e04042-22. https://doi.org/10.1128/spectrum.04042-22

Gillis, J. A. (2023). Scales, scutes, and embryonic origins of the vertebrate dermal skeleton. Proceedings of the National Academy of Sciences, 120(33), e2310552120. https://doi.org/10.1073/pnas.2310552120

Gollnisch, R., Wallenius, J., Gribble, K. E., Ahrén, D., & Rengefors, K. (2023). SAG-RAD: A method for single-cell population genomics of unicellular eukaryotes. Molecular Biology and Evolution, msad095. https://doi.org/10.1093/molbev/msad095

Goodheart, J. A., Collins, A. G., Cummings, M. P., Egger, B., & Rawlinson, K. A. (2023). A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution. Royal Society Open Science, 10(3), 220939. https://doi.org/10.1098/rsos.220939

Hehenberger, E., Guo, J., Wilken, S., Hoadley, K., Sudek, L., Poirier, C., Dannebaum, R., Susko, E., & Worden, A. Z. (2023). Phosphate limitation responses in marine green algae are linked to reprogramming of the tRNA epitranscriptome and codon usage bias. Molecular Biology and Evolution, msad251. https://doi.org/10.1093/molbev/msad251

Hubbard, C. J., Harrison, J. G., McMinn, R., Bennett Ponsford, J. C., Maignien, L., Ewers, B., & Weinig, C. (2023). Rhizosphere microbial community composition shifts diurnally and in response to natural variation in host clock phenotype. mSystems, e0148721. https://doi.org/10.1128/msystems.01487-21

Itano, M. S., Kumar, A., & Maddox, P. S. (2023). Editorial: Live cell imaging: Cell and developmental research bridging education, optical engineering, industry, software, shared facilities. Frontiers in Cell and Developmental Biology, 11. https://www.frontiersin.org/articles/10.3389/fcell.2023.1191235

Jiang, X., Gallager, S., Pàmies, R. P., Ruff, S. E., & Liu, Z. (2024). Laboratory-Simulated Photoirradiation Reveals Strong Resistance of Primary Macroplastics to Weathering. Environmental Science & Technology. https://doi.org/10.1021/acs.est.3c09891

Kiefl, E., Esen, O., Miller, S., Kroll, K., Willis, A., Rappé, M., Pan, T., & Eren, A. (2023). Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution. Science Advances, 9(8), eabq4632. https://doi.org/10.1126/sciadv.abq4632

Lundgren, S. N., Madan, J. C., Karagas, M. R., Morrison, H. G., Christensen, B. C., & Hoen, A. G. (2023). Human milk-associated bacterial communities associate with the infant gut microbiome over the first year of life. Frontiers in Microbiology, 14. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1164553

Mark Welch, D., Gould, T., Olins, A., & Olins, D. (2023). The transcriptome of acute dehydration in myeloid leukemic cells. Postepy Biochemii. https://doi.org/10.18388/pb.2021_507

Miller, S. E., Colman, A. S., & Waldbauer, J. R. (2023). Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities. mSystems, 0(0), e01238-22. https://doi.org/10.1128/msystems.01238-22

Mincer, T. J., Bos, R. P., Zettler, E. R., Zhao, S., Asbun, A. A., Orsi, W. D., Guzzetta, V. S., & Amaral-Zettler, L. A. (2023). Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat. Water Research, 120033. https://doi.org/10.1016/j.watres.2023.120033

Peña-Montenegro, T. D., Kleindienst, S., Allen, A. E., Eren, A. M., McCrow, J. P., Sánchez-Calderón, J. D., Arnold, J., & Joye, S. B. (2023). Species-specific responses of marine bacteria to environmental perturbation. ISME Communications, 3(1), 1–10. https://doi.org/10.1038/s43705-023-00310-z

Pérez Castro, S., Peredo, E., Mason, O., Vineis, J., Bowen, J., Mortazavi, B., Ganesh, A., Ruff, S., Paul, B., Giblin, A., & Cardon, Z. (2023). Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes. Applied Environmental Microbiology, e0098823. https://doi.org/10.1128/aem.00988-23

Rees, J. M., Palmer, M. A., & Gillis, J. A. (2023). Fgf signalling is required for gill slit formation in the skate, Leucoraja erinacea. Developmental Biology. https://doi.org/10.1016/j.ydbio.2023.11.008

Rees, J. M., Sleight, V. A., Clark, S. J., Nakamura, T., & Gillis, J. A. (2023). Ectodermal Wnt signaling, cell fate determination, and polarity of the skate gill arch skeleton. eLife, 12. https://doi.org/10.7554/eLife.79964

Ruff, S., & Baker, B. (2023). Editorial: Rising stars in hydrothermal vents and cold seeps: 2021. Frontiers in Microbiology, 14, 1297372. https://doi.org/10.3389/fmicb.2023.1297372

Ruff, S. E., Humez, P., de Angelis, I. H., Diao, M., Nightingale, M., Cho, S., Connors, L., Kuloyo, O. O., Seltzer, A., Bowman, S., Wankel, S. D., McClain, C. N., Mayer, B., & Strous, M. (2023). Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems. Nature Communications, 14(1), 3194. https://doi.org/10.1038/s41467-023-38523-4

Runde, J., Veseli, I., Fogarty, E. C., Watson, A. R., Clayssen, Q., Yosef, M., Shaiber, A., Verma, R., Quince, C., Gerasimidis, K., Rubin, D. T., & Eren, A. M. (2023). Transient suppression of bacterial populations associated with gut health is critical in success of exclusive enteral nutrition for children with Crohn’s disease. Journal of Crohn’s & Colitis, jjad031. https://doi.org/10.1093/ecco-jcc/jjad031

Strauss, J., Choi, C. J., Grone, J., Wittmers, F., Jimenez, V., Makareviciute-Fichtner, K., Bachy, C., Jaeger, G. S., Poirier, C., Eckmann, C., Spezzano, R., Löscher, C. R., Sarma, V. V. S. S., Mahadevan, A., & Worden, A. Z. (2023). The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients. Environmental Microbiology, 25(11), 2118–2141. https://doi.org/10.1111/1462-2920.16431

Torres-Morales, J., Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G. (2023). Site-specialization of human oral Gemella species. Journal of Oral Microbiology, 15(1), 2225261. https://doi.org/10.1080/20002297.2023.2225261

Trouche, B., Schauberger, C., Bouderka, F., Auguet, J.-C., Belser, C., Poulain, J., Thamdrup, B., Wincker, P., Arnaud-Haond, S., Glud, R. N., & Maignien, L. (2023). Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments. ISME Communications, 3(1), 1–12. https://doi.org/10.1038/s43705-023-00341-6

Watson, A. R., Füssel, J., Veseli, I., DeLongchamp, J. Z., Silva, M., Trigodet, F., Lolans, K., Shaiber, A., Fogarty, E., Runde, J. M., Quince, C., Yu, M. K., Söylev, A., Morrison, H. G., Lee, S. T. M., Kao, D., Rubin, D. T., Jabri, B., Louie, T., & Eren, A. M. (2023). Metabolic independence drives gut microbial colonization and resilience in health and disease. Genome Biology, 24(1), 78. https://doi.org/10.1186/s13059-023-02924-x

Wu-Woods, N. J., Barlow, J. T., Trigodet, F., Shaw, D. G., Romano, A. E., Jabri, B., Eren, A. M., & Ismagilov, R. F. (2023). Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples. Nature Methods, 20(12), 1672–1682. https://doi.org/10.1038/s41592-023-02025-4

Zhang, Y., Ruff, S. E., Oskolkov, N., Tierney, B. T., Ryon, K., Danko, D., Mason, C. E., & Elhaik, E. (2023). The microbial biodiversity at the archeological site of Tel Megiddo (Israel). Frontiers in Microbiology, 14. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1253371