JBPC Publications 2023

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鈥83). Springer.

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鈥934). Springer Nature.

Arkhipova, I. R., Burns, K. H., Chiappinelli, K. B., Chuong, E. B., Goubert, C., Guarn茅, 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.

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鈥2137.

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鈥1762.

Arkhipova, I., Yushenova, I., & Rodriguez, F. (2023). Shaping eukaryotic epigenetic systems by horizontal gene transfer. Bioessays, 45(7), e2200232.

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鈥16.

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.

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.

DeWolf, E., Brock, M., Calder, W., Kliebenstein, D., Katz, E., Li, B., Morrison, H., Ma茂gnien, L., & Weinig, C. (2023). The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa. Molecular Ecology, 32(3), 741鈥751.

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.

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.

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.

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鈥5.

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.

Gillis, J. A. (2023). Scales, scutes, and embryonic origins of the vertebrate dermal skeleton. Proceedings of the National Academy of Sciences, 120(33), e2310552120.

Gollnisch, R., Wallenius, J., Gribble, K. E., Ahr茅n, D., & Rengefors, K. (2023). SAG-RAD: A method for single-cell population genomics of unicellular eukaryotes. Molecular Biology and Evolution, 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.

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.

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.

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.

Jiang, X., Gallager, S., P脿mies, R. P., Ruff, S. E., & Liu, Z. (2024). Laboratory-Simulated Photoirradiation Reveals Strong Resistance of Primary Macroplastics to Weathering. Environmental Science & Technology.

Kiefl, E., Esen, O., Miller, S., Kroll, K., Willis, A., Rapp茅, M., Pan, T., & Eren, A. (2023). Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution. Science Advances, 9(8), eabq4632.

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.

Mark Welch, D., Gould, T., Olins, A., & Olins, D. (2023). The transcriptome of acute dehydration in myeloid leukemic cells. Postepy Biochemii.

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.

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.

Pe帽a-Montenegro, T. D., Kleindienst, S., Allen, A. E., Eren, A. M., McCrow, J. P., S谩nchez-Calder贸n, J. D., Arnold, J., & Joye, S. B. (2023). Species-specific responses of marine bacteria to environmental perturbation. ISME Communications, 3(1), 1鈥10.

P茅rez 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.

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.

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.

Ruff, S., & Baker, B. (2023). Editorial: Rising stars in hydrothermal vents and cold seeps: 2021. Frontiers in Microbiology, 14, 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.

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鈥檚 disease. Journal of Crohn鈥檚 & Colitis, 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., L枚scher, 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鈥2141.

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.

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鈥12.

Watson, A. R., F眉ssel, J., Veseli, I., DeLongchamp, J. Z., Silva, M., Trigodet, F., Lolans, K., Shaiber, A., Fogarty, E., Runde, J. M., Quince, C., Yu, M. K., S枚ylev, 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.

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鈥1682.

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.