Publications

Below is a list of publications from research supported by GEMS. You can also view these publications on our Google Scholar page.

GEMS Institute profile on Google Scholar

2025

  • Aleshintsev et al., 2025

    Aleshintsev, A., Way, L. E., Guerra, B., Serwaa, L. A., Molina, M., Wang, X., & Kim, H. J. (2025). ParB C-terminal lysine residues are essential for dimerization, in vitro DNA sliding and in vivo function. bioRxiv.

    https://doi.org/10.1101/2025.06.10.659001

  • Boehm Vock et al., 2025

    Boehm Vock, L. F., Mossman, L. M., Rapti, Z., Dolezal, A. G., & Clifton, S. M. (2025). Spatiotemporal, environmental, and behavioral predictors of Varroa mite intensity in managed honey bee apiaries. PLOS ONE 20(8): e0325801.

    https://doi.org/10.1371/journal.pone.0325801

  • Caesar et al., 2025

    Caesar, L., Barksdale, C., Valiati, V. H., & Newton, I. (2025). Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly. bioRxiv.

    https://doi.org/10.1101/2025.03.07.642116

  • Farley et al., 2025

    Farley, K. R., Buechler, A. K., Bianco, C. M., & Vanderpool, C. K. (2025). Small RNAs positively and negatively control transcription elongation through modulation of Rho utilization site accessibility. mBio 0:e02921-25.

    https://doi.org/10.1128/mbio.02921-25

  • Ganote et al., 2025

    Ganote, C., Caesar, L., Rice, D. W., Whitaker, R. J., & Newton, I. L. G. (2025). Evolutionary trends in Bombella apis CRISPR-Cas systems. mSystems 0:e00166-25.

    https://doi.org/10.1128/msystems.00166-25

  • Hughes et al., 2025

    Hughes, A. G., Cullum, J. E., Fredericks, M. J., Wilson, P. J., Schwarzenberger, A., & Cáceres, C. E. (2025). Influence of melatonin on the successful infection of Daphnia dentifera by Metschnikowia bicuspidata. Ecosphere, 16 (2), e70192.

    https://doi.org/10.1002/ecs2.70192

  • Izquierdo-Martinez et al., 2025

    Izquierdo-Martinez, A., Schäper, S., Brito, A. D., Liao, Q., Tesseur, C., Sorg, M., Botinas, D. S., Wang, X., & Pinho, M. G. (2025). Chromosome segregation dynamics during the cell cycle of Staphylococcus aureus. bioRxiv.

    https://doi.org/10.1101/2025.02.18.638847

  • Lennon et al, 2025

    Lennon, J. T., Lehmkuhl, B. K., Chen, L., Illingworth, M., Kuo, V., & Muscarella, M.E. (2025). Resuscitation-promoting factor (Rpf) terminates dormancy among diverse soil bacteria. mSystems 10:e01517-24.

    https://doi.org/10.1128/msystems.01517-24

  • Li et al., 2025

    Li, S., Laderman, E., Markle, H., Yang, Y., Bergelson, J., & Pascual, M. (2025). Negative frequency-dependent selection contributes to modular structure of effector repertoires in Pseudomonas syringae. bioRxiv.

    https://doi.org/10.1101/2025.01.16.632277

  • Liaghat et al., 2025

    Liaghat, A., Guillemet, M., Whitaker, R., Gandon, S., & Pascual, M. (2025). Host competitive assymetries accelerate viral evolution in a microbe-virus coevolutionary system. Ecology Letters, 28 (6): e70153.

    https://doi.org/10.1111/ele.70153

  • Liao et al., 2025

    Liao, Q., Brandão, H. B., Ren, Z., & Wang, X. (2025). Replisomes restrict SMC-mediated DNA-loop extrusion in vivo. bioRxiv.

    https://doi.org/10.1101/2025.02.23.639750

  • Mishra et al., 2025

    Mishra, A., Jackson, A. E., Wang, X., & Kearns, D. B. (2025). The SinR-SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis. Journal of Molecular Biology, 437 (12): 169123.

    https://doi.org/10.1016/j.jmb.2025.169123

  • Mueller et al., 2025

    Mueller, E. A., & Lennon, J. T. (2025). Residence time structures microbial communities through niche partitioning. Ecology Letters, 28 (2): e70093.

    https://doi.org/10.1111/ele.70093

  • O’Neal et al., 2025

    O’Neal, L. G., Drucker, M. N., Khanh Lai, N. Clemente, A. F., Campbell, A. P., Way, L. E., Hong, S., Holmes, E. E., Rancic, S. J., Sawyer, N., Wang, X., & Thrall, E. S. (2025). The B. subtilis replicative polymerases bind the sliding clamp with different strengths to tune replication processivity and fidelity. bioRxiv.

    https://doi.org/10.1101/2025.03.10.642433

  • Payne et al., 2025

    Payne, A.N., Prayugo, V., & Dolezal, A. G. (2025). A honey bee-associated virus remains infectious and quantifiable in postmortem hosts. Journal of Invertebrate Pathology, 209: 108258.

    https://doi.org/10.1016/j.jip.2024.108258

  • Riaz et al., 2025

    Riaz, M. R., Sosa Marquez, I., Lindgren, H., Levin, G., Doyle, R., Cerón Romero, M., Paoli, J.C., Drnevich, J., Fields, C.J., Geddes, B.A., Marshall-Colón, A., & Heath, K.D. (2025). Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis. Proc Natl Acad Sci U S A., 122(31):e2411831122.

    https://doi.org/10.1073/pnas.2411831122

  • Robinson et al., 2025

    Robinson, C. R. P., Dolezal, A. G., Liachko, I., & Newton, I. L. G. (2025). Mobile genetic elements exhibit associated patterns of host range variation and sequence diversity within the gut microbiome of the European honey bee. bioRxiv.

    https://doi.org/10.1101/2025.01.31.635958

  • Sanath-Kumar et al, 2025

    Sanath-Kumar, R., Rahman, A., Ren, Z., Reynolds, I. P., Augusta, L., Fuqua, C., Weisberg, A. J., & Wang, X. (2025). Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion. mBio 16:e01046-25.

    https://doi.org/10.1128/mbio.01046-25

  • Schakel et al., 2025

    Schakel, O. F., Fritts, R. K., Zmuda, A. J., Setayeshgar, S., & McKinlay, J. B. (2025). Microbial cross-feeding is stabilized when a dependent mutant is segregated from its independent ancestor. The ISME Journal, Volume 19, Issue 1, January 2025, wraf131.

    https://doi.org/10.1093/ismejo/wraf131

  • Sosa Marquez et al., 2025

    Sosa Marquez, I., Griesbaum, K., Clark, L. V., Ainsworth, E. A., Christian, N., & Heath, K. D. (2025). Dominant foliar endophytes influence soybean yield and transcriptome. FEMS Microbiology Ecology, Volume 101 (Issue 6): fiaf053.

    https://doi.org/10.1093/femsec/fiaf053

  • Vereau Gorbitz et al., 2025

    Vereau Gorbitz, D., Schwarz, C., McMullen, J. G., Cerón-Romero, M., Doyle, R. T., Lau, J. A., Whitaker, R. J., Vanderpool, C. K., & Heath, K. (2025). Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum. mBio 0:e02497-25.

    https://doi.org/10.1128/mbio.02497-25

  • Weiner et al, 2025

    Weiner, B. G., Märkle, H., Laderman, E., Demirjian, C., & Bergelson, J. (2025). A physical model links structure and function in the plant immune system. Proc Natl Acad Sci U S A. 122(24):e2502872122.

    https://doi.org/10.1073/pnas.2502872122

  • Zang et al., 2025

    Zang, Z., Zhang, C., Park, K. J., Schwartz, D. A., Podicheti, R., Lennon, J. T., & Gerdt, J. P. (2025). Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection. Nature Microbiology, 10: 362-373.

     

    https://doi.org/10.1038/s41564-024-01910-8

2024

  • Baglivo et al., 2024

    Baglivo, I., Malgieri, G., Roop, R. M. 2nd, Barton, I. S., Wang, X., Russo, V., Pirone, L., Pedone, E. M., & Pedone, P. V. (2024). MucR protein: Three decades of studies have led to the identification of a new H-NS-like protein. Molecular Microbiology, 00, 1-14.

    https://doi.org/10.1111/mmi.15261

  • Basu et al., 2024

    Basu, A., Adams, A. N. D., Degnan, P. H., & Vanderpool, C. K. (2024). Determinants of raffinose family oligosaccharide use in Bacteroides species. Journal of Bacteriology, 206 (10): e0023524.

    https://doi.org/10.1128/jb.00235-24

  • Caesar et al., 2024

    Caesar, L., Rice, D. W., McAfee, A., Underwood, R., Ganote, C., Tarpy, D. R., Foster, L. J., & Newton, I. R. L. (2024). Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phage. mSystems, 9:e01182-23.

    https://doi.org/10.1128/msystems.01182-23

  • Hill et al., 2024

    Hill, C. A., McMullen, J. G., & Lennon, J. T. (2024). Nitrogen enrichment alters selection on rhizobial genes. bioRxiv.

    https://doi.org/10.1101/2024.11.25.625319

  • Kosmopoulos et al., 2024

    Kosmopoulos, J. C., Batsone-Doyle, R. T., & Heath, K. D. (2024). Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis. Canadian Journal of Microbiology, 70, 275-288.

    https://doi.org/10.1139/cjm-2023-0209

  • Lennon et al., 2024

    Lennon, J. T., Abramoff, R.Z., Allison, S. D., Burckhardt, R. M., DeAngelis, K. M., Dunne, J. P., Frey, S. D., Friedlingstein, P., Hawkes, C. V., Hungate, B. A., Khurana, S., Kivlin, S. N., Levine, N. M., Manzoni, S., Martiny, A. C., Martiny, J. B. H., Nguyen, N. K., Rawat, M., Talmy, D., Todd-Brown, K., Vogt, M., Wieder, W. R., Zakem, E. J. (2024). Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction. mBio, 15 (5):e0045524.

    https://doi.org/10.1128/mbio.00455-24

  • Liaghat et al., 2024

    Liaghat, A., Yang, J., Whitaker, R., & Pascual, M. (2024). Punctuated virus-driven succession generates dynamical alternations in CRISPR-mediated microbe-virus coevolution. Journal of The Royal Society Interface, 21(217), 20240195.

    https://doi.org/10.1098/rsif.2024.0195

  • Mishra et al., 2024

    Mishra, A., Hughes, A. C.. Amon, J. D., Rudner, D. Z., Wang, X., & Kearns, D. B. (2024). SwrA-mediated multimerization of DegU and an upstream activation sequence enhance flagellar gene expression in Bacillus subtilis. Journal of Molecular Biology, 436 (4), 168419.

    https://doi.org/10.1016/j.jmb.2023.168419

  • Robinson et al., 2024

    Robinson, C. R. P., Dolezal, A. G., & Newton, I. L. G. (2024). Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations. ISME Communications, 4(1), 1-14.

    https://doi.org/10.1093/ismeco/ycad003

  • Schwing et al., 2024

    Schwing, C. D., Holmes, C. J., Muturi, E. J., Dunlap, C., Holmes, J. R., & Cáceres, C. E. (2024). Causes and consequences of microbiome formation in mosquito larvae. Ecological Entomology, 49:857–868.

    https://doi.org/10.1111/een.13360

  • St. Clair et al., 2024

    St. Clair, A. L., Dwyer, B., Shapiro, M., & Dolezal, A. G. (2024). Adult honey bee queens consume pollen and nectar. bioRxiv.

    https://doi.org/10.1101/2024.12.04.626851

  • Suttenfield et al., 2024

    Suttenfield, L. C., Rapti, Z., Chandrashekhar, J. H., Steinlein, A. C., Vera, J. C., Kim, T., & Whitaker, R. J. (2024). Phage-mediated resolution of genetic conflict alters the evolutionary trajectory of Pseudomonas aeruginosa lysogens. mSystems, 9:e00801-24.

    https://doi.org/10.1128/msystems.00801-24

  • Wilson et al., 2024

    Wilson, P. J., Cáceres, C. E., & Stewart Merrill, T. E. (2024). Exposure to fungal infection decreases eye size in the zooplankton, Daphnia. Journal of Plankton Research, 46 (6): 596-603.

    https://doi.org/10.1093/plankt/fbae058

2023

  • Barton et al., 2023

    Barton, I. S., Ren, Z., Cribb, C. B., Pitzer, P. E., Baglivo, I., Martin, D. W., Wang, X., & Roop, R. M. (2023). Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid. mBio, 14(6), Article e02201-23.

    https://doi.org/10.1128/mbio.02201-23

  • Cáceres & Stewart Merrill, 2023

    Cáceres, C. E., & Stewart Merrill, T. E. (2023). The role of varying resources on Daphnia dentifera immune responses. Fundamental and Applied Limnology, 196(3-4), 217-228.

    https://doi.org/10.1127/fal/2022/1458

  • Collins & Whitaker, 2023

    Collins, A. J., & Whitaker, R. J. (2023). CRISPR Comparison Toolkit: Rapid identification, visualization, and analysis of CRISPR array diversity. The CRISPR Journal, 6(4), 386–400.

    https://doi.org/10.1089/crispr.2022.0080

  • Fishman et al., 2023

    Fishman, F. J., & Lennon, J. T. (2023). Macroevolutionary constraints on global microbial diversity. Ecology and Evolution, 13(8), e10403.

    https://doi.org/10.1002/ece3.10403

  • Măgălie et al., 2023

    Măgălie, A., Schwartz, D. A., Lennon, J. T., & Weitz, J. S. (2023). Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching. Journal of Theoretical Biology, 561, Article 111413.

    https://doi.org/10.1016/j.jtbi.2023.111413

  • Ren et al., 2023

    Ren, Z., Takacs, C. N., Brandão, H. B., Jacobs-Wagner, C., & Wang, X. (2023). Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. PLoS Genetics, 19(7), Article e1010857.

    https://doi.org/10.1371/journal.pgen.1010857

  • Ricks & Yannarell, 2023

    Ricks, K. D., & Yannarell, A. C. (2023). Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response. Proceedings of the Royal Society B: Biological Sciences, 290(2001).

    https://doi.org/10.1098/rspb.2023.0469

  • Ricks et al., 2023

    Ricks, K. D., Ricks, N. J., & Yannarell, A. C. (2023). Patterns of plant salinity adaptation depend on interactions with soil microbes. The American Naturalist, 202(3), 276-287.

    https://doi.org/10.1086/725393

  • Schwartz et al., 2023

    Schwartz, D. A., Rodríguez-Ramos, J. A., Shaffer, M., Flynn, R. M., Daly, R. A., Wrighton, K. C., & Lennon, J. T. (2023). Human-gut phages harbor sporulation genes. mBio, 14(3).

    https://doi.org/10.1128/mbio.00182-23

  • Schwartz et al, 2023

    Schwartz, D. A., Shoemaker, W. R., Măgălie, A., Weitz, J. S., & Lennon, J. T. (2023). Bacteria-phage coevolution with a seed bank. The ISME Journal, Volume 17 (Issue 8), pages 1315–1325.

    https://doi.org/10.1038/s41396-023-01449-2

  • Terrill Sondag et al., 2023

    Terrill Sondag, E. E., Stuart Merrill, T. E., Drnevich, J., Holmes, J. R., Fischer, E. K., Cáceres, C. E., & Strickland, L. R. (2023). Differential gene expression in response to fungal pathogen exposure in the aquatic invertebrate, Daphnia dentifera. Ecology and Evolution, 13(8).

    https://doi.org/10.1002/ece3.10354

  • Wisnoski & Lennon, 2023

    Wisnoski, N. I., & Lennon, J. T. (2023). Scaling up and down: Movement ecology for microorganisms. Trends in Microbiology, 31(3), 242-253.

    https://doi.org/10.1016/j.tim.2022.09.016

2022

  • Bolin et al., 2022

    Bolin, L. G., Lennon, J. T., & Lau, J. A. (2022). Traits of soil bacteria predict plant responses to soil moisture. Ecology, 104(2).

    https://doi.org/10.1002/ecy.3893

  • Halloway et al., 2022

    Halloway, A. H., Heath, K. D., & McNickle, G. G. (2022). When does mutualism offer a competitive advantage? A game-theoretic analysis of host–host competition in mutualism. AoB Plants, 14(2), 1-9.

    https://doi.org/10.1093/aobpla/plac010

  • Heath et al., 2022

    Heath, K. D., Batstone, R. T., Cerón Romero, M., & McMullen, J. G. (2022). MGEs as the MVPs of partner quality variation in legume-Rhizobium symbiosis. mBio, 13(4).

    https://doi.org/10.1128/mbio.00888-22

  • Massey & Newton, 2022

    Massey, J. H., & Newton, I. L. G. (2022). Diversity and function of arthropod endosymbiont toxins. Trends in Microbiology, 30(2), 185–198.

    https://doi.org/10.1016/j.tim.2021.06.008

  • McMullen & Lennon, 2022

    McMullen, II, J. G., & Lennon, J. T. (2022). Mark‐recapture of microorganisms. Environmental Microbiology, 25(1), 150-157.

    https://doi.org/10.1111/1462-2920.16267

  • Parish et al., 2022

    Parish, A. J., Rice, D. W., Tanquary, V. M., Tennessen, J. M., & Newton, I. L. G. (2022). Honey bee symbiont buffers larvae against nutritional stress and supplements lysine. ISME Journal, 16(9), 2160–2168.

    https://doi.org/10.1038/s41396-022-01268-x

  • Schwartz et al., 2022

    Schwartz, D. A., Lehmkuhl, B. K., & Lennon, J. T. (2022). Phage-encoded sigma factors alter bacterial dormancy. mSphere, 7(4).

    https://doi.org/10.1128/msphere.00297-22