Publications

Google Scholar - Jennifer Bowen

• Sullivan, H. L., Holtzer, J., Deegan, L. A., & Bowen, J. L. (2025). The Effect of Runnels on Salt Marsh Sediment Dynamics, Vegetation, and Nitrogen Cycling. Estuaries and Coasts, 48(3), 73. https://doi.org/10.1007/s12237-025-01511-6

• Bowen, J. L., Spivak, A. C., Bernhard, A. E., Fulweiler, R. W., & Giblin, A. E. (2024). Salt marsh nitrogen cycling: Where land meets sea. Trends in Microbiology, 32, 565–576.

• Bulseco, A. N., Murphy, A. E., Giblin, A. E., Tucker, J., Sanderman, J., & Bowen, J. L. (2024). Marsh sediments chronically exposed to nitrogen enrichment contain degraded organic matter that is less vulnerable to decomposition via nitrate reduction. Science of The Total Environment, 915, 169681.

• Crump, B. C., & Bowen, J. L. (2024). The microbial ecology of estuarine ecosystems. Annual Review of Marine Science, 16, 335–360.

• Weston, N. B., Troy, C., Kearns, P. J., Bowen, J. L., Porubsky, W., Hyacinthe, C., Meile, C., Van Cappellen, P., & Joye, S. B. (2024). Physicochemical Perturbation Increases Nitrous Oxide Production in Soils and Sediments. EGUsphere 2024, 1–20.

• Pérez Castro, S., Peredo, E. L., Mason, O. U., Vineis, J., Bowen, J. L., Mortazavi, B., Ganesh, A., Ruff, S. E., Paul, B. G., & Giblin, A. E. (2023). Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes. Applied and Environmental Microbiology, 89, e00988-23.

• Vineis, J., Martins, S., Calaza, C., Gaspar, J., Bowen, J., & Goluch, E. (2023). Machined silicon traps for capturing novel bacterial communities and strainsin-situ.

• Vineis, J. H., Bulseco, A. N., & Bowen, J. L. (2023). Microbial chemolithoautotrophs are abundant in salt marsh sediment following long-term experimental nitrate enrichment. FEMS Microbiology Letters, 370, fnad082.

• Fremin, B. J., Bhatt, A. S., Kyrpides, N. C., Sengupta, A., Sczyrba, A., da Silva, A. M., Buchan, A., Gaudin, A., Brune, A., Hirsch, A. M., et al. (2022). Thousands of small, novel genes predicted in global phage genomes. Cell Reports, 39.

• Hurtado-McCormick, V., Trevathan-Tackett, S. M., Bowen, J. L., Connolly, R. M., Duarte, C. M., & Macreadie, P. I. (2022). Pathways for understanding blue carbon microbiomes with amplicon sequencing. Microorganisms, 10, 2121.

• Neri, U., Wolf, Y. I., Roux, S., Camargo, A. P., Lee, B., Kazlauskas, D., Chen, I. M., Ivanova, N., Allen, L. Z., Paez-Espino, D., et al. (2022). Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell, 185, 4023–4037.

• Unzueta-Martínez, A., Scanes, E., Parker, L. M., Ross, P. M., O’Connor, W., & Bowen, J. L. (2022a). Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission. Animal Microbiome, 4, 32.

• Unzueta-Martínez, A., Welch, H., & Bowen, J. L. (2022b). Determining the composition of resident and transient members of the oyster microbiome. Frontiers in Microbiology, 12, 828692.

• Hanley, T. C., Bowen, J. L., Kearns, P. J., & Hughes, A. R. (2021). Short‐and long‐term effects of nutrient enrichment on salt marsh plant production and microbial community structure. Journal of Ecology, 109, 3779–3793.

• McNally, K. L., Bowen, J. L., Brisson, J. O., Kennedy, A., & Innis, C. J. (2021a). Evaluation of the respiratory microbiome and the use of tracheal lavage as a diagnostic tool in Kemp’s ridley sea turtles (Lepidochelys kempii). Animals, 11, 2927.

• McNally, K. L., Innis, C. J., Kennedy, A., & Bowen, J. L. (2021b). Characterization of oral and cloacal microbial communities in cold-stunned Kemp’s ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation. PLoS One, 16, e0252086.

• McNally, K. L., Mott, C. R., Guertin, J. R., & Bowen, J. L. (2021c). Microbial communities of wild-captured Kemp’s ridley (Lepidochelys kempii) and green sea turtles (Chelonia mydas). Endangered Species Research, 45, 21–36.

• Peng, X., Ji, Q., Angell, J. H., Kearns, P. J., Bowen, J. L., & Ward, B. B. (2021). Long-term fertilization alters nitrous oxide cycling dynamics in salt marsh sediments. Environmental Science & Technology, 55, 10832–10842.

• Unzueta‐Martínez, A., Downey‐Wall, A. M., Cameron, L. P., Ries, J. B., Lotterhos, K. E., & Bowen, J. L. (2021). Ocean acidification alters the diversity and structure of oyster associated microbial communities. Limnology and Oceanography Letters, 6, 348–359.

• Vineis, J. H., Bulseco, A. N., & Bowen, J. L. (2021). Microbial dark carbon fixation fueled by nitrate enrichment. bioRxiv, 2021–08.1

• Bowen, J. L., Giblin, A. E., Murphy, A. E., Bulseco, A. N., Deegan, L. A., Johnson, D. S., Nelson, J. A., Mozdzer, T. J., & Sullivan, H. L. (2020). Not all nitrogen is created equal: differ2ential effects of nitrate and ammonium enrichment in coastal wetlands. BioScience, 70, 1108–1119.

• Bulseco, A. N., Vineis, J. H., Murphy, A. E., Spivak, A. C., Giblin, A. E., Tucker, J., & Bowen, J. L. (2020). Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments. Limnology and Oceanography, 65, S321–S339.

• Lynum, C. A., Bulseco, A. N., Dunphy, C. M., Osborne, S. M., Vineis, J. H., & Bowen, J. L. (2020). Microbial community response to a passive salt marsh restoration. Estuaries and Coasts, 43, 1439–1455.3

• Murphy, A. E., Bulseco, A. N., Ackerman, R., Vineis, J. H., & Bowen, J. L. (2020). Sulphide addition favours respiratory ammonification (DNRA) over co4mplete denitrification and alters the active microbial community in salt marsh sediments. Environmental Microbiology, 22, 2124–2139.

• Bowen, J., Baillie, C., Grabowski, J., Hughes, A., Scyphers, S., Gilbert, K., Gorney, S., Slevin, J., Geigley, K. (2019). Boston Harbor, Boston, Massachusetts, USA: Transformation from ‘the harbor of shame’to a vibrant coastal resource. Regional Studies in Marine Science, 25, 100482.

• Bulseco, A. N., Giblin, A. E., Tucker, J., Murphy, A. E., Sanderman, J., Hiller‐Bittrolff, K., & Bowen, J. L. (2019). Nitrate addition stimulates microbial decomposition of organic matter in salt marsh sediments. Global Change Biology, 25, 3224–3241.

• Kearns, P. J., Bulseco-McKim, A. N., Hoyt, H., Angell, J. H., & Bowen, J. L. (2019). Nutrient enrichment alters salt marsh fungal communities and promotes putative fungal denitrifiers. Microbial Ecology, 77, 358–369.

• Murphy, A. E., Kolkmeyer, R., Song, B., Anderson, I. C., & Bowen, J. (2019). Bioreactivity and microbiome of biodeposits from filter-feeding bivalves. Microbial Ecology, 77, 343–357.

• Paynter, I., Schaaf, C., Bowen, J. L., Deegan, L., Peri, F., & Cook, B. (2019). Characterizing a New England saltmarsh with NASA G-LiHT airborne lidar. Remote Sensing, 11, 509.

• Spivak, A., Sanderman, J., Bowen, J., Canuel, E., & Hopkinson, C. (2019). Global-change controls on soil-carbon accumulation and loss in coastal vegetated ecosystems. Nat. Geosci., 12, 685–692.

• Angell, J. H., Peng, X., Ji, Q., Craick, I., Jayakumar, A., Kearns, P. J., Ward, B. B., & Bowen, J. L. (2018). Community composition of nitrous oxide-related genes in salt marsh sediments exposed to nitrogen enrichment. Frontiers in microbiology, 9, 170.

• Feinman, S. G., Farah, Y. R., Bauer, J. M., & Bowen, J. L. (2018). The influence of oyster farming on sediment bacterial communities. Estuaries and coasts, 41, 800–814.

• Hiller-Bittrolff, K., Foreman, K., Bulseco-McKim, A. N., Benoit, J., & Bowen, J. L. (2018). Effects of mercury addition on microbial community composition and nitrate removal inside permeable reactive barriers. Environmental Pollution, 242, 797–806.

• Jayakumar, A., Balachandran, D., Rees, A. P., Kearns, P. J., Bowen, J. L., & Ward, B. B. (2018). Community composition of nitrous oxide reducing bacteria investigated using a functional gene microarray. Deep Sea Research Part II: Topical Studies in Oceanography, 156, 44–50.

• Poynton, H. C., Hasenbein, S., Benoit, J. B., Sepulveda, M. S., Poelchau, M. F., Hughes, D. S., Murali, S. C., Chen, S., Glastad, K. M., Goodisman, M. A., et al. (2018). The toxicogenome of Hyalella azteca: a model for sediment ecotoxicology and evolutionary toxicology. Environmental science & technology, 52, 6009–6022.

• Bowen, J. L., Kearns, P. J., Byrnes, J. E., Wigginton, S., Allen, W. J., Greenwood, M., Tran, K., Yu, J., Cronin, J. T., & Meyerson, L. A. (2017). Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant. Nature communications, 8, 433.5

• Feinman, S. G., Martínez, A. U., Bowen, J. L., & Tlusty, M. F. (2017). Fine-scale transition to lower bacterial diversity and altered community compo6sition precedes shell disease in laboratory-reared juvenile American lobster. Diseases of Aquatic Organisms, 124, 41–54.

• Kearns, P. J., Bowen, J. L., & Tlusty, M. F. (2017). The skin microbiome of cow‐nose rays (Rhinoptera bonasus) in an aquarium touch‐tank exhibit. Zoo Biology, 36, 226–230.

• Kearns, P. J., Fischer, S., Fernández-Beaskoetxea, S., Gabor, C. R., Bosch, J., Bowen, J. L., Tlusty, M. F., & Woodhams, D. C. (2017b). Fight fungi with fungi: antifungal properties of the amphibian mycobiome. Frontiers in Microbiology, 8, 2494.

• Kearns, P. J., Holloway, D., Angell, J. H., Feinman, S. G., & Bowen, J. L. (2017c). Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond. Aquatic microbial ecology, 80, 29–41.

• Tlusty, M., Rhyne, A., Szczebak, J. T., Bourque, B., Bowen, J. L., Burr, G., Marx, C. J., & Feinberg, L. (2017). A transdisciplinary approach to the initial validation of a single cell protein as an alternative protein source for use in aquafeeds. PeerJ, 5, e3170.

• Kearns, P. J., Angell, J. H., Howard, E. M., Deegan, L. A., Stanley, R. H., & Bowen, J. L. (2016). Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments. Nature communications, 7, 12881.

• Kearns, P. J., Weston, N. B., Bowen, J. L., Zivlivic, T., & Vile, M. A. (2016). Tidal freshwater marshes harbor phylogenetically unique clades of sulfate reducers that are resistant to climate induced salinity intrusion. Estuaries and Coasts, 39, 981–991.

• Peng, X., Ji, Q., Angell, J. H., Kearns, P. J., Yang, H. J., Bowen, J. L., & Ward, B. B. (2016). Long‐term fertilization alters the relative importance of nitrate reduction pathways in salt marsh sediments. Journal of Geophysical Research: Biogeosciences, 121, 2082–2095.

• Bowen, J. L., Weisman, D., Yasuda, M., Jayakumar, A., Morrison, H. G., & Ward, B. B. (2015). Marine oxygen-deficient zones harbor depauperate denitrifying communities compared to novel genetic diversity in coastal sediments. Microbial Ecology, 70, 311–321.

• Hiller, K. A., Foreman, K. H., Weisman, D., & Bowen, J. L. (2015). Permeable reactive barriers designed to mitigate eutrophication alter bacterial community composition and aquifer redox conditions. Applied and Environmental Microbiology, 81, 7114–7124.

• Ji, Q., Babbin, A. R., Peng, X., Bowen, J. L., & Ward, B. B. (2015). Nitrogen substrate dependent nitrous oxide cycling in salt marsh sediments. Journal of Marine Research, 73, 71–92.

• Kearns, P. J., Angell, J. H., Feinman, S. G., & Bowen, J. L. (2015). Long-term nutrient addition differentially alters community composition and diversity of genes that control nitrous oxide flux from marsh sediments. Estuarine, Coastal, and Shelf Science, 154, 39–47.

• Bowen, J. L., Babbin, A. R., Kearns, P. J., & Ward, B. B. (2014). Connecting the dots: linking nitrogen cycle gene expression to nitrogen fluxes in marine sediments. Frontiers in Microbiology, 5, 429.

• Bowen, J. L, Kearns, P. J., Holcomb, M., & Ward, B. B. (2013). Acidifcation alters composition of ammonia oxidizing assemblages in marine mesocosms. Marine Ecology Progress Series, 492, 1–8.

• Bowen, J. L., Byrnes, J. E. K., Weisman, D., & Colaneri, C. (2013). Functional gene pyrosequencing and network analysis shed light on denitrifying bacteria in salt marsh sediments and their response to increased nitrogen supply. Frontiers in Microbiology, 4, 342.

• Weisman, D., Yasuda, M., & Bowen, J. L. (2013). FunFrame: Functional Gene Ecological Analysis Pipeline. Bioinformatics, 29, 1212–1214.

• Bowen, J. L., Hobbie, J. E., Morrison, H. G., & Sogin, M. L. (2012). Salt marsh sediment diversity: a test of the variability of the rarebiosphere among environmental replicates. The ISME Journal, 6, 2014–2023.

• Bowen, J. L., Ward, B. B., Morrison, H. G., Hobbie, J. E., Valiela, I., Deegan, L. A., & Sogin, M. L. (2011). Microbial community composition in sediments resisits perturbation by nutrient enrichment. The ISME Journal, 5, 1540–1548.

• van Ooij, S. (2011). This article was also featured in Nature Reviews Microbiology.

• Bowen, J. L., & Valiela, I. (2008). Using 15N to assess coupling between land use and estuaries in temperate and tropical systems. Journal of Coastal Research, 24, 804–813.

• Bowen, J. L., Crump, B. C., Deegan, L. A., & Hobbie, J. E. (2009). Increased supply of ambient nitrogen has minimal effect on salt marsh bacterial production. Limnology and Oceanography, 54, 713–722.

• Bowen, J. L., Crump, B. C., Deegan, L. A., & Hobbie, J. E. (2009). Response of salt marsh sediment bacteria to external nitrogen inputs as measured by denaturing gradient gel electrophoresis. The ISME Journal, 3, 924–934.

• Bowen, J. L., Kroeger, K. D., Tomasky, G., Pabich, W. J., Cole, M. L., Carmichael, R. H., & Valiela, I. (2007). A review of land-estuary coupling by ground water discharge: Mechanisms and effects. Applied Geochemistry, 22, 175–191.

• Bowen, J. L., Ramstack, J. M., Mazzilli, S., & Valiela, I. (2007). NLOAD: An interactive, web-based modeling tool to estimate nitrogen loads and concentrations, and explore options for nitrogen management in estuaries. Ecological Applications, 17, S17–S30.

• Deegan, L. A., Bowen, J. L., Drake, D., Fleeger, J. W., Friedrichs, C. T., Galvan, K. A., Hobbie, J. E., Hopkinson, C., Johnson, J. M., Johnson, D. S., Lemay, D. E., Miller, E., Peterson, B. J., Picard, C., Sheldon, S., Vallino, J., & Warren, R. S. (2007). Susceptibility of salt marshes to nutrient enrichment and predator removal. Ecological Applications, 17, S42–S63.

• Bowen, J. L., & Valiela, I. (2004). Nitrogen loads to estuaries: Using loading models to assess the effectiveness of management options to restore estuarine water quality. Estuaries, 27, 482–500.

• Serveiss, V., J. L. Bowen, D. Dow, and I. Valiela. (2004). Waquoit Bay Watershed Ecological Risk Assessment: Effect of land-derived nitrogen loads on estuarine eutrophication. Environmental Management, 33, 730–740.

• Valiela, I., Mazzilli, S., Bowen, J. L., Kroeger, K. D., Cole, M. L., Tomasky, G., & Isaji, T. (2004). ELM, an estuarine nitrogen loading model: Formulation, and verification of predicted concentrations of dissolved inorganic nitrogen. Water Air and Soil Pollution, 157, 365–391.

• Bowen, J. L., Dow, D., Serveiss, V. B., & Valiela, I. (2003). Waquoit Bay watershed ecological risk assessment: The effect of watershed derived nitrogen loads on estuarine eutrophication. Washington, DC: US Environmental Protection Agency. Office of Research and Development. National Center for Environmental Assessment; report no EPA/600/R-02/079.

• Valiela, I., & Bowen, J. L. (2003). Recent shifts in winter distributions of birds: Effects of global warming and local habitat change. Ambio, 32, 476–480.

• Valiela, I., & Bowen, J. L. (2002). Nitrogen sources to watersheds and estuaries: Role of land cover mosaics and losses within watersheds. Environmental Pollution, 18, 239–248.

• Valiela, I., Bowen, J. L., & Kroeger, K. D. (2002). Assessment of different models for estimation of land-derived nitrogen loads to shallow estuaries. Applied Geochemistry, 17, 935–953.7

• Bowen, J. L., & Valiela, I. (2001). The ecological effects of urbanization o8f coastal watersheds: Historical increases in nitrogen loads and eutrophication of Waquoit Bay estuaries. Canadian Journal of Fisheries and Aquatic Sciences, 58, 1489–1500.

• Bowen, J. L., & Valiela, I. (2001). Historical changes in atmospheric nitrogen deposition to Cape Cod, Massachusetts, USA. Atmospheric Environment, 35, 1039–1051.

• Valiela, I., J. L. Bowen, and J. K. York. (2001). Mangrove forests: One of the world's most threatened major tropical environments. BioScience, 51, 807–815.

• Valiela, I., Bowen, J. L., Cole, M. L., Kroeger, K. D., Lawrence, D., Pabich, W. J., Tomasky, G. L., & Mazzilli, S. (2001). Following up on a Margalevian concept: Interactions and exchanges among adjacent parcels of coastal landscapes. Scientia Marina, 65, 217–231.9

• Evgenidou, A., Konkle, A., DiAmbrosio, A., Corcoran, A., Bowen, J., Brown, E., Corcoran, D., Dearholt, C., Fern, S., Lamb, A., Michalowski, J., Ruegg, I., & Cebrian, J. (1999). Effects of increased nitrogen loading on the abundance of diatoms and dinoflagellates in estuarine phytoplankton communities. Biological Bulletin, 197, 292–294.10

• Kroeger, K.,11 J. L. Bowen, D. Corocoran, J. Michelowski, J. Moorman, C. Rose, and I. Valiela. (1999). Nitrogen loading to Green Pond: Sources and management options. Environment Cape Cod, 2, 15–26.