Publications

*Thompson, M., Valentine, D.L., and Peng, X.. (2024). Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean. FEMS Microbes: xtae028. [Link]
Peng, X., Yousavich, D.J., Bourbonnais, A., Wenzhoefer, F., Janssen, F., Treude, T., and Valentine, D.L. (2024). The fate of fixed nitrogen in Santa Barbara Basin sediments during seasonal anoxia. Biogeosciences, 21: 3041–3052. [Link]
Peng, X., Amend, A.S., Baltar, F., Blanco-Bercial, L., Breyer, E., Burgaud, G., Cunliffe, M., Edgcomb, V.P., Grossart, H., Mara, P., Masigol, H., Pang, K., Retter, A., Roberts, C., van Bleijswijk, J., Walker, A.K., and Whitner, S. (2024). Planktonic marine fungi: A review. JGR Biogeosciences, 129: e2023JG007887. [Link] (Part of the Celebrating 20 Years at JGR: Biogeosciences special collection)
Yousavich, D.J., Robinson, D., Peng, X., Krause, S.J.E., Wenzhoefer, F., Janßen, F., Liu, N., Tarn, J., Kinnaman, F., Valentine, D.L., and Treude, T. (2024). Marine anoxia initiates giant sulfur-bacteria mat proliferation and associated changes in benthic nitrogen, sulfur, and iron cycling in the Santa Barbara Basin, California Borderland. Biogeosciences, 21: 789-809. [Link]
Liu, N., Kivenson, V., Peng, X., Cui, Z., Lankiewicz, T., Gosselin, K., English, C., Blair, E., O'Malley, M.A., and Valentine, D.L. (2024). Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen. Applied and Environmental Microbiology, 90: e00914-23. [Link]
*Lane, D.M., Valentine, D.L., and Peng, X.. (2023). Genomic analysis of the marine yeast Rhodotorula sphaerocarpa ETNP2018 reveals adaptation to the open ocean. BMC Genomics, 24: 695. [Link]
Tang, W., Ward, B. B., Beman, M., Bristow, L., Clark, D., Fawcett, S., Frey, C., Fripiat, F., Herndl, G. J., Mdutyana, M., Paulot, F., Peng, X., Santoro, A. E., Shiozaki, T., Sintes, E., Stock, C., Sun, X., Wan, X. S., Xu, M. N., and Zhang, Y. (2023). Database of nitrification and nitrifiers in the global ocean, Earth System Science Data, 15: 5039-5077. [Link]
Xenopoulos, M.A., Bond-Lamberty, B., Huntzinger, D., Desai, A.R., Feng, X., Hammond, W.M., Moore, D.J.P., Peng, X., Sahagian, D., Santin, C., Vargas, R., Wells, N.S., and Wooden, P. (2023). Update on Our Action Plan for Equity, Inclusion, and Diversity in Publishing at JGR: Biogeosciences. JGR Biogeosciences, 128: e2023JG007712. [Link]
*Lazo-Murphy, B., *Larson, S., *Staines, S., *Bruck, H., *McHenry, J., Bourbonnais, B., and Peng, X. (2022). Nitrous oxide production and isotopomer composition by fungi isolated from salt marsh sediments. Frontiers in Marine Science, 9: 1098508. [Link]
Burgaud, G., Edgcomb, V., Hassett, B.T., Kumar, A., Li, W., Mara, P., Peng, X., Philippe, A., Phule, P., Prado, S., Quéméner, M., and Roullier, C. (2022). Marine Fungi. In: Stal, L.J., Cretoiu, M.S. (eds) The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, vol 3. Springer, Cham [Link]
Peng, X., Ji, Q., Angell, J., Kearns, P., Bowen, J.L., and Ward, B.B. (2021). Long-term fertilization alters nitrous oxide cycling dynamics in salt marsh sediments. Environmental Science and Technology, 55(15): 10832-10842. [Link]
Peng, X., Gat, D., Paytan, A., and Rudich, Y. (2021). The response of airborne mycobiome to dust storms in the Eastern Mediterranean. Journal of Fungi, 7(10): 802. [Link]
Peng, X. and Valentine, D.L. (2021). Diversity and N₂O production potential of fungi in an oceanic oxygen minimum zone. Journal of Fungi, 7(3): 218. [Link]
Roux, S., Paul, B.G., Bagby, S.C., Nayfach, S., Allen, M.A., Attwood, G., Cavicchioli, R., Chistoserdova, L., Gruninger, R.J., Hallam, S.J., Hernandez, M.E., Hess, M., Liu, W-T., McAllister, T.A., O’Malley, M.A., Peng, X., Rich, V.I., Saleska, S., and Eloe-Fadrosh, E.A. (2021). Ecology and molecular targets of hypermutation in the global microbiome. Nature Communications, 12: 3076. [Link]
Peng, X., Wilken, S.E., Lankiewicz, T.S., Gilmore, S.P., Brown, J.L., Henske, J.K., Swift, C.L., Salamov, A., Barry, K., Grigoriev, I.V., Theodorou, M.K., Valentine, D.L., O’Malley, M.A. (2021). Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. Nature Microbiology 6: 499-511. [Link]
Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I.-M., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T.B.K., Nielsen, T., Kirton, E., Faria, J.P., Edirisinghe, J.N., Henry, C.S., Jungbluth, S.P., Chivian, D., Dehal, P., Wood-Charlson, E.M., Arkin, A.P., Tringe, S.G., Visel, IMG/M Data Consortium (including Peng, X.), Woyke, T., Mouncey, N.J., Ivanova, N.N., Kyrpides, N.C., Eloe-Fadrosh, E.A. (2020). A genomic catalog of Earth’s microbiomes. Nature Biotechnology, 39: 499–509. [Link]
Hassett, B.T., Vonnahme, T.R., Peng, X., Jones, E.B.G., and Heuzé, C. (2020). Global diversity and geography of the planktonic marine fungi. Botanica Marina, 63(2): 121-139. [Link]
Peng, X., Fawcett, S.E., van Oostende, N., Wolf, M.J., Marconi, D., Sigman, D.M, and Ward, B.B. (2018). Nitrogen uptake and nitrification in the subarctic North Atlantic Ocean. Limnology and Oceanography, 63(4): 1462-1487. [Link]
Angell, J.H., Peng, X., Ji, Q., Craick, I., Jayakumar, A., Kearns, P.J., Ward, B.B., and Bowen, J.L. (2018). Community composition of nitrous oxide-related genes in salt marsh sediments exposed to nitrogen enrichment, Frontiers in Microbiology, 9: 170. [Link]
Peng, X., Swift, C.L., Theodorou, M.K., O’Malley, M.A. (2018). Methods for genomic characterization and maintenance of anaerobic fungi. In: de Vries R., Tsang A., Grigoriev I. (eds) Fungal Genomics. Methods in Molecular Biology, vol 1775. Humana Press, New York, NY. [Link]
Gilmore, S.P., Henske, J.K., Sexton, J.A., Solomon, K.V., Seppala, S., Yoo, J.I., Huyett, L.M., Pressman, A., Cogan, J.Z., Kivenson, V., Peng, X., Tan, Y., Valentine, D.L., and O’Malley, M.A. (2017). Genomic analysis of methanogenic archaea reveals a shift towards energy conservation. BMC Genomics 18: 639. [Link]
Peng, X., Ji, Q., Angell, J., Kearns, P., Yang, H.J., Bowen, J.L., and 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(8), 2082-2095. [Link]
Peng, X., Gilmore, S.P., O’Malley, M.A. (2016). Microbial communities for bioprocessing: Lessons learned from nature. Current Opinion in Chemical Engineering, 14, 103-109. [Link]
Peng, X., Fuchsman, C.A., Jayakumar, A., Warner, M.J., Devol, A.H., and Ward, B.B. (2016). Revisiting Nitrification in the Eastern Tropical South Pacific: A focus on controls. Journal of Geophysical Research: Oceans, 121, 1667-1684. [Link]
Peng, X., Fuchsman, C.A., Jayakumar, A., Oleynik, S., Martens-Habbena, W., Devol, A.H., and Ward, B.B. (2015). Ammonia and nitrite oxidation in the Eastern Tropical North Pacific. Global Biogeochemical Cycles, 29, 2034-2049. [Link]
Ji, Q., Babbin, A.R., Peng, X., Bowen, J.L., and Ward, B.B. (2015) Nitrogen substrate-dependent nitrous oxide cycling in salt marsh sediments. Journal of Marine Research 73: 71-92. [Link]
Jayakumar, A., Peng X., and Ward, B.B. (2013). Community composition of bacteria involved in fixed nitrogen loss in the water column of two major oxygen minimum zones in the ocean. Aquatic Microbial Ecology 70: 245-259. [Link]
Peng, X., Jayakumar, A., and Ward, B.B. (2013). Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones. Frontiers in Microbiology 4: 177. [Link]
Peng, X., Yando, E., Hildebrand, E., Dwyer, C., Kearney, A., Waciega, A., Valiela, I., and Bernhard, A.E. (2013). Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh. Frontiers in Microbiology 3: 445. [Link]