Publications

In revision.  Genco, B.M., M.E. White, I. Koester, L. Aluwihare, and J.M. Beman.  Tropical cyclones drive phytoplankton blooms and simultaneous oxygen minimum zone shoaling.  Nature Communications

2023  White, M.E., et al. Refractory dissolved organic matter has similar chemical characteristics but different radiocarbon signatures with depth in the marine water column.  Global Biogeochemical Cycles 37: e2022GB007603 ::HTML::

2022  Perez-Coronel, E. and J.M. Beman.  Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis.  Nature Communications 13: 6454 ::HTML::

2022  Fremin, B.J. et al.  Thousands of small, novel genes predicted in global phage genomes.  Cell Reports 39: 110984 ::HTML::

2021  Beman, J.M. et al.  Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones.  Nature Communications 12: 7043 ::HTML::

2021  Montiel-Molina, J.A.M., J.P. Sexton, A.C. Frank, and J.M. Beman.  Archaeal and bacterial diversity and distribution patterns in Mediterranean-climate vernal pools of Mexico and the western USA.  Microbial Ecology ::HTML::

2021  Schorn, M.A. et al.  A community resource for paired genomic and metabolomic data mining.  Nature Chemical Biology 17: 363-368.  ::HTML::

2021  Perez-Coronel, E., S.C. Hart, and J.M. Beman.  Methane dynamics of high elevation lakes in the Sierra Nevada California: the role of elevation, temperature, and inorganic nutrients.  Inland Waters 11: 267-277. ::HTML::

2020  Nayfach, S. et al.  A genomic catalog of Earth’s microbiomes.  Nature Biotechnology 39: 499-509.  ::HTML::

2020  Beman, J.M. et al.  Biogeochemistry and hydrography shape microbial community assembly and activity in the eastern tropical North Pacific Ocean oxygen minimum zone.  Environmental Microbiology  ::HTML::

2019  Rapacciuolo, G., J.M. Beman, L.M. Schiebelhut, and M.N. Dawson.  Microbes and macro-invertebrates show parallel β-diversity but contrasting α-diversity patterns in a marine natural experiment.  Proceedings of the Royal Society B 286: 20190999. ::RAPACCIUOLO19_PROCB::

2019  Wilson, J.M., G. Ucharm, and J.M. Beman.  Climatic, physical, and biogeochemical changes drive rapid oxygen loss and recovery in a marine ecosystem.  Scientific Reports 9: 16114. ::WILSON19_SCIREP::

2019  Stephens, B.M., S.D. Wankel, J.M. Beman, A.J. Rabines, A.E. Allen and L.I. Aluwihare.  Euphotic zone nitrification in the California Current Ecosystem.  Limnology and Oceanography. ::STEPHENS19_LO::

2019  Ul-Hasan, S., R.M. Bowers, A. Figueroa-Montiel, A.F. Licea-Navarro, J.M. Beman, T. Woyke, and C.J. Nobile. Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California.  PloS One 14: e0212355. ::HTML::

2018  Wilson, J. M., S.Y. Litvin, and J.M. Beman, J. M. Microbial community networks associated with variations in community respiration rates during upwelling in nearshore Monterey Bay, California.  Environmental Microbiology Reports 10: 272-282.  ::HTML::

2017  Wilson, J.M., S. Abboud., and J.M. Beman.  Primary Production, Community Respiration, and Net Community Production along Oxygen and Nutrient Gradients: Environmental Controls and Biogeochemical Feedbacks within and across “Marine Lakes.”  Frontiers in Marine Science 4: 12.  ::HTML::

2016  Meyerhof, M.S., J.M. Wilson, M.N. Dawson, and J.M. Beman.  Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau.  Environmental Microbiology 18: 4907–4919.  ::HTML::

2016  Carey, C.J., N.C. Dove, J.M. Beman, S.C. Hart, and E.L. Aronson. Meta-analysis reveals ammonia-oxidizing bacteria respond more strongly to nitrogen addition than ammonia-oxidizing archaea.  Soil Biology and Biochemistry 9: 158-166. ::PDF::

2016  Moulton, O.M., M.A. Altabet, J.M. Beman, L.A. Deegan, J. Lloret, M.K. Lyons, J.A. Nelson, and C.A. Pfister. Microbial associations with macrobiota in coastal ecosystems: patterns and implications for nitrogen cycling. Frontiers in Ecology and the Environment 4: 200-208 ::PDF::

2016  Smith, B., M. Beman, D. Gravano and Y. Chen. Development and validation of a microbe detecting UAV payload. 2015 Workshop on Research, Education and Development of Unmanned Aerial Systems (RED-UAS), Cancun, Mexico: 258-264. ::PDF::

2016  Graham, E.B. et al. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Frontiers in Microbiology 7: 214. ::HTML::

2015 Hayden, C.J. and J.M. Beman. Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park, California, USA. Environmental Microbiology doi 10.1111/1462-2920.12938. ::HTML::

2015 Carey, C.J., J.M. Beman, V.T. Eviner, C.S. Malmstrom, and S.C. Hart. Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands. Frontiers in Microbiology 6: 466. ::HTML::

2015 Carolan, M.T., J.M. Smith and J.M. Beman.  Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone. Frontiers in Microbiology 6: 334. ::HTML::

2014 Hayden, C.J. and J.M. Beman. High abundances of potentially active ammonia-oxidizing bacteria and archaea in oligotrophic, high-altitude lakes of the Sierra Nevada, California, USA. PLOS ONE 9(11): e111560.  ::HTML::

2014 Wilson, J.M., R. Severson, and J.M. Beman. Ocean-scale patterns in community respiration rates along continuous transects across the Pacific Ocean. PLOS ONE 9(7): e99821. ::HTML::

2014 Beman, J.M. Activity, abundance, and diversity of nitrifying archaea and denitrifying bacteria in sediments of a subtropical estuary: Bahía del Tóbari, Mexico. Estuaries and Coasts (invited submission to thematic issue) 37: 1343-1352.  ::PDF::

2013 Beman, J.M. and M.T. Carolan. Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone. Nature Communications 4: 2705. ::BEMAN13_NCOMM::

2013 Beman, J.M., J.L. Shi, B.N. Popp.  Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean. ISME Journal 7: 2192-2205. ::BEMAN13_ISMEJ::

2013 Gilly, W.F., J.M. Beman, S.Y. Litvin, B. Robison.  Oceanographic and biological effects of shoaling of the oxygen minimum zone.  Annual Review of Marine Science 5: 393-420.  ::HTML::

2012 Beman, J.M., V.J. Bertics, T. Braunschweiler, and J.M. Wilson. Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California. Frontiers in Microbiology 3: 263.  ::HTML::

2012 Beman, J.M., B.N. Popp, and S.E. Alford. Quantification of ammonia oxidation rates and ammonia-oxidizing archaea and bacteria at high resolution in the Gulf of California and eastern tropical North Pacific Ocean. Limnology and Oceanography 57: 711-726.  ::BEMAN12_LO.pdf::

2011 Beman, J.M., C.-E. Chow, A.L. King, Y. Feng, J.A. Fuhrman, A. Andersson, N.R. Bates, B.N. Popp, and D.A. Hutchins. Global declines in oceanic nitrification rates as a consequence of ocean acidification. Proceedings of the National Academy of Sciences 108: 209-213.  ::BEMAN11_PNAS::

2011 Steele, J.A., P.D. Countway, L. Xia, P. Vigil, J.M. Beman, et al. Marine bacterial, archaeal, and protistan association networks reveal ecological linkages. ISME Journal 5: 1414-1425.  ::STEELE11_ISMEJ.pdf::

2011 Beman, J.M., J.A. Steele, and J.A. Fuhrman. Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. ISME Journal 5: 1077-1085.  ::BEMAN11_ISMEJ::

2010 Beman, J.M., R. Sachdeva, and J.A. Fuhrman. Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight. Environmental Microbiology 12: 1282-1292.  ::HTML::

2008 Ahrens, T.D., J.M. Beman, J.A. Harrison, P.K. Jewett, and P.A. Matson. A synthesis of nitrogen transformations and transfers from land to sea in the Yaqui Valley agricultural region of Northwest Mexico. Water Resources Research 44: W00A05 (invited).  ::PDF::

2008 Beman, J.M., B.N. Popp, and C.A. Francis. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME Journal 2: 429-441.  ::BEMAN08_ISMEJ::

2007 Beman, J.M., K.J. Roberts, L. Wegley, F. Rohwer, and C.A. Francis. Distribution and diversity of archaeal ammonia monooxygenase (amoA) genes associated with corals. Applied and Environmental Microbiology 73: 5642-5647.  ::BEMAN07_AEM.pdf::

2007 Francis, C.A., J.M. Beman, and M.M.M. Kuypers. New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME Journal 1: 19-27.  ::FRANCIS07_ISMEJ.pdf::

2006 Beman, J.M. and C.A. Francis. Diversity of ammonia-oxidizing Archaea and Bacteria in the sediments of a hyper-nutrified subtropical estuary: Bahía del Tóbari, Mexico. Applied and Environmental Microbiology 72: 7677-7777.  ::BEMAN06_AEM.pdf::

2006 Gilly, W.F., C.A. Elliger, C.A. Salinas, S. Camarillo-Coop, G. Bazzino and J.M. Beman. Spawning by jumbo squid Dosidicus gigas in San Pedro Mártir Basin, Gulf of California, Mexico. Marine Ecology Progress Series 313: 125-133.  ::GILLY06_MEPS.pdf::

2005 Francis, C.A., K.J. Roberts, J.M. Beman, A.E. Santoro and B.B. Oakley. Ubiquity and diversity of ammonia-oxidizing Archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences 102: 14683-14688.  ::FRANCIS05_PNAS::

2005 Beman, J.M., K.R. Arrigo and P.A. Matson. Agricultural runoff fuels large phytoplankton blooms in vulnerable areas of the ocean. Nature 434: 211-214.  ::BEMAN05_Nature::