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Santoro AE, Francis CA, De Sieyes NR, Boehm AB.  2008.  Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environmental Microbiology. 10:1068–1079.
Santoro AE, Lombardero MJ, Ayres MP, Ruel JJ.  2001.  Interactions between fire and bark beetles in an old growth pine forest. Forest Ecology and Management. 144:245–254.
Santoro AE, Boehm AB, Francis CA.  2006.  Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer. Applied and Environmental Microbiology. 72:2102–2109.
Santoro AE, Boehm AB.  2007.  Frequent occurrence of the human-specific Bacteroides fecal marker at an open coast marine beach: relationship to waves, tides and traditional indicators. Environmental Microbiology. 9:2038–2049.
Santoro AE, Casciotti KL, Francis CA.  2010.  Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environmental Microbiology. 12:1989–2006.
Santoro AE.  2010.  Microbial nitrogen cycling at the saltwater–freshwater interface. Hydrogeology Journal. 18:187–202.
Santoro AE, Casciotti KL.  2011.  Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation. The ISME journal. 5:1796–1808.
Santoro AE, Nidzieko NJ, Van Dijken GL, Arrigo KR, Boehm AB, .  2010.  Contrasting spring and summer phytoplankton dynamics in the nearshore Southern California Bight. Limnology and Oceanography. 55:264.
Santoro AE, Buchwald C, McIlvin MR, Casciotti KL.  2011.  Isotopic signature of N2O produced by marine ammonia-oxidizing archaea. Science. 333:1282–1285.
Santoro AE, Dupont CL, R Richter A, Craig MT, Carini P, McIlvin MR, Yang Y, Orsi WD, Moran DM, Saito MA.  2015.  Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean. Proceedings of the National Academy of Sciences. 112:1173–1178.
Santoro AE.  2016.  The do-it-all nitrifier. Science. 351:342–343.
Santoro AE, Saito MA, Goepfert TJ, Lamborg CH, Dupont CL, DiTullio GR.  2017.  Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation. Limnology and Oceanography.
Santoro AE.  2019.  Crystal ball: the microbial map of the ocean.. Environ Microbiol Rep. 11(1):35-37.