Publications and Projects - San Pedro Ocean Time-series (SPOT)

Teel, EN, X Liu, BN Seegers, MA Ragan, WZ Haskell, BH Jones, NM Levine. (2018). Contextualizing time-series data: quantification of short-term regional variability in the San Pedro Channel using high-resolution in situ glider data. Biogeosciences 15.20:6151-6165.

Haskell WZ, MG Prokopenko, DE Hammond, RHR Stanley, and ZO Sandwith. (2017). Annual cyclicity in export efﬁciency in the inner Southern California Bight. Global Biogeochemical Cycles 31.2:357-376.

Connell, PE, V Campbell, AG Gellene, SK Hu, DA Caron. (2017). Planktonic food web structure at a coastal time-series site: II. Spatiotemporal variability of microbial trophic activities. Deep Sea Research Part I 121:210-223.

Caron, DA, PE Connell, RA Schaffner, A Schnetzer, JA Fuhrman, PD Countway, DK Kim. (2017). Deep-Sea Research Part I 121:14-29.

Hu, SK, V Campbell, PE Connell, AG Gellene, Z Liu, R Terrado and DA Caron. (2016). Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific. FEMS Microbial Ecology 92.4:1-13.

Haskell, WZ, DE Hammond, MG Prokopenko. (2015). A dual-tracer approach to estimate upwelling velocity in coastal Southern California. Earth and Planetary Science Letters 422:138-140.

Fuhrman, JA, JA Cram, DM Needham. (2015). Marine microbial community dynamics and their ecological interpretation. Nature Reviews 13:133-146.

Cram, JA, CET Chow, R Sachdeva, DM Needham, AE Parada, JA Steele, JA Fuhrman. (2015). Seasonal and interannual variability of the marine bacterioplantkon community throughout the water column over ten years. ISME 9:563-580.

Chow, CET, DY Kim, R Sachdeva, DA Caron and JA Fuhrman. (2014). Top-down controls on bacterial community structure: microbial network analysis of bacteria, T-4like viruses and protists. ISME 8:816-829.

Needham, DM, CET Chow, JA Cram, R Sachdeva, A Parada, FA Fuhrman. (2013). Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. ISME 7:1274-1285.

Xia, LC, D Ai, JA Cram, JA Fuhrman, F Sun. (2013). Efficient statistical significance approximation for local similarity analysis of high-throughput time-series data. Bioinformatics 29:230-237.

Lie, AAY, DY Kim, A Schnetzer, and DA Caron. (2013). Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of Southern California. Aquatic Microbial Ecology 70:93-110.

Kim, DY, PD Countway, AC Jones, A Schnetzer, W Yamashita, C Tung, and DA Caron. (2013). Monthly to interannual variability of microbial eukaryote assemblages at four depths in the eastern north pacific. ISME 1:16.

Chow, CET, R Sachdeva, JA Cram, JA Steele, DM Needham, A Patel, AE Parada, and JA Fuhrman. (2013). Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. ISME J doi: 10.1038/ismej.2013.122

Seth, JG, J Mendez, J Moffett, and J Adkins. (2012). The flux of iron and iron isotopes from San Pedro Basin sediments. Geochimica et Cosmochimica Acta 93:14-29.

Koid, A, WC Nelson, A Mraz, and KB Heidelberg. (2012). Comparative analysis of eukaryotic marine assemblages from 18S rRNA gene and gene transcript clone libraries by using different methods of extraction. Applied Environmental Microbiology 78:3958-3965.

Kim, DY, PD Countway, W Yamashita, and DA Caron. (2012). A combined sequence-based and fragment-based characterization of microbial eukaroyote assemblages provides taxonomic context for the terminal restriction fragment length polymorphism (T-RFLP) method. Journal of Microbiological Methods 91:527-536.

Xia, LC, JA Steele, JA Cram, ZG Cardon, SL Simmons, JJ Vallino, JA Fuhrman, and F Sun. (2011). Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Systems Biology doi:10.1186/1752-0509-5-S2-S15.

Steele, JA, PD Countway, L Xia, PD Vigil, JM Beman, DY Kim, CET Chow, R Sachdeva, AC Jones, MS Schwalbach, JM Rose, I Hewson, A Patel, F Sun, DA Caron and JA Fuhrman. (2011). Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME 5, 1414–1425; doi:10.1038/ismej.2011.24.

Schnetzer, A, SD Moorthi, PD Countway, RJ Gast, IC Gilg, DA Caron. (2011). Depth matters: microbial eukaryote diversity and community structure in the eastern north pacific revealed through environmental gene libraries. Deep Sea Research I 58:16-26.

Hamersley, MR, KA Turk, A Leinweber, N Gruber, JP Zehr, T Gunderson, and DG Capone. (2011). Nitrogen fixation within the water column associated with two hypoxic basins in the Southern California Bight. Aquat Microb Ecol 63: 193-205.

Collins, LE, W Berelson, DE Hammond, A Knapp, R Schwartz, and D Capone. (2011). Particle fluxes in San Pedro Basin, California: A four year record of sedimentation and physical forcing. Deep-Sea Research I 58:898-914.

Beman, JM, JA Steele, and JA Fuhrman. (2011). Co-occurrence patterns for abundant marine archael and bacterial lineages in the deep chlorophyll maximum of coastal California. ISME 5:1077-1085.

Fitzpatrick, E, DA Caron, and A Schnetzer. (2010). Development and environmental application of a genus-specific quantitative PCR approach for Pseudo-nitzchia species. Mar Biol 157:1161-1169.

Gilg, BC, LA Amaral-Zettler, PD Countway, S Moorthi, A Schnetzer, DA Caron. (2010). Phylogenetic affiliations of mesopelagic Acantharia and Acantharian-like environmental 18S rRNA genes off the Southern California Coast. Protist 161:197-211.

Countway, PD, PD Vigil, A Schnetzer, SD Moorthi, and DA Caron. (2010). Seasonal analysis of protistan community structure and diversity at the USC Microbial Observatory (San Pedro Channel, North Pacific Ocean). Limol Oceanogr 55(6): 2381-2396.

Fuhrman JA. (2009). Microbial community structure and its functional implication. Nature 459:193-199.

Caron, DA, PD Countway, P Saval, RJ Gast, A Schnetzer, SD Moorthl, MR Dennett, DM Moran, and AC Jones. (2009). Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Applied and Environmental Microbiology 75: 5797-5808.

Beman, JM. R Sachdeva, and JA Fuhrman. (2010). Population ecology of nitrifying Archae and Bacteria in the Southern California bight. Environmental Microbiology 12:1282-1292.

Fuhrman, JA, MS Schwalbach, and U Stingl. (2008). Proteorhodopsins: an array of physiological roles? Nature 6:488-494.

Fuhrman, JA, JA Steele, I Hewson, MS Schwalbach, MV Brown, JL Green, and JH Brown. (2008). A latitudinal diversity gradient in planktonic marine bacteria. PNAS 105:7774-7778.

Fuhrman, JA, JA Steele. (2008). Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquatic Microbial Ecology 53:69-81.

Hewson, I, ME Jacobson/Meyers, and JA Fuhrman. (2007). Diversity and biogeograph of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California borderlands. Environmental Microbiology 9:923-933.

Ruan, Q, D Dutta, MS Schwalbach, JA Steele, JA Fuhrman, and F Sun. (2006). Local similarity analysis reveals unique applications among marine bacterioplankton species and environmental factors. Bioinformatics 22:2532-2538.

Hewson, I, JA Steele, DG Capone, and JA Fuhrman. (2006). Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition. Limol Oceanogr 51:1274-1283.

Fuhrman, JA, I Hewson, MS Schwalbach, JA Steele, MV Brown, and S Naeem. (2006). Annually reoccurring bacterial communities are predictable from ocean conditions. PNAS 103:13104-13109.

Countway, PD, DA Caron. (2006). Abundance and distribution of ostreococcus sp. in the San Pedro Channel, California, as revealed by quantitative PCR. Applied and Environmental Microbiology 72:2496-2506.

Schwalbach, MS, M Brown, and JA Fuhrman. (2005). Impact of light on marine bacterioplankton community structure. Aquatic Microbial Ecology 39:235-245.

Schnetzer, A, DA Caron. (2005). Copepod grazing impact on the trophic structure of the microbial assemblage of the San Pedro Channel, California. Journal of Plankton Research 27:969-971.

Brown, MV, MS Schwalbach, I Hewson, and JA Fuhrman. (2005). Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environmnetal Microbiology 7:1466-1479.

Brown, MV, Fuhrman JA. (2005). Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquatic Microbial Ecology 41:15-23.

Research Projects

Research activities affiliated with the USC Wrigley Institute SPOT program have received more than $10 million in grant funding to date. Please see below for a summary of funded activities.

Project Title	Investigator(s)	NSF Program(s)
Collaborative Research: New Constraints on Marine Oxygen Cycling	William Berelson (Principal Investigator)	Chemical Oceanography
Can B-vitamins control phyto-and-bacterioplankton successions in a coastal upwelling region?	Sergio Sanudo-Wilhelmy (Principal Investigator) David Hutchins (Co-Principal Investigator) Feixue Fu (Co-Principal Investigator)	Biological Oceanography
Collaborative Research: New Approaches to New Production	Douglas Capone (Principal Investigator)	Biological Oceanography
EAGER: Direct Identification and Characterization of Marine Heterotrophic Nitrogen Fixers by Stable Isotope Probing	Douglas Capone (Principal Investigator)	Biological Oceanography
Collaborative Research: Use of Triple Oxygen Isotopes and O2/Ar to constrain Net/Gross Oxygen Production during upwelling and non-upwelling periods in a Coastal Setting	Douglas Hammond (Principal Investigator)	Chemical Oceanography
Collaborative Research: Use of Triple Oxygen Isotopes and O2/Ar to constrain Net/Gross Oxygen Production during upwelling and non-upwelling periods in a Coastal Setting	Maria Prokopenko (Principal Investigator)	Chemical Oceanography
Dimensions: Pattern and Process in Marine Bacterial, Archaeal, and Protistan Biodiversity, and Effects of Human Impacts	Jed Fuhrman (Principal Investigator) Fengzhu Sun (Co-Principal Investigator) William Nelson (Co-Principal Investigator) John Heidelberg (Co-Principal Investigator) David Caron (Co-Principal Investigator)	Biological Oceanography, Dimensions of Biodiversity
Marine viral dynamics and incorporation into microbial association networks	Jed Fuhrman (Principal Investigator)	Biological Oceanography
The Oceanography of B-Vitamins: evaluating how nutrients and trace metals influence their synthesis, cycling, and biogeochemical impact	Sergio Sanudo-Wilhelmy (Principal Investigator) Eric Webb (Co-Principal Investigator)	Chemical Oceanography
MO: Assembly of Marine Microbial Communities	Jed Fuhrman (Principal Investigator) David Caron (Co-Principal Investigator)	Micro Obs & Micro Inter & Pro, Microbial Genome Sequencing
Genomic Analysis of Unculturable Microbial Eukaryotic Plankton of the San Pedro Ocean Time Series Station	Karla Heidelberg (Principal Investigator) David Caron (Co-Principal Investigator) John Heidelberg (Co-Principal Investigator)	Microbial Genome Sequencing
Experimentally linking identification and function of marine bacteria	Jed Fuhrman (Principal Investigator)	Micro Obs & Micro Inter & Pro, Biological Oceanography
Biogeochemical roles of planktonic archaea	Jed Fuhrman (Principal Investigator)	Biological Oceanography
Collaborative Research: Relating Microbial Biodiversity to Biological Oceanographic Processes	Jed Fuhrman (Principal Investigator) Douglas Capone (Co-Principal Investigator)	Biological Oceanography, Environmental Genomics
Discovery and Characterization of Uncultivated Bacteria, Archaea and Protista from the San Pedro Channel Time Series	Jed Fuhrman (Principal Investigator) David Caron (Co-Principal Investigator)	Micro Obs & Micro Inter & Pro