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Genomes and Genes | Jonathan P ZehrSummaryAffiliation: University of California Country: USA Publications
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Publications
Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem IIJonathan P Zehr
Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
Science 322:1110-2. 2008....
Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genesJonathan P Zehr
Department of Ocean Sciences and Institute of Marine Science, Earth and Marine Sciences, Bldg A438, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
Biotechniques 35:996-1002, 1004-5. 2003....- Nitrogen cycle of the open ocean: from genes to ecosystemsJonathan P Zehr
Ocean Sciences Department, University of California, Santa Cruz, California 95064, USA
Ann Rev Mar Sci 3:197-225. 2011..The nitrogen cycle in the oceans is an integral feature of the function of ocean ecosystems and will be a central player in how oceans respond during global environmental change... 
Low genomic diversity in tropical oceanic N2-fixing cyanobacteriaJonathan P Zehr
Department of Ocean Sciences, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
Proc Natl Acad Sci U S A 104:17807-12. 2007..Although genomic diversity seems to be the rule in many, if not most, marine microbial lineages, different forces may control the evolution and diversification in low abundance microorganisms, such as the nitrogen-fixing cyanobacteria...- Nitrogen fixation by marine cyanobacteriaJonathan P Zehr
Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
Trends Microbiol 19:162-73. 2011..The major cyanobacterial groups have different physiological and ecological constraints that result in highly variable geographic distributions, with implications for the marine N-cycle budget... - Phylogenetic diversity of cyanobacterial narB genes from various marine habitatsRyan W Paerl
Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street EMS D446, Santa Cruz, CA 95064, USA
Environ Microbiol 10:3377-87. 2008..Using a reverse transcription PCR method, narB mRNA sequences were amplified from Heron Island samples, indicating that narB expression can be detected in environmental samples... - Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domainPia H Moisander
Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
Science 327:1512-4. 2010..These findings have implications for the geographic extent and magnitude of basin-scale oceanic N2 fixation rates... - Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacteriumH James Tripp
Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
Nature 464:90-4. 2010..The UCYN-A cyanobacterium is a paradox in evolution and adaptation to the marine environment, and is an example of the tight metabolic coupling between microorganisms in oligotrophic oceanic microbial communities... - Comparison of diazotroph community structure in Lyngbya sp. and Microcoleus chthonoplastes dominated microbial mats from Guerrero Negro, Baja, MexicoEnoma O Omoregie
Department of Ocean Sciences and Institute of Marine Sciences, University of California, Santa Cruz, 95064, USA
FEMS Microbiol Ecol 47:305-8. 2004.... - Abundance and distribution of major groups of diazotrophic cyanobacteria and their potential contribution to N₂ fixation in the tropical Atlantic OceanNicole L Goebel
University of California at Santa Cruz, Ocean Sciences Department, Santa Cruz, CA 95064, USA
Environ Microbiol 12:3272-89. 2010..Modelled contributions of Trichodesmium, UCYN-B and UCYN-A to total N₂ fixation suggested that Trichodesmium had the largest input, except for the potential of UCYN-A at the Cape Verde Islands... - In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsoniiIan Hewson
Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
ISME J 3:618-31. 2009.... - Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial matsPia H Moisander
Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
Environ Microbiol 8:1721-35. 2006..The nifH microarray is a powerful tool for diazotroph community analysis in the marine environment... - Unicellular cyanobacterium symbiotic with a single-celled eukaryotic algaAnne W Thompson
Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
Science 337:1546-50. 2012.... - Genome-wide analysis of diel gene expression in the unicellular N(2)-fixing cyanobacterium Crocosphaera watsonii WH 8501Tuo Shi
Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
ISME J 4:621-32. 2010..This study represents the first whole-genome expression profiling in cultivated Crocosphaera, and the results will be useful in determining the basal physiology and ecology of the endemic Crocosphaera populations... - Spatial-temporal variability in diazotroph assemblages in Chesapeake Bay using an oligonucleotide nifH microarrayPia H Moisander
Ocean Sciences Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
Environ Microbiol 9:1823-35. 2007..Higher diversity in the freshwater end of the system may reflect variability in disturbance rates and environmental conditions such as forms and concentrations of organic matter, nutrients and oxygen... - Analogous nutrient limitations in unicellular diazotrophs and Prochlorococcus in the South Pacific OceanPia H Moisander
Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
ISME J 6:733-44. 2012.... - Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North AtlanticKendra A Turk
Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
ISME J 5:1201-12. 2011.... - Distribution and activity of diazotrophs in the Eastern Equatorial AtlanticRachel A Foster
Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
Environ Microbiol 11:741-50. 2009..The distribution of the diazotroph groups, especially the three strains of symbiotic cyanobacteria, was different, and appeared largely controlled by riverine inputs and upwelling... - Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarrayBethany D Jenkins
University of California, Santa Cruz, Santa Cruz, California 95064, USA
Appl Environ Microbiol 70:1767-76. 2004..M. Short, B. D. Jenkins, and J. P. Zehr, Appl. Environ. Microbiol., in press). The results show that DNA macroarrays have great potential for mapping the spatial and temporal variability of functional gene diversity in the environment... - Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression and response to phosphate enrichmentIan Hewson
Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, USA
ISME J 1:78-91. 2007..The presence of typical open ocean phylotype transcripts in lagoon bacterioplankton may indicate that they are an important component of the N cycle of the coral reef... - Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCRRyan W Paerl
Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Environ Microbiol 14:580-93. 2012..Therefore, non-measured environmental factors (e.g. metals, mortality) likely had different influences on subgroups, which led to their distinct abundance patterns at M0... - Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoonPia H Moisander
Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
ISME J 2:954-67. 2008..The SCS diazotroph community has a relatively low diversity and is a mixture of both estuarine and oceanic fingerprints... - Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake BaySteven M Short
Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, California 95064, USA
Appl Environ Microbiol 70:2186-92. 2004.... - Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific OceanIan Hewson
Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
ISME J 3:1286-300. 2009..The results provide insight into aggregate microbial communities in contrast to planktonic free-living assemblages that are the focus of other studies... - Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentationJulie C Robidart
Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, USA
ISME J 6:513-23. 2012.... - Determination of nitrogen-fixing phylotypes in Lyngbya sp. and Microcoleus chthonoplastes cyanobacterial mats from Guerrero Negro, Baja California, MexicoEnoma O Omoregie
Department of Ocean Sciences and Institute of Marine Sciences, University of California, Santa Cruz, California 95064, USA
Appl Environ Microbiol 70:2119-28. 2004..The results of this study indicate that several different organisms, some of which were not previously known to fix nitrogen, are likely to be responsible for the observed dark-period nitrogenase activity in these cyanobacterial mats... - Nitrogenase gene diversity and microbial community structure: a cross-system comparisonJonathan P Zehr
Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
Environ Microbiol 5:539-54. 2003..The broad analysis of nitrogenase genes provides a basis for developing molecular assays and bioinformatics approaches for the study of nitrogen fixation in the environment... - Diel cycling of DNA staining and nifH gene regulation in the unicellular cyanobacterium Crocosphaera watsonii strain WH 8501 (Cyanophyta)Kory Pennebaker
Ocean Sciences Department, University of California, Santa Cruz, CA 95064, USA
Environ Microbiol 12:1001-10. 2010..Thus, nifH gene expression in C. watsonii WH 8501 appears to be influenced by both circadian and environmental factors... - Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbiosesRachel A Foster
Ocean Sciences Department, University of California, Santa Cruz, CA, USA
ISME J 5:1484-93. 2011..Further, this is the first demonstration of N transfer from an N(2) fixer to a unicellular partner. These symbioses are important models for molecular regulation and nutrient exchange in symbiotic systems... - Characterization of cyanobacterial glnA gene diversity and gene expression in marine environmentsAngela H Gibson
Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
FEMS Microbiol Ecol 55:391-402. 2006..Results showed that the glnA gene can be used to characterize the diversity of natural populations of cyanobacteria, and to characterize gene expression patterns of individual species or strains... - Modeled contributions of three types of diazotrophs to nitrogen fixation at Station ALOHANicole L Goebel
Institute of Marine Sciences, University of California, Santa Cruz, CA, USA
ISME J 1:606-19. 2007.... - Modelling the vertical distribution of Prochlorococcus and Synechococcus in the North Pacific Subtropical OceanSophie Rabouille
Ocean Sciences Department, University of California, Santa Cruz, CA 95064, USA
Environ Microbiol 9:2588-602. 2007..Results support the idea that intermittent mixing events may have important ecological and geochemical impacts on the phytoplankton community at Station ALOHA... - Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studiesH James Tripp
Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
Nucleic Acids Res 39:8792-802. 2011..We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets... - Characterization of diatom-cyanobacteria symbioses on the basis of nifH, hetR and 16S rRNA sequencesRachel A Foster
Institute of Marine Science, University of California, Santa Cruz, CA 95064, USA
Environ Microbiol 8:1913-25. 2006..clevei, H. hauckii and the Calothrix symbiont of Chaetoceros sp. respectively... - Nitrogenase (nifH) gene expression in diazotrophic cyanobacteria in the Tropical North Atlantic in response to nutrient amendmentsKendra A Turk-Kubo
Department of Ocean Sciences, University of California at Santa Cruz Santa Cruz, CA, USA
Front Microbiol 3:386. 2012..This has important implications for our current understanding of controls on N(2) fixation in the TNAtl and may partially explain why it appears to be intermittently limited by Fe, P, or both... - Two Strains of Crocosphaera watsonii with Highly Conserved Genomes are Distinguished by Strain-Specific FeaturesShellie R Bench
Department of Ocean Sciences, University of California, Santa Cruz Santa Cruz, CA, USA
Front Microbiol 2:261. 2011..The strain-specific sequences found in this study provide tools for future physiological studies, as well as genetic markers to help determine the relative abundance of phenotypes in natural populations... - Differential distributions of synechococcus subgroups across the california current systemRyan W Paerl
Department of Ocean Sciences, University of California Santa Cruz Santa Cruz, CA, USA
Front Microbiol 2:59. 2011..The presented biogeographic data provides insight on the distributions and ecologies of Synechococcus present in an eastern boundary current system... - Nitrogen cycling in the ocean: new perspectives on processes and paradigmsJonathan P Zehr
Department of Ocean Sciences, Earth and Marine Sciences Building, Room A438, University of California, Santa Cruz, CA 95064, USA
Appl Environ Microbiol 68:1015-24. 2002 - Quantitative analysis of nifH genes and transcripts from aquatic environmentsSteven M Short
Diversa Corp, San Diego, California 92121, USA
Methods Enzymol 397:380-94. 2005.... - Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific OceanMatthew J Church
Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
Appl Environ Microbiol 71:5362-70. 2005..The temporal separation of nifH expression by the various phylotypes suggests that open ocean diazotrophic cyanobacteria have unique in situ physiological responses to daily fluctuations of light in the upper ocean... - Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environmentsBethany D Jenkins
Department of Cell and Molecular Biology and Graduate School of Oceanography, University of Rhode Island, 45 Lower College Road, Kingston, RI 02881, USA
Environ Microbiol 8:2083-95. 2006.... - Nitrogenase gene expression in the Chesapeake Bay EstuarySteven M Short
Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
Environ Microbiol 9:1591-6. 2007..This study provides the first evidence of nifH expression in the Chesapeake Bay, and suggests that diazotrophic unicellular cyanobacteria have a broader distribution and activity than previously recognized... - Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversityGrieg F Steward
Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
Appl Environ Microbiol 70:1455-65. 2004..Our results indicate that macroarray hybridization can be a highly reproducible, semiquantitative method for assessing the diversity of functional genes represented in mixed pools of PCR products amplified from the environment... - Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific OceanAllison A Fong
Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
ISME J 2:663-76. 2008..These results suggest that mesoscale physical variability can play an important role in modifying the abundances of N(2) fixing microorganisms and associated rates of N(2) fixation in open ocean ecosystems... - High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific OceanJoseph P Montoya
School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
Nature 430:1027-32. 2004....