Jonathan P Zehr

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies
    H James Tripp
    Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 39:8792-802. 2011
  2. pmc Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont
    Jason A Hilton
    Department of Ocean Sciences, University of California, 1156 High Street, Santa Cruz, California 95064, USA
    Nat Commun 4:1767. 2013
  3. pmc Two Strains of Crocosphaera watsonii with Highly Conserved Genomes are Distinguished by Strain-Specific Features
    Shellie R Bench
    Department of Ocean Sciences, University of California, Santa Cruz Santa Cruz, CA, USA
    Front Microbiol 2:261. 2011
  4. doi request reprint Nitrogen fixation by marine cyanobacteria
    Jonathan P Zehr
    Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
    Trends Microbiol 19:162-73. 2011
  5. ncbi request reprint Nitrogen cycle of the open ocean: from genes to ecosystems
    Jonathan P Zehr
    Ocean Sciences Department, University of California, Santa Cruz, California 95064, USA
    Ann Rev Mar Sci 3:197-225. 2011
  6. doi request reprint Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II
    Jonathan P Zehr
    Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Science 322:1110-2. 2008
  7. ncbi request reprint Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes
    Jonathan 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
  8. pmc Low genomic diversity in tropical oceanic N2-fixing cyanobacteria
    Jonathan 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
  9. doi request reprint Phylogenetic diversity of cyanobacterial narB genes from various marine habitats
    Ryan 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
  10. doi request reprint Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain
    Pia H Moisander
    Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Science 327:1512-4. 2010

Collaborators

Detail Information

Publications52

  1. pmc Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies
    H 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...
  2. pmc Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont
    Jason A Hilton
    Department of Ocean Sciences, University of California, 1156 High Street, Santa Cruz, California 95064, USA
    Nat Commun 4:1767. 2013
    ..The genome of Richelia is an example of metabolic streamlining that has implications for the evolution of N₂-fixing symbiosis and potentially for manipulating plant-cyanobacterial interactions...
  3. pmc Two Strains of Crocosphaera watsonii with Highly Conserved Genomes are Distinguished by Strain-Specific Features
    Shellie 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...
  4. doi request reprint Nitrogen fixation by marine cyanobacteria
    Jonathan 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...
  5. ncbi request reprint Nitrogen cycle of the open ocean: from genes to ecosystems
    Jonathan 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...
  6. doi request reprint Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II
    Jonathan P Zehr
    Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Science 322:1110-2. 2008
    ....
  7. ncbi request reprint Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes
    Jonathan 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
    ....
  8. pmc Low genomic diversity in tropical oceanic N2-fixing cyanobacteria
    Jonathan 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...
  9. doi request reprint Phylogenetic diversity of cyanobacterial narB genes from various marine habitats
    Ryan 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...
  10. doi request reprint Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain
    Pia 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...
  11. doi request reprint Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium
    H 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...
  12. ncbi request reprint Comparison of diazotroph community structure in Lyngbya sp. and Microcoleus chthonoplastes dominated microbial mats from Guerrero Negro, Baja, Mexico
    Enoma 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
    ....
  13. ncbi request reprint Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats
    Pia 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...
  14. doi request reprint In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii
    Ian Hewson
    Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
    ISME J 3:618-31. 2009
    ....
  15. doi request reprint Abundance and distribution of major groups of diazotrophic cyanobacteria and their potential contribution to N₂ fixation in the tropical Atlantic Ocean
    Nicole 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...
  16. ncbi request reprint Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga
    Anne W Thompson
    Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
    Science 337:1546-50. 2012
    ....
  17. ncbi request reprint Spatial-temporal variability in diazotroph assemblages in Chesapeake Bay using an oligonucleotide nifH microarray
    Pia 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...
  18. doi request reprint Genome-wide analysis of diel gene expression in the unicellular N(2)-fixing cyanobacterium Crocosphaera watsonii WH 8501
    Tuo 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...
  19. pmc Analogous nutrient limitations in unicellular diazotrophs and Prochlorococcus in the South Pacific Ocean
    Pia H Moisander
    Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
    ISME J 6:733-44. 2012
    ....
  20. ncbi request reprint Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression and response to phosphate enrichment
    Ian 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...
  21. pmc Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray
    Bethany 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...
  22. pmc Distribution and activity of diazotrophs in the Eastern Equatorial Atlantic
    Rachel 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...
  23. pmc Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic
    Kendra A Turk
    Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
    ISME J 5:1201-12. 2011
    ....
  24. doi request reprint Non-cyanobacterial nifH phylotypes in the North Pacific Subtropical Gyre detected by flow-cytometry cell sorting
    Deniz Bombar
    Ocean Sciences Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
    Environ Microbiol Rep 5:705-15. 2013
    ..This approach enables the detection of rare nifH phylotypes, identifies possible associations with larger cells or particles and offers a possible solution for distinguishing reagent contaminants from real microbial community components...
  25. doi request reprint Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR
    Ryan 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...
  26. ncbi request reprint Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean
    Ian 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...
  27. pmc Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay
    Steven M Short
    Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Appl Environ Microbiol 70:2186-92. 2004
    ....
  28. doi request reprint Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon
    Pia 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...
  29. ncbi request reprint Nitrogenase gene diversity and microbial community structure: a cross-system comparison
    Jonathan 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...
  30. pmc Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation
    Julie C Robidart
    Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    ISME J 6:513-23. 2012
    ....
  31. pmc Determination of nitrogen-fixing phylotypes in Lyngbya sp. and Microcoleus chthonoplastes cyanobacterial mats from Guerrero Negro, Baja California, Mexico
    Enoma 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...
  32. doi request reprint 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...
  33. ncbi request reprint Characterization of diatom-cyanobacteria symbioses on the basis of nifH, hetR and 16S rRNA sequences
    Rachel 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...
  34. pmc Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus
    Elif Demir-Hilton
    Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
    ISME J 5:1095-107. 2011
    ..In situ growth rate estimates using these primer-probes and better comprehension of physiology will enhance ecological understanding of Ostreococcus Clades OII and OI which appear to be oceanic and coastal clades, respectively...
  35. ncbi request reprint Characterization of cyanobacterial glnA gene diversity and gene expression in marine environments
    Angela 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...
  36. pmc Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses
    Rachel 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...
  37. ncbi request reprint Modeled contributions of three types of diazotrophs to nitrogen fixation at Station ALOHA
    Nicole L Goebel
    Institute of Marine Sciences, University of California, Santa Cruz, CA, USA
    ISME J 1:606-19. 2007
    ....
  38. ncbi request reprint Modelling the vertical distribution of Prochlorococcus and Synechococcus in the North Pacific Subtropical Ocean
    Sophie 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...
  39. pmc Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean
    Julie C Robidart
    1 Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA 2 Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA 3 Center for Microbial Oceanography Research and Education, University of Hawaii, Honolulu, HI, USA
    ISME J 8:1175-85. 2014
    ..These results underscore the value of high-resolution sampling and its applications for modeling the effects of global change...
  40. pmc Differential distributions of synechococcus subgroups across the california current system
    Ryan 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...
  41. pmc Nitrogen cycling in the ocean: new perspectives on processes and paradigms
    Jonathan 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
  42. pmc Nitrogenase (nifH) gene expression in diazotrophic cyanobacteria in the Tropical North Atlantic in response to nutrient amendments
    Kendra 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...
  43. pmc A microarray for assessing transcription from pelagic marine microbial taxa
    Irina N Shilova
    Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
    ISME J 8:1476-91. 2014
    ..The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions. ..
  44. pmc Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity
    Grieg 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...
  45. ncbi request reprint High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean
    Joseph P Montoya
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
    Nature 430:1027-32. 2004
    ....
  46. pmc Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean
    Matthew 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...
  47. ncbi request reprint Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments
    Bethany 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
    ....
  48. ncbi request reprint Nitrogenase gene expression in the Chesapeake Bay Estuary
    Steven 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...
  49. doi request reprint Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific Ocean
    Allison 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...
  50. ncbi request reprint Quantitative analysis of nifH genes and transcripts from aquatic environments
    Steven M Short
    Diversa Corp, San Diego, California 92121, USA
    Methods Enzymol 397:380-94. 2005
    ....