Jizhong Zhou

Summary

Affiliation: University of Oklahoma
Country: USA

Publications

  1. pmc Elevated CO₂ influences microbial carbon and nitrogen cycling
    Meiying Xu
    State Key Laboratory of Applied Microbiology, Ministry Guangdong Province Jointly Breeding Base, South China, Guangdong Institute of Microbiology, Guangzhou, China
    BMC Microbiol 13:124. 2013
  2. pmc Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau
    Yuguang Zhang
    Institute of Forestry Ecology, Environment and Protection, and The Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing 100091, China
    BMC Microbiol 13:72. 2013
  3. pmc Genome-wide analysis of acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system
    Bareket Dassa
    Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
    BMC Genomics 13:210. 2012
  4. pmc Random sampling process leads to overestimation of β-diversity of microbial communities
    Jizhong Zhou
    State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
    MBio 4:e00324-13. 2013
  5. pmc Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions
    Bo Li
    School of Computing, Clemson University, Clemson, SC 29634, USA
    BMC Syst Biol 5:73. 2011
  6. pmc Pellicle formation in Shewanella oneidensis
    Yili Liang
    School of Minerals Processing and Bioengineering, Central South University, Changsha, PR China
    BMC Microbiol 10:291. 2010
  7. pmc Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site
    Jessica E Butler
    Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
    BMC Genomics 8:180. 2007
  8. pmc Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1
    Weimin Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Genomics 7:76. 2006
  9. pmc Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach
    Debora F Rodrigues
    Michigan State University, NASA Astrobiology Institute and Center for Microbial Ecology, East Lansing, MI 48824, USA
    BMC Genomics 9:547. 2008
  10. pmc Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory
    Feng Luo
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    BMC Bioinformatics 8:299. 2007

Detail Information

Publications114 found, 100 shown here

  1. pmc Elevated CO₂ influences microbial carbon and nitrogen cycling
    Meiying Xu
    State Key Laboratory of Applied Microbiology, Ministry Guangdong Province Jointly Breeding Base, South China, Guangdong Institute of Microbiology, Guangzhou, China
    BMC Microbiol 13:124. 2013
    ..0) was used to examine the composition, structure, and metabolic potential of soil microbial communities from a grassland field experiment after ten-year field exposure to ambient and elevated CO₂ concentrations...
  2. pmc Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau
    Yuguang Zhang
    Institute of Forestry Ecology, Environment and Protection, and The Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing 100091, China
    BMC Microbiol 13:72. 2013
    ..0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau...
  3. pmc Genome-wide analysis of acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system
    Bareket Dassa
    Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
    BMC Genomics 13:210. 2012
    ..The recently sequenced genome of the cellulolytic mesophile, Acetivibrio cellulolyticus, allows detailed comparison of the cellulosomes of these two select cellulosome-producing bacteria...
  4. pmc Random sampling process leads to overestimation of β-diversity of microbial communities
    Jizhong Zhou
    State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
    MBio 4:e00324-13. 2013
    ..In summary, the results presented in this study should have important implications for examining microbial biodiversity to address both basic theoretical and applied management questions...
  5. pmc Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions
    Bo Li
    School of Computing, Clemson University, Clemson, SC 29634, USA
    BMC Syst Biol 5:73. 2011
    ..Synthetic lethal genetic interactions among proteins have been widely used to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interactions is still unclear...
  6. pmc Pellicle formation in Shewanella oneidensis
    Yili Liang
    School of Minerals Processing and Bioengineering, Central South University, Changsha, PR China
    BMC Microbiol 10:291. 2010
    ..The goal of this work was to understand basic requirements and mechanism of pellicle formation in S. oneidensis...
  7. pmc Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site
    Jessica E Butler
    Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
    BMC Genomics 8:180. 2007
    ..Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known...
  8. pmc Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1
    Weimin Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Genomics 7:76. 2006
    ....
  9. pmc Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach
    Debora F Rodrigues
    Michigan State University, NASA Astrobiology Institute and Center for Microbial Ecology, East Lansing, MI 48824, USA
    BMC Genomics 9:547. 2008
    ..We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5 degrees C to 39 degrees C to study its thermal adaptation...
  10. pmc Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory
    Feng Luo
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    BMC Bioinformatics 8:299. 2007
    ....
  11. pmc Reproducibility and quantitation of amplicon sequencing-based detection
    Jizhong Zhou
    Department of Environmental Science and Engineering, Tsinghua University, Beijing, China
    ISME J 5:1303-13. 2011
    ..However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities...
  12. pmc Spatial scaling of functional gene diversity across various microbial taxa
    Jizhong Zhou
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Proc Natl Acad Sci U S A 105:7768-73. 2008
    ..0475-0.0959). However, the z values are several times lower than those commonly observed in plants and animals. These results suggest that the turnover in space of microorganisms may be, in general, lower than that of plants and animals...
  13. doi request reprint How sulphate-reducing microorganisms cope with stress: lessons from systems biology
    Jizhong Zhou
    Stephenson Research and Technology Center, 101 David L Boren Blvd, Institut for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    Nat Rev Microbiol 9:452-66. 2011
    ....
  14. doi request reprint GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer
    Joy D Van Nostrand
    Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    Environ Microbiol 11:2611-26. 2009
    ..This biostimulation approach may potentially offer an effective means for the bioremediation of U(VI)-contaminated sites...
  15. pmc Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer
    Joy D Van Nostrand
    University of Oklahoma, 101 David L Boren Blvd, SRTC 2022, Norman, OK 73019, USA
    Appl Environ Microbiol 77:3860-9. 2011
    ....
  16. doi request reprint GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
    Zhili He
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, 101 David L Boren Boulevard, Norman, OK 73019, USA
    ISME J 4:1167-79. 2010
    ..As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning...
  17. ncbi request reprint Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels
    Patricia J Waldron
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    Environ Sci Technol 43:3529-34. 2009
    ..This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination...
  18. pmc Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities
    Yuting Liang
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 76:1088-94. 2010
    ..The developed CORS provides a useful approach for microarray data normalization and comparison for studies of complex microbial communities...
  19. pmc Molecular ecological network analyses
    Ye Deng
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    BMC Bioinformatics 13:113. 2012
    ....
  20. pmc Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands
    Kai Xue
    Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
    Appl Environ Microbiol 79:1284-92. 2013
    ....
  21. doi request reprint Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2
    Zhili He
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Ecol Lett 13:564-75. 2010
    ..This study provides insights into potential activity of microbial community and associated feedback responses of terrestrial ecosystems to eCO2...
  22. pmc Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico
    Liyou Wu
    Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 74:4516-29. 2008
    ....
  23. doi request reprint Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough
    Aifen Zhou
    Virtual Institute of Microbial Stress and Survival, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Environ Microbiol 12:2645-57. 2010
    ..In addition, a conceptual cellular model of D. vulgaris responses to H(2)O(2) stress was constructed to illustrate that this bacterium may employ a complicated molecular mechanism to defend against the H(2)O(2)-induced stresses...
  24. pmc The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide
    Zhili He
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    ISME J 6:259-72. 2012
    ..This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure...
  25. doi request reprint Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments
    Sanghoon Kang
    Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
    FEMS Microbiol Ecol 86:200-14. 2013
    ..These populations therefore appear to contribute significantly to the resistance and stability of the microbial communities throughout the gradient of metal contamination in Lake DePue...
  26. doi request reprint Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community
    Christopher L Hemme
    Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
    ISME J 4:660-72. 2010
    ....
  27. doi request reprint StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses
    Aifen Zhou
    Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
    Environ Sci Technol 47:9841-9. 2013
    ..In summary, StressChip provides a new tool for accessing microbial community functional structure and responses to environmental changes. ..
  28. pmc Microbial functional gene diversity with a shift of subsurface redox conditions during In Situ uranium reduction
    Yuting Liang
    School of Environment, Tsinghua University, Beijing, China
    Appl Environ Microbiol 78:2966-72. 2012
    ..Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation...
  29. pmc Elevated carbon dioxide alters the structure of soil microbial communities
    Ye Deng
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
    Appl Environ Microbiol 78:2991-5. 2012
    ..The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO(2), which was closely associated with soil and plant properties...
  30. pmc Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough
    Aifen Zhou
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
    Appl Environ Microbiol 78:1168-77. 2012
    ..vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses...
  31. pmc Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution
    Aifen Zhou
    Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
    ISME J 7:1790-802. 2013
    ..Taken together, these data suggest that the accumulation of osmolytes, increased membrane fluidity, decreased cell motility and possibly an increased exclusion of Na(+) contribute to increased NaCl tolerance in NaCl-evolved D. vulgaris. ..
  32. doi request reprint Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness
    Liyou Wu
    Department of Botany and Microbiology, Institute for Environmental Genomics, Stephenson Research and Technology Center, University of Oklahoma, Norman, OK 73019, USA
    ISME J 2:642-55. 2008
    ..These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms...
  33. pmc Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses
    Haichun Gao
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    BMC Genomics 9:42. 2008
    ..Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene...
  34. doi request reprint Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation
    Meiying Xu
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
    ISME J 4:1060-70. 2010
    ....
  35. doi request reprint The microbial gene diversity along an elevation gradient of the Tibetan grassland
    Yunfeng Yang
    State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
    ISME J 8:430-40. 2014
    ....
  36. pmc Strain/species-specific probe design for microbial identification microarrays
    Qichao Tu
    Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
    Appl Environ Microbiol 79:5085-8. 2013
    ..The method can also be used to select strain/species-specific probes for sequenced genomes in any environments, such as soil and water. ..
  37. pmc Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields
    Christopher L Hemme
    Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
    Appl Environ Microbiol 77:7998-8008. 2011
    ..The availability of whole-genome sequence and comparative genomic analyses will aid in engineering and optimizing Thermoanaerobacter strains for viable CBP strategies...
  38. doi request reprint Development of functional gene microarrays for microbial community analysis
    Zhili He
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Curr Opin Biotechnol 23:49-55. 2012
    ..In this review, we first summarize currently reported FGAs, and then focus on the FGA development. We will also discuss several key issues of FGA technology as well as challenges and directions in future FGA development...
  39. doi request reprint Assimilatory nitrate utilization by bacteria on the West Florida Shelf as determined by stable isotope probing and functional microarray analysis
    Boris Wawrik
    Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    FEMS Microbiol Ecol 79:400-11. 2012
    ..e. nirS, nirK, narG, nosZ, napA, and nrfA was detected. These data directly implicate several bacterial populations in nitrate uptake, but suggest a more complex pattern for N flow than traditionally implied...
  40. pmc Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation
    Zhili He
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    Appl Environ Microbiol 76:1574-86. 2010
    ..A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels...
  41. pmc Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis
    Zhili He
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 74:2957-66. 2008
    ..This study provides general guidance for users to select appropriate SNR thresholds for different samples under different hybridization conditions...
  42. pmc The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control
    Yunfeng Yang
    Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084, China
    BMC Microbiol 10:264. 2010
    ..This down-regulation is mediated by a Fur-regulated small regulatory RNA named RyhB. It is unclear in the γ-proteobacterium S. oneidensis whether TCA is also regulated by Fur and RyhB...
  43. pmc Design and analysis of mismatch probes for long oligonucleotide microarrays
    Ye Deng
    Institute for Environmental Genomics, Department of Botany and Microbiology, The University of Oklahoma, Norman, OK 73019, USA
    BMC Genomics 9:491. 2008
    ..One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes...
  44. pmc Generation and validation of a Shewanella oneidensis MR-1 clone set for protein expression and phage display
    Haichun Gao
    Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
    PLoS ONE 3:e2983. 2008
    ..g., mass spectrometry-based proteomic analysis), and facilitates a wide variety of integrated studies, including protein expression, purification, and functional analyses of proteins both in vivo and in vitro...
  45. pmc Microarray-based evaluation of whole-community genome DNA amplification methods
    Jian Wang
    State Key Joint Laboratory of Environmental Stimulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
    Appl Environ Microbiol 77:4241-5. 2011
    ..For pure-culture DNA, REPLI-g and Templiphi showed less bias than Bst. For community DNA, REPLI-g showed the least bias and highest number of genes, while Bst had the highest success rate and was suitable for low-quality DNA...
  46. doi request reprint The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities
    Yong Jin Lee
    Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
    ISME J 7:1974-84. 2013
    ....
  47. ncbi request reprint GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
    Zhili He
    Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    ISME J 1:67-77. 2007
    ..It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions...
  48. doi request reprint Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin
    Boris Wawrik
    Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    FEMS Microbiol Ecol 81:26-42. 2012
    ..These data suggest that coal methanogenesis is unlikely to be limited by methanogen biomass, but rather the activation and degradation of coal constituents...
  49. doi request reprint Applications of functional gene microarrays for profiling microbial communities
    Zhili He
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Curr Opin Biotechnol 23:460-6. 2012
    ..We also discuss challenges and future directions of FGA applications...
  50. pmc Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume
    Zhenmei Lu
    College of Life Sciences, Zhejiang University, Hangzhou, China
    ISME J 6:451-60. 2012
    ..Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments...
  51. ncbi request reprint Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes
    Yuguang Zhang
    Institute of Forestry Ecology, Environment and Protection, Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
    FEMS Microbiol Lett 266:144-51. 2007
    ..cluster analysis demonstrated that primitive forest soil was clustered more closely to soil from the spruce plantation established in 1960s...
  52. doi request reprint Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction
    Yunfeng Yang
    State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
    BMC Microbiol 13:267. 2013
    ..To explore new features of iron reduction pathways, we experimentally analyzed Shewanella putrefaciens W3-18-1 since its gene cluster is considerably different from that of MR-1 in that the gene cluster encodes only four ORFs...
  53. pmc Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1
    Dongru Qiu
    Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
    Appl Environ Microbiol 79:5250-7. 2013
    ..These results indicate that Shewanella putrefaciens W3-18-1 is well adapted to habitats with higher oxygen levels. Taken together, the results of this study provide valuable insights into bacterial genome evolution. ..
  54. doi request reprint Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil
    Yuting Liang
    Department of Environmental Science and Engineering, Tsinghua University, Beijing, China
    Chemosphere 75:193-9. 2009
    ..These changes demonstrate the feasibility of an integrated ozonation and biodegradation treatment to remove recalcitrant soil contaminants...
  55. doi request reprint Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection
    Aihua Liu
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Anal Bioanal Chem 401:2003-11. 2011
    ..1 pM, enhancing microarray hybridization sensitivity over tenfold. This promising technology may be potentially applied to other binding events such as specific interactions between proteins...
  56. doi request reprint Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland
    Yunfeng Yang
    School of Environment, Tsinghua University, Beijing, China
    Glob Chang Biol 19:637-48. 2013
    ....
  57. pmc Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone
    Xinyu Li
    State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
    ISME J 7:660-71. 2013
    ..This study provides new insight into our understanding of the influence of eO(3) and wheat cultivars on soil microbial communities...
  58. pmc Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination
    Jinbo Xiong
    State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
    PLoS ONE 7:e50507. 2012
    ..This study provides new insights about the heterogeneity of microbial community metabolic potential and future biodiversity preservation for arsenic bioremediation management...
  59. pmc Use of functional gene arrays for elucidating in situ biodegradation
    Joy D Van Nostrand
    Institute for Environmental Genomics, University of Oklahoma Norman, OK, USA Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
    Front Microbiol 3:339. 2012
    ..This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation...
  60. pmc Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production
    Christopher L Hemme
    Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    J Bacteriol 192:6494-6. 2010
    ..The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology...
  61. pmc Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins
    Haichun Gao
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    J Bacteriol 188:4560-9. 2006
    ..Mutational analyses confirmed that the small cold shock proteins, So1648 and So2787, are involved in the cold shock response of S. oneidensis. The analyses also indicated that So1648 may function only at very low temperatures...
  62. doi request reprint Contrasting responses of heterotrophic and autotrophic respiration to experimental warming in a winter annual-dominated prairie
    Dejun Li
    Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
    Glob Chang Biol 19:3553-64. 2013
    ..Across the 3 years, warming increased Rh/Rs by 29.1% but clipping did not affect Rh/Rs. Our study highlights that climate warming may have contrasting effects on Rh and Ra in association with responses of plant productivity to warming. ..
  63. pmc Metal reduction and iron biomineralization by a psychrotolerant Fe(III)-reducing bacterium, Shewanella sp. strain PV-4
    Yul Roh
    Institute for Environmental Genomics, and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 72:3236-44. 2006
    ..The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation...
  64. pmc Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation
    Xingyuan Li
    PerkinElmer Life and Analytical Sciences, 549 Albany Street, Boston, MA 02118, USA
    Nucleic Acids Res 33:6114-23. 2005
    ..The program was used to design probes for both whole-genome and highly homologous sequence data. CommOligo and CommOligo_PE are freely available to academic users upon request...
  65. pmc Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris
    Yasuhiro Oda
    Department of Microbiology, University of Washington, Seattle, 98195 7242, USA
    J Bacteriol 187:7784-94. 2005
    ....
  66. ncbi request reprint Improving solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 proteins expressed into Esherichia coli
    Irina Kataeva
    Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
    J Proteome Res 4:1942-51. 2005
    ..A suggestion has been made that the Wilkinson-Harrison model is not applicable to C. thermocellum proteins because it did not account for the peculiarities of protein sequences from thermophiles...
  67. pmc Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction
    Rizlan Bencheikh-Latmani
    Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093 0202, USA
    Appl Environ Microbiol 71:7453-60. 2005
    ..This study sheds light on the multifaceted response of MR-1 to U(VI) and Cr(VI) under anaerobic conditions and suggests that the same electron transport pathway can be used for more than one electron acceptor...
  68. ncbi request reprint Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric acid-uranium waste
    Matthew W Fields
    Department of Microbiology, Miami University, Pearson Hall, Room 32, Oxford, OH 45056, USA
    FEMS Microbiol Ecol 53:417-28. 2005
    ....
  69. pmc Use of microarrays with different probe sizes for monitoring gene expression
    Zhili He
    Environmental Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, TN 37831 6038, USA
    Appl Environ Microbiol 71:5154-62. 2005
    ..The results demonstrated that 70-mer oligonucleotides can provide the performance most comparable to the performance obtained with PCR-generated probes...
  70. ncbi request reprint Effects of a strong static magnetic field on bacterium Shewanella oneidensis: an assessment by using whole genome microarray
    Weimin Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
    Bioelectromagnetics 26:558-63. 2005
    ..Among these genes, 21 were upregulated while other 44 were downregulated, compared with control...
  71. pmc Empirical establishment of oligonucleotide probe design criteria
    Zhili He
    Environmental Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, TN 37831 6038, USA
    Appl Environ Microbiol 71:3753-60. 2005
    ....
  72. pmc Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress
    Dorothea K Thompson
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Appl Environ Microbiol 68:881-92. 2002
    ..These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems...
  73. pmc Microbial genomics--challenges and opportunities: the 9th International Conference on Microbial Genomes
    Jizhong Zhou
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    J Bacteriol 184:4327-33. 2002
  74. ncbi request reprint PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis
    Dong Xu
    Protein Informatics Group, Life Sciences Division Environmental Sciences Division, Oak Ridge, TN 37831, USA
    Bioinformatics 18:1432-7. 2002
    ..A bioinformatic tool, PRIMEGENS, has recently been developed for the automatic design of PCR primers using DNA fragments that are specific to individual open reading frames (ORFs)...
  75. pmc Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough
    Kelly S Bender
    Department of Biochemistry, 117 Schweitzer Hall, Columbia, MO 65211, USA
    Appl Environ Microbiol 73:5389-400. 2007
    ..Both the physiological and transcriptional data implicate a global regulatory role for Fur in the sulfate-reducing bacterium D. vulgaris...
  76. pmc Microbial diversity and heterogeneity in sandy subsurface soils
    Jizhong Zhou
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Appl Environ Microbiol 70:1723-34. 2004
    ..Finally, the overall diversity of the subsurface samples was much lower than that of the corresponding surface soil samples...
  77. pmc Global transcriptome analysis of the heat shock response of Shewanella oneidensis
    Haichun Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    J Bacteriol 186:7796-803. 2004
    ..Finally, a putative regulatory site with high conservation to the Escherichia coli sigma32-binding consensus sequence was identified upstream of a number of heat-inducible genes...
  78. pmc Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis
    Xiu Feng Wan
    Environmental Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, TN 37831 6038, USA
    J Bacteriol 186:8385-400. 2004
    ....
  79. ncbi request reprint Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications
    Liyou Wu
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Environ Sci Technol 38:6775-82. 2004
    ..The results suggest that CGA hybridization has potential as a specific, sensitive, and quantitative tool for detection and identification of microorganisms in environmental samples...
  80. pmc Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Proc Natl Acad Sci U S A 102:2099-104. 2005
    ..We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins with each newly sequenced genome...
  81. pmc Cellular response of Shewanella oneidensis to strontium stress
    Steven D Brown
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Appl Environ Microbiol 72:890-900. 2006
    ....
  82. pmc Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference
    Yunfeng Yang
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Genomics 9:S5. 2008
    ..Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality...
  83. pmc Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels
    Erick Cardenas
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Appl Environ Microbiol 74:3718-29. 2008
    ..Spatial differences in community structure within the treatment zone were likely related to the hydraulic pathway and to electron donor metabolism during biostimulation...
  84. ncbi request reprint Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems
    Huaqun Yin
    School of Minerals Processing and Bioengineering, Central South University Changsha, Hunan, 410083 China
    J Microbiol Methods 70:165-78. 2007
    ....
  85. ncbi request reprint Unravelling microbial communities with DNA-microarrays: challenges and future directions
    Michael Wagner
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, A 1090, Wien, Austria
    Microb Ecol 53:498-506. 2007
    ..Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities...
  86. ncbi request reprint Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect
    Etienne Yergeau
    Center for Terrestrial Ecology, Netherlands Institute for Ecology NIOO KNAW, Heteren, The Netherlands
    ISME J 1:163-79. 2007
    ....
  87. pmc Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1
    Karuna Chourey
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Appl Environ Microbiol 72:6331-44. 2006
    ....
  88. ncbi request reprint Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean
    Haichun Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
    Int J Syst Evol Microbiol 56:1911-6. 2006
    ..nov. is proposed. The type strain is PV-4(T) (=ATCC BAA-1088(T)=DSM 17748(T))...
  89. ncbi request reprint Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico
    Tingfen Yan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
    FEMS Microbiol Ecol 57:251-9. 2006
    ....
  90. pmc Response of Desulfovibrio vulgaris to alkaline stress
    Sergey Stolyar
    University of Washington, Department of Civil and Environmental Engineering, 616 NE North Lake Place, Box 355014, Seattle, WA 98195 2700, USA
    J Bacteriol 189:8944-52. 2007
    ....
  91. pmc Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response
    Yunfeng Yang
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Genomics 9:S11. 2008
    ..In many bacterial species, coordinate regulation of iron homeostasis depends on the protein product of a Fur gene. Fur also plays roles in virulence, acid tolerance, redox-stress responses, flagella chemotaxis and metabolic pathways...
  92. ncbi request reprint Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions
    Patricia M Pereira
    Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Lisbon, Portugal
    Arch Microbiol 189:451-61. 2008
    ..vulgaris as a consequence of oxidative damage to their metal clusters...
  93. ncbi request reprint Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs)
    Mary Beth Leigh
    Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
    ISME J 1:134-48. 2007
    ....
  94. ncbi request reprint Molecular diversity of 16S rRNA and gyrB genes in copper mines
    Huaqun Yin
    School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
    Arch Microbiol 189:101-10. 2008
    ..Moreover, our results also indicated that gyrB sequence analysis may be very useful for differentiating very closely related species in the study of microbial communities...
  95. pmc Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach
    Aindrila Mukhopadhyay
    Virtual Institute of Microbial Stress and Survival, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    J Bacteriol 188:4068-78. 2006
    ..vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms...
  96. pmc Transcriptome of a Nitrosomonas europaea mutant with a disrupted nitrite reductase gene (nirK)
    Catherine Mee Hie Cho
    Department of Environmental Sciences, Geology 2207, University of California, Riverside, CA 92521, USA
    Appl Environ Microbiol 72:4450-4. 2006
    ..Relationships of differentially regulated genes to the nirK mutant phenotype are discussed...
  97. pmc Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
    Sean M Caffrey
    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
    J Bacteriol 189:6159-67. 2007
    ..In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase...
  98. pmc Microarray transcription profiling of a Shewanella oneidensis etrA mutant
    Alex S Beliaev
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 6038, USA
    J Bacteriol 184:4612-6. 2002
    ..This is the first microarray study indicating a possible involvement of EtrA in the regulation of gene expression in S. oneidensis MR-1...
  99. pmc Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants
    Orianna Bretschger
    Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
    Appl Environ Microbiol 73:7003-12. 2007
    ..Overall, these data suggest a very complex picture of electron transfer to solid and soluble substrates by S. oneidensis MR-1...
  100. ncbi request reprint A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins
    Christal Yost
    The Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 6480, USA
    OMICS 7:177-91. 2003
    ..This method, which uses a suite of computational tools that are freely available to academic users, can be used to annotate hypothetical proteins in general...
  101. ncbi request reprint Microarrays for bacterial detection and microbial community analysis
    Jizhong Zhou
    Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831 6038, USA
    Curr Opin Microbiol 6:288-94. 2003
    ..However, more rigorous and systematic assessment and development are needed to realize the full potential of microarrays for microbial detection and community analysis...