Eoin L Brodie

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance
    Katherine C Goldfarb
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
    Front Microbiol 2:94. 2011
  2. doi request reprint Microbial community response to addition of polylactate compounds to stimulate hexavalent chromium reduction in groundwater
    Eoin L Brodie
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, CA 94720, United States
    Chemosphere 85:660-5. 2011
  3. pmc Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation
    Eoin L Brodie
    Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:6288-98. 2006
  4. ncbi request reprint Influences of organic carbon supply rate on uranium bioreduction in initially oxidizing, contaminated sediment
    Tetsu K Tokunaga
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, and University of California, Berkeley, California 94720, USA
    Environ Sci Technol 42:8901-7. 2008
  5. doi request reprint Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata
    Shinichi Sunagawa
    School of Natural Sciences, University of California, Merced, CA 95344, USA
    ISME J 3:512-21. 2009
  6. pmc Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
    Kimberlee A West
    Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720 1170, USA
    Appl Environ Microbiol 74:3533-40. 2008
  7. pmc Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray
    Patrick K H Lee
    Department of Civil and Environmental Engineering, University of California, Berkeley, USA
    ISME J 5:1014-24. 2011
  8. pmc Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus
    Javier A Ceja-Navarro
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    ISME J 8:6-18. 2014
  9. pmc PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip
    Kristen M DeAngelis
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Appl Environ Microbiol 77:6313-22. 2011
  10. doi request reprint Selective progressive response of soil microbial community to wild oat roots
    Kristen M DeAngelis
    Ecology Department, Lawrence Berkeley National Lab, Berkeley, CA, USA
    ISME J 3:168-78. 2009

Detail Information

Publications45

  1. pmc Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance
    Katherine C Goldfarb
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
    Front Microbiol 2:94. 2011
    ..Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition...
  2. doi request reprint Microbial community response to addition of polylactate compounds to stimulate hexavalent chromium reduction in groundwater
    Eoin L Brodie
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, CA 94720, United States
    Chemosphere 85:660-5. 2011
    ..The results of these experiments demonstrate that amendment with the pHRC and MRC forms result in effective removal of Cr(VI) from solution most likely by both direct (enzymatic) and indirect (microbially generated reductant) mechanisms...
  3. pmc Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation
    Eoin L Brodie
    Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    Appl Environ Microbiol 72:6288-98. 2006
    ..High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner...
  4. ncbi request reprint Influences of organic carbon supply rate on uranium bioreduction in initially oxidizing, contaminated sediment
    Tetsu K Tokunaga
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, and University of California, Berkeley, California 94720, USA
    Environ Sci Technol 42:8901-7. 2008
    ..These offsetting influences will require careful control of OC supply rates in order to optimize bioreduction-based U stabilization...
  5. doi request reprint Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata
    Shinichi Sunagawa
    School of Natural Sciences, University of California, Merced, CA 95344, USA
    ISME J 3:512-21. 2009
    ..faveolata colonies and resulted in (or be a result of) an increase in opportunistic pathogens...
  6. pmc Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
    Kimberlee A West
    Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720 1170, USA
    Appl Environ Microbiol 74:3533-40. 2008
    ....
  7. pmc Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray
    Patrick K H Lee
    Department of Civil and Environmental Engineering, University of California, Berkeley, USA
    ISME J 5:1014-24. 2011
    ..Overall, the microarrays are a valuable high-throughput tool for comparative genomics of unsequenced Dehalococcoides-containing samples to provide insights into their gene content and dechlorination functions...
  8. pmc Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus
    Javier A Ceja-Navarro
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    ISME J 8:6-18. 2014
    ..We provide evidence for the microbial fixation of N2 that is important for this beetle to subsist on woody biomass. ..
  9. pmc PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip
    Kristen M DeAngelis
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Appl Environ Microbiol 77:6313-22. 2011
    ....
  10. doi request reprint Selective progressive response of soil microbial community to wild oat roots
    Kristen M DeAngelis
    Ecology Department, Lawrence Berkeley National Lab, Berkeley, CA, USA
    ISME J 3:168-78. 2009
    ..This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones...
  11. doi request reprint A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells
    Kelly C Wrighton
    Department of Plant and Microbial Biology, University of California, Berkeley CA 94720, USA
    ISME J 2:1146-56. 2008
    ..Consequently, we revealed a previously unidentified functional role for Gram-positive bacteria in MFC current generation...
  12. doi request reprint Environmental genomics reveals a single-species ecosystem deep within Earth
    Dylan Chivian
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Science 322:275-8. 2008
    ....
  13. pmc Metagenomic analysis of a stable trichloroethene-degrading microbial community
    Vanessa L Brisson
    Department of Civil and Environmental Engineering, University of California Berkeley, CA 94720, USA
    ISME J 6:1702-14. 2012
    ..Genes for hydrogenase components (271 in total) were widespread, highlighting the importance of hydrogen metabolism in this community. PhyloChip analysis confirmed the stability of this microbial community...
  14. ncbi request reprint High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment
    Todd Z DeSantis
    Lawrence Berkeley National Laboratory, Center for Environmental Biotechnology, 1 Cyclotron Road, Mail Stop 70A 3317, Berkeley, CA 94720, USA
    Microb Ecol 53:371-83. 2007
    ..Furthermore, the microarray allowed samples to be rapidly evaluated with replication, a significant advantage in studies of microbial ecology...
  15. pmc Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata
    Collin J Closek
    1 Department of Biology, The Pennsylvania State University, University Park, PA, USA 2 School of Natural Sciences, University of California, Merced, CA, USA
    ISME J 8:2411-22. 2014
    ..HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD...
  16. pmc Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups
    Sarah A Placella
    Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 109:10931-6. 2012
    ..Microbial response patterns displayed phylogenetic clustering and were primarily conserved at the subphylum level, suggesting that resuscitation strategies after wet-up of dry soil may be a phylogenetically conserved ecological trait...
  17. ncbi request reprint Uranium reduction in sediments under diffusion-limited transport of organic carbon
    Tetsu K Tokunaga
    Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Environ Sci Technol 39:7077-83. 2005
    ....
  18. pmc Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators
    Cindy H Wu
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS ONE 5:e11285. 2010
    ..A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring...
  19. ncbi request reprint In situ long-term reductive bioimmobilization of Cr(VI) in groundwater using hydrogen release compound
    Boris Faybishenko
    Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Environ Sci Technol 42:8478-85. 2008
    ..The degree of sustainability of Cr(VI) reductive bioimmobilization under different redox conditions at this and other contaminated sites is currently under study...
  20. doi request reprint Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland
    Karelyn Cruz-Martínez
    Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
    ISME J 3:738-44. 2009
    ....
  21. pmc Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought
    Nicholas J Bouskill
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    ISME J 7:384-94. 2013
    ..Soluble iron declined in treatment plots and was correlated with decreased soluble phosphorus concentrations, which may have significant implications for microbial productivity in these P-limited systems...
  22. pmc Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition
    Nicholas J Bouskill
    Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
    Front Microbiol 7:323. 2016
    ..This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO2 efflux following wet-up in drought plots relative to control plots. ..
  23. pmc Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism
    Nicholas J Bouskill
    Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
    Front Microbiol 7:525. 2016
    ..Significantly, some of these drought-induced functional shifts in the soil microbiota are attenuated by prior exposure to a short-term drought suggesting that acclimation may occur despite a lack of longer-term drought history. ..
  24. pmc Exometabolite niche partitioning among sympatric soil bacteria
    Richard Baran
    Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, California 94720, USA
    Nat Commun 6:8289. 2015
    ..These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity. ..
  25. doi request reprint Divergent aquifer biogeochemical systems converge on similar and unexpected Cr(VI) reduction products
    Harry R Beller
    Earth Sciences Division and Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
    Environ Sci Technol 48:10699-706. 2014
    ..This study indicates that the bulk redox status and biogeochemical regime, as categorized by the dominant electron-accepting process, do not necessarily control the final product of Cr(VI) reduction. ..
  26. doi request reprint Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes
    George F Wells
    Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
    Appl Microbiol Biotechnol 98:4723-36. 2014
    ..Our results provide compelling evidence that substantial immigration between coupled process units occurs and may exert significant influence over microbial community dynamics within staged bioreactors...
  27. pmc Urban aerosols harbor diverse and dynamic bacterial populations
    Eoin L Brodie
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:299-304. 2007
    ..Finally, using multivariate regression techniques, we demonstrate that temporal and meteorological influences can be stronger factors than location in shaping the biological composition of the air we breathe...
  28. pmc Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee
    Javier A Ceja-Navarro
    Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nat Commun 6:7618. 2015
    ..hampei, and re-inoculation of antibiotic-treated insects with an isolated Pseudomonas strain reinstates caffeine-degradation ability confirming their key role. ..
  29. pmc Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota
    Susan V Lynch
    Colitis and Crohn s Disease Center, Division of Gastroenterology, Department of Medicine University of California, San Francisco, San Francisco, CA, USA
    Gut Microbes 4:41-7. 2013
    ..Thus, these data provide the first indications that GI bacterial colonization is strongly impacted by the loss of functional CFTR and opens up avenues for alternative therapeutic approaches to improve CF disease management...
  30. pmc Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust
    Lara Rajeev
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    ISME J 7:2178-91. 2013
    ....
  31. pmc Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1
    Harry R Beller
    Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Appl Environ Microbiol 79:63-73. 2013
    ....
  32. doi request reprint Physiological and transcriptional studies of Cr(VI) reduction under aerobic and denitrifying conditions by an aquifer-derived pseudomonad
    Ruyang Han
    Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Environ Sci Technol 44:7491-7. 2010
    ..We also report incomplete removal of reduced Cr from solution and on artifacts in the widely used diphenylcarbazide assay for Cr(VI), most notably, its complete inactivation in the presence of millimolar nitrite...
  33. pmc Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase
    David R Johnson
    Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 1710, USA
    Appl Environ Microbiol 74:2864-72. 2008
    ....
  34. doi request reprint Field evidence for co-metabolism of trichloroethene stimulated by addition of electron donor to groundwater
    Mark E Conrad
    E O Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Environ Sci Technol 44:4697-704. 2010
    ..The results of these studies indicate that electron donor amendment designed to stimulate reductive dechlorination of TCE may also stimulate co-metabolism of TCE...
  35. pmc Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma
    Yvonne J Huang
    Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California, San Francisco, Calif, USA
    J Allergy Clin Immunol 127:372-381.e1-3. 2011
    ..However, the airway might be populated by a more diverse microbiota, and clinical features of asthma might be associated with characteristics of the airway microbiota present...
  36. pmc Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons
    Shengjing Shi
    Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
    MBio 6:e00746. 2015
    ....
  37. pmc Simrank: Rapid and sensitive general-purpose k-mer search tool
    Todd Z DeSantis
    Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, USA
    BMC Ecol 11:11. 2011
    ..However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available...
  38. pmc Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus
    Ping Hu
    Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A3317, Berkeley, CA 94720, USA
    J Bacteriol 187:8437-49. 2005
    ..Several differentially regulated transcripts from regions previously not known to encode proteins were identified, demonstrating the advantage of evaluating the transcriptome by using whole-genome microarrays...
  39. pmc Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer
    Talia N M Jewell
    Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    ISME J 10:2106-17. 2016
    ....
  40. doi request reprint Metabolite identification in Synechococcus sp. PCC 7002 using untargeted stable isotope assisted metabolite profiling
    Richard Baran
    Life Sciences Division and Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
    Anal Chem 82:9034-42. 2010
    ..PCC 7002 but not included in databases of metabolism (MetaCyc or KEGG). ..
  41. pmc Microbial legacies alter decomposition in response to simulated global change
    Jennifer Bh Martiny
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
    ISME J . 2016
    ..The ISME Journal advance online publication, 14 October 2016; doi:10.1038/ismej.2016.122...
  42. pmc Avian incubation inhibits growth and diversification of bacterial assemblages on eggs
    Matthew D Shawkey
    Department of Environmental Science, Ecosystem Science Division, University of California, Berkeley, California, United States of America
    PLoS ONE 4:e4522. 2009
    ..Thus, incubation inhibits all of the relatively few bacteria that grow on eggshells, and does not appear to promote growth of any bacteria...
  43. pmc Environmental whole-genome amplification to access microbial populations in contaminated sediments
    Carl B Abulencia
    Diversa, 4955 Directors Place, San Diego, CA 92121, USA
    Appl Environ Microbiol 72:3291-301. 2006
    ..The reported SSU rRNA sequences and library clone end sequences are listed with their respective GenBank accession numbers, DQ 404590 to DQ 404652, DQ 404654 to DQ 404938, and DX 385314 to DX 389173...
  44. ncbi request reprint Long-term sustainability of a high-energy, low-diversity crustal biome
    Li Hung Lin
    Department of Geosciences, Princeton University, Princeton, NJ, USA
    Science 314:479-82. 2006
    ..These sulfate reducers were sustained by geologically produced sulfate and hydrogen at concentrations sufficient to maintain activities for millions of years with no apparent reliance on photosynthetically derived substrates...