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Prof. dr. G.A. (George) Kowalchuk

Professor 
Science
Biology
Environmental Biology
Ecology and Biodiversity
Ecology and Biodiversity
Hugo R. Kruytgebouw
Padualaan 8
Kamer N 304
3584 CH Utrecht

Prof. dr. G.A. (George) Kowalchuk

Professor
Ecology and Biodiversity
+31 30 253 6856
g.a.kowalchuk@uu.nl
Profile CV Publications Activities In the media Research Teaching Ancillary activities Contact
Profile CV Publications Activities In the media Research Teaching Ancillary activities Contact

Professional appointments and education:

-   01/2013-present: Professor of Ecology & Biodiversity, Utrecht University. Institute of Environmental Biology (IEB), Dept. of Biology.

-  01/2013-present: Guest researcher, Netherlands Institute of Ecology (NIOO-KNAW), Dept. of Microbial Ecology, Wageningen.  

-  02/2005-12/2014: Professor of Plant-Microbe Interactions: Free University Amsterdam: Institute for Ecological Sciences (IEW).

-   12/2005-6/2006: Guest researcher: University of Adelaide, Adelaide Australia.

-   9/96-12/2013: Senior Researcher / Microbial ecologist; Dept. of Plant Microorganism Interactions. Centre for Terrestrial Ecology: Netherlands Institute of Ecology.

-   9/94-9/96: Post-doctoral researcher; Centre for Terrestrial Ecology;

Netherlands Institute of Ecology, Dept. of Plant Microorganism Interactions.

Topics: Molecular characterisation of bacterial and fungal communities.

-   1/94-8/94: Guest lecturer / researcher; Dept. of Microbiology; University of Amsterdam. Topics: evolution of metabolic pathways; microbial degradation of xenobiotic compounds; natural transformation.

-   8/1993-12/1993: Postdoctoral Fellow; Yale University, Dept. of Biology.

topic: Evolution of pathways for aerobic aromatic catabolism

-   9/1988-7/1993; Research Trainee; Department of Biology, Yale University, New Haven, Connecticut, U.S.A. MS 1990; M.Phil. 1991 (with honors); Thesis topic: Bacterial degradation of aromatic compounds.

-   9/1984-5/1988; 1988, Duke University Durham, NC.

BS with Double Major: Biology, Psychology magna cum laude

Undergraduate Research Project.  Zinc Finger DNA binding proteins of Saccharomyces cerevisiae   

    

 

Services:

-          Professional associations

American Society for Microbiology

Netherlands Association for Microbiology

International Society for Microbial Ecology (Netherlands Ambassador)

 

-          Editorial positions

The ISME Journal (co-editor-in-chief)

Molecular Microbial Ecology Manual (editor-in-chief)

Microbial Ecology (editor: 2005-2007)

Environmental Microbiology and Environment Microbiology Reports (editorial board)

Applied & Environmental Microbiology (editorial board)

FEMS Microbiology Ecology (editorial board)

Journal of Genomics Standards (editorial board)

Journal of Microbiological Methods (editorial board 1997-2007)

 

 

Peer-reviewed Publications

 

  1. Weedon JT, Aerts R, Kowalchuk GA, van Bodegom PM (2014) No effects of experimental warming but contrasting seasonal patterns for soil peptidase and glycosidase enzymes in a sub-arctic peat bog. Biogeochemistry, 117: 55-66. DOI 10.1007/s10533-013-9870-0.
  2. Wolf AB, Vos M, de Boer W, Kowalchuk GA (2013) Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria. PLoS ONE. 8(12): DOI: 10.1371/journal.pone.008366.
  3. van Grunsven R, Yuwati T, Kowalchuk GA, van der Putten W, Veenendaal E (2013) The northward shifting neophyte Tragopogon dubius is just as effective in forming mycorrhizal associations as the native T. pratensis. Plant Ecology & Diversity, DOI: 10.1080/17550874.2013.824517
  4. Kuramae EE, Verbruggen E, Hillekens R, de Hollander M, Röling WFM, der Heijden MGA, Kowalchuk GA (2013) Tracking Fungal Community Responses to Maize Plants by DNA- and RNA-Based Pyrosequencing. PLoS ONE 8(7): e69973. doi:10.1371/journal.pone.0069973.
  5. Vos M, Wolf AB, Jennings SJ, Kowalchuk GA (2013) Micro-scale determinants of bacterial diversity in soil. FEMS Microbiology Reviews, 37: 936–954. doi: 10.1111/1574-6976.12023.
  6. Kuramae EE, Hillekens RHE, de Hollander M, van der Heijden MGA, van den Berg M, van Straalen NM, Kowalchuk GA (2013) Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf. FEMS Microbiology Ecology, 84: 519-531.
  7. García-Villaraco Velascoa A, Kowalchuk GA, Gutierrez Ma˜neroa FJ, Ramosa B, Yergeau E, Lucas García JA (2013) Increased microbial activity and nitrogen mineralization coupled to changes in microbial community structure in the rhizosphere of Bt corn. Applied Soil Ecology 68: 46– 56.
  8. Weedon JT, Aerts R, Kowalchuk GA, van Logtestijn R, Andringa D, van Bodegom PM (2013) Temperature sensitivity of peatland C and N cycling: Does substrate supply play a role? Soil Biology and Biochemistry. 61: 109-120.http://dx.doi.org/10.1016/j.soilbio.2013.02.019
  9. Remus-Emsermann MNP, Kowalchuk GA, Leveau JHJ (2013) Single-cell versus population-level reproductive success of bacterial immigrants to pre-colonized leaf surfaces. Environmental Microbiology Reports 5: 387–392. doi:10.1111/1758-2229.12040.
  10. Wakelin SA, Barratt BIP, Gerard E, Gregg AL, Brodie EL, Andersen GL, DeSantis TZ, Zhou J, He Z, Kowalchuk GA, O'Callaghan M (2013). Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems. Soil Biology and Biochemistry. 57: 675-682.
  11. Drigo B, Kowalchuk GA, Knapp, BA, Pijl AS, Boschker HTS, van Veen JA (2013) Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow .and microbial community dynamics. Global Change Biology, 19: 621-636.
  12. Verbruggen E, Kuramaea EE, Hillekens R, de Hollander M, Kiers ET, Röling WFM, Kowalchuk GA, van der Heijden MGA (2012) Testing Potential Effects of Maize Expressing the Bacillus thuringiensis Cry1Ab Endotoxin (Bt Maize) on Mycorrhizal Fungal Communities via DNA- and RNA-Based Pyrosequencing and Molecular Fingerprinting. Applied Environmental Microbiology, 78: 7384-7392.
  13. Kowalchuk GA (2012) Bad news for soil carbon sequestration? Science, 337:1019-1050. 
  14. Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, Bailey MJ, Gordon JI, Kowalchuk GA, Gilbert JA (2012) Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology, 30:513-20.
  15. Epelde l, Becerril JM, Kowalchuk GA, Garbisu C (2012) Links between pseudometallophytes and rhizosphere microbial communities in a metalliferous soil. Pedobiologia, 55: 219-225.
  16. Verbruggen E, van der Heijden MGA, Kowalchuk GA, Röling, WFM (2012) Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils. Molecular Ecology, 21: 2341–2353.
  17. Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA (2012) A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity. PLoS ONE 7(2): e30600. doi:10.1371/journal.pone.0030600.
  18. Weedon JT, Kowalchuk GA, Aerts R, van Hal J, van Logtestijn R, Tas N, Röling WFM, van Bodegom PM (2012) Summer warming accelerates sub-arctic peatland nitrogen cycling without changing enzyme pools or microbial community structure. Global Change Biology. 18: 138-150.
  19. Yergeau E, Bokhorst S, Kang S, Zhou J, Greer CW, Aerts R,  Kowalchuk GA (2012) Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. The ISME Journal, 6: 692–702. 
  20. Kuramae EE, Yergeau E, Wonga LC, Pijl AS, van Veen JA, Kowalchuk GA (2012) Soil characteristics more strongly influence soil microbial communities than land management. FEMS Microbiology Ecology. 79: 12-24.  
  21. Kiers TE, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E, Fellbaum CR, Kowalchuk GA, Hart MM, Bago A, Palmer TM, West SA, Vandenkoornhuyse P, Jansa J, Bücking H (2011) Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science. 333: 880-882. 
  22. Kuramae EE, Gamper HA, van Veen JA, Kowalchuk GA (2011) Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with neutral pH. FEMS Microbiology Ecology. 77: 285–294.
  23. Garbeva P, Hol WHG, Termorshuizen AJ, Kowalchuk GA, de Boer W (2011) Fungistasis and general soil biostasis - A new synthesis. Soil Biology & Biochemistry 43, 469-477.
  24. Weedon, JT, Aerts R, Kowalchuk GA, van Bodegom PM (2011) Enzymology under global change: organic nitrogen turnover in alpine and sub-Arctic soils. Biochemical Society Transactions 39, 309–314.
  25. Epelde L, Becerril JM, Kowalchuk GA, Deng Y, Zhou J, Garbisu C (2010) Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities. Applied Environmental Microbiology 76: 7843–7853.
  26. Kielak AM, van Veen JA, Kowalchuk GA (2010) Comparative Analysis of Acidobacterial Genomic Fragments from Terrestrial and Aquatic Metagenomic Libraries, with Emphasis on Acidobacteria Subdivision 6. Applied Environmental Microbiology 76: 6769–6777.
  27. Drigo B,  van Veen JA, Pijl AS,Kielak AM, Gamper HA, Houtekamer MJ, Bodelier PLE, Boschker HTS, Whiteley AS, Kowalchuk GA (2010) Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2. PNAS USA. 107:10938-10942; doi: 10.1073/pnas.0912421107.
  28. Verbruggen E, Röling WFM, Gamper HA, Kowalchuk GA, Verhoef HA, van der Heijden MGA (2010) Positive effects of organic farming on below-ground mutualists: large-scale comparison of mycorrhizal fungal communities in agricultural soils. New Phytologist. 186: 868-979. DOI 10.1111/j.1469-8137.2010.03230.x.
  29. Mello, A, Miozzibc L, Vizzinib A, Napolib C, Kowalchuk G, Bonfante P (2010) Bacterial and fungal communities associated with Tuber magnatum productive niches. Plant Biosystems, 144: 323–332.
  30. Kuramae EE, Gamper HA, Yergeau E, Piceno YM, Brodie EL, DeSantis TZ, Andersen GL, van Veen JA, Kowalchuk GA (2010) Microbial secondary succession in a chronosequence of chalk grasslands.The ISME Journal, 4: 711-715.
  31. Yergeau E, Bezemer TM, Hedlund K, Mortimer SR, Kowalchuk GA, van der Putten WH (2010) Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils. Environmental Microbiology,12: 2096-2106; DOI: 10.1111/j.1462-2920.2009.02053.x
  32. Gamper HA, van der Heijden MGA, Kowalchuk GA (2010) Molecular trait indicators: moving beyond phylogeny in arbuscular mycorrhizal ecology. New Phylogist 185: 67-82.
  33. Kielak A, Rodrigues JLM, Kuramae EE, Chain PSG, van Veen JA, Kowalchuk GA (2010) Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiology Ecology, 71: 23-33.
  34. Rinnan R, Rousk J, Yergeau E, Kowalchuk GA, Baath E (2009) Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming. Global Change Biology, 15: 2615–2625.
  35. van DoornR, Klerks M, van Gent-Pelzer M, Speksnijder AGCL, Kowalchuk GA, Schoen CD (2009) Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts using a novel Internal Amplification Control approach on Biotrove OpenArraysTM. Applied Environmental Microbiology,75: 7253-7260.
  36. Drigo, B, van Veen JA, Kowalchuk GA (2009) Specific rhizosphere bacterial and fungal groups respond differently to elevated atmospheric CO2. ISME Journal, 3: 1204-1217.
  37. Mertens J, Broos K, Wakelin SA, Kowalchuk GA, Springael D, Smolders E (2009) Bacteria, not archaea, restore nitrification in a zinc contaminated soil. The ISME Journal, 3: 916-923.
  38. van Doorn R, Slawiak M, Szemes M, Dullemans A, Bonants P, Kowalchuk GA, and Schoen CD (2009) Robust detection and identification of multiple oomycetes and fungi in environmental samples using a novel cleavable padlock probe-based ligation-detection assay. Applied Environmental Microbiology,75: 4185-4193.
  39. Yergeau E, Schoondermark-Stolk SA, Brodie EL, Déjean S, DeSantis TZ, Gonçalves O, Piceno YM, Andersen GL, Kowalchuk GA (2009) Environmental microarray analyses of Antarctic soil microbial communities. The ISME Journal, 3, 340-351.
  40. Kielak A, Pijl AS, van Veen JA, Kowalchuk, GA (2009) Phylogenetic diversity of Acidobacteria in a former agricultural soil. The ISME Journal, 3: 378–382.
  41. Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glockner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O (2008) Toward a standards-compliant genomic and metagenomic publication record. Omics - A Journal of Integrative Biology 12: 157-160.
  42. Yergeau E, Kowalchuk GA (2008) Responses of Antarctic soil microbial communities and associated functions to temperature and freeze-thaw cycle frequency. Environmental Microbiology. 9: 2670-2682.
  43. Drigo B, Kowalchuk GA, van Veen JA (2008) Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere. Biology and Fertility of Soils 44: 667-679.
  44. Kielak A, Pijl AS, van Veen JA, Kowalchuk GA (2008) Plant species identity and diversity lead to only minor changes in soil-borne microbial communities in a former arable field. FEMS Microbiology Ecology, 63: 372-382.
  45. Drigo, B, Kowalchuk GA, Yergeau E, Bezemer TM, Boschker HTS, van Veen JA (2007) Impact of Elevated CO2 on the Rhizosphere Communities of Carex arenaria and Festuca rubra. Global Change Biology, 13:2396-2410.
  46. Field D, GarrityG, Gray T, et alKowalchuk GA … (30 of 59 authors) (2008) Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nature Biotechnology, 26:541 – 547.
  47. van Doorn R, Szemes M, Bonants P, Kowalchuk GA, Sallas J, Ortenberg E, Schoen CD (2007) Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time PCR on OpenArraysTM. BMC Genomics, 8:276.
  48. Yergeau E, Newsham KK, Pearce DA, Kowalchuk GA (2007) Patterns of bacterial diversity across a range of Antarctic terrestrial habitats. Environmental Microbiology, 9:2670-2682.
  49. Yergeau E, Kang S, He Z, Zhou J, Kowalchuk GA (2007) Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME Journal, 1: 163-179.
  50. Kowalchuk GA, Heidelberg JF, Bailey MJ (2007) The ISME Journal: Multidisciplinary Journal of Microbial Ecology. The ISME Journal, 1: 1-3.      
  51. Kowalchuk GA, Speksnijder AGCL, Zhang K, Goodman RM, van Veen JA (2007) Finding the needles in the meta-genome haystack. Microbial Ecology, 53: 475-485.
  52. Nelson KE, Methe´ BM, Kowalchuk GA (2007) Microbial Environmental Genomics. Microbial Ecology, 53: 367-368.
  53. Nelson KE, Methe´ BM, Kowalchuk GA (2007) Environmental Microbial Ecology in an “Omics” Era: Summary report of MicroEnGen-II (Shanghai, June 12–15, 2006). Microbial Ecology, 53: 369-370.
  54. van der Putten WH, Kowalchuk GA, Brinkman EP, Doodeman GTA, Van der Kaaij RM, Kamp ADF, Menting FBJ, Veenendaal EM (2007) Soil feedback of exotic savannah grass relates to the absence of pathogens and selective mycorrhizal fungi. Ecology, 88: 978-988.
  55. Yergeau E, Bokhorst S, Huiskes AHL, Boschker HTS, Aerts R, Kowalchuk GA (2007) Size and structure of bacterial, fungal and nematode communities along an Antarctic environmental gradient. FEMS Microbiology Ecology, 59: 436–451.
  56. Kowalchuk GA, Hol WHG, van Veen JA (2006) Rhizosphere fungal communities are influenced by Senecio jacobaea pyrrolizidine alkaloid content and composition. Soil Biology & Biochemistry. 38:2852-2859.
  57. Bezemer TM, Harvey JA, Kowalchuk GA, Korpershoek H, Van der Putten WH (2006) Interplay between population dynamics of Senecio jacobaea and plant, soil and aboveground insect herbivore community composition. Ecology, 87:2002-2013.
  58. De Boer W, Kowalchuk GA, van Veen JA (2006) `Root-Food` and the rhizosphere microbial community composition. New Phytologist, 170: 3-6.  
  59. Kowalchuk GA, Nelson KE, Bailey MJ (2006) Introducing the ‘New’ Microbial Ecology. Microbial Ecology, 51:1-3.
  60. De Souza FA,Smit E, Kowalchuk GA, Declerck S (2005) Morphological ontogenetic and molecular characterization of Scutellospora reticulata (Glomeromycota). Mycological Research, 109:697-706 .
  61. Duine AS, Kowalchuk GA, Klein Gunnewiek PJA, Smant W, van Veen JA, de Boer W (2005) Rhizosphere bacterial community compositions in natural stands of Carex arenaria (sand sedge) is determined by bulk soil. Soil Biology and Biochemistry, 37:349-357.
  62. Kowalchuk GA (2004)International group emphasizes microbial environmental genomics. ASM NEWS 70 (11): 507-508.
  63. De Souza FA,Kowalchuk GA, Leefland P, van Veen JA, Smit E (2004) PCR-DGGE profiling of inter- and intra-species 18S rDNA sequence heterogeneity as an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora. Applied Environmental Microbiology, 70: 1413-1424.
  64. De Boer W, Leveau JHJ, Kowalchuk GA, Klein Gunnewiek PJA, Abeln ECA,  Figge MJ, Sjollema K, Janse JD, Van Veen JA (2004) Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on intact fungal hyphae. International Journal of Applied and Systematic Microbiology, 54: 857-864.
  65. Kowalchuk GA, Bruinsma M, Van Veen JA (2003) Assessing Soil Ecosystem Responses to GM Plants. Trends in Ecology & Evolution, 18:403-410.
  66. Bruinsma M, Kowalchuk GA, Van Veen JA. 2003. Effects of genetically modified plants on microbial communities and processes in soil. Biology & Fertility of Soils, 37:329-337.
  67. De Boer W, Verheggen P, Klein-Gunnewiek PJA, Kowalchuk GA, Van Veen JA (2003) Microbial Community Composition Affects Soil Fungistasis. Applied Environmental Microbiology, 69:835-844.
  68. Kowalchuk GA, Van Os GJ, Van Aartrijk J, Van Veen JA (2003) Microbial community responses to disease management soil treatments used in flower bulb cultivation. Biology & Fertility of Soils, 37: 55-63.
  69. Kowalchuk GA, Buma DS, De Boer W, Klinkhamer PGL, Van Veen JA (2002) Effects of Aboveground Plant Species Composition and Diversity on the Diversity of Soil-borne Microorganisms. Antonie van Leeuwenhoek, 81: 509-520.
  70. Carnol M, Kowalchuk GA, De Boer W (2002) Nitrosomonas europaea-like bacteria detected as the dominant ß-subclass Proteobacteria ammonia oxidisers in reference and limed acid forest soils. Soil Biology and Biochemistry, 34: 1047-1050.
  71. Kowalchuk GA, de Souza FA, van Veen JA (2002) Community analysis of arbuscular mycorrhizal fungi associated with Ammophila arenaria in Dutch coastal sand dunes. Molecular Ecology, 11:571-581.
  72. De Boer W, Gunnewiek PJAK, Kowalchuk GA, Van Veen JA (2001) Growth of chitinolytic dune soil beta-subclass Proteobacteria in response to invading fungal hyphae. Applied Environmental Microbiology, 67: 3358-3362.
  73. Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: A model for molecular microbial ecology. Annual Review of Microbiology, 55: 485-529.
  74. De Boer W, Kowalchuk GA (2001) Nitrification in acid soils: microorganisms and mechanisms. Soil Biology and Biochemistry, 33:853-866.
  75. Laverman AM, Speksnijder AGCL, Braster M, Kowalchuk GA, Verhoef HA, Van Verseveld HW (2001) Spatio-temporal stability of an ammonia oxidizing community in a nitrogen-saturated forest soil. Microbial Ecology, 42: 35-45.
  76. De Bie M, Speksnijder, AGCL, Kowalchuk GA, Schuurman T, Zwart G, Stephen JR, Diekmann O, Laanbroek HJ (2001) Shifts in the dominant populations of ammonia-oxidizing ß-subclass proteobacteria along the eutrophic Schelde estuary. Aquatic Microbial Ecology, 23:225-236.   
  77. Speksnijder AGCL, Kowalchuk GA, De Jong S, Kline E, Stephen JR, Laanbroek HJ (2001) Micro-variation artifacts introduced by PCR and cloning of closely related 16S rDNA sequences. Applied Environmental. Microbiology, 67: 469-472.
  78. Duineveld BM, Kowalchuk GA, Keizer A, Van Elsas JD, Van Veen JA (2001) Analysis of the bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR amplified 16S ribosomal RNA and DNA fragments. Applied Environmental Microbiology, 67: 172-178.
  79. Kowalchuk GA, Stienstra AW, Heilig GHJ, Stephen JR, Woldendorp JW (2000) Changes in the community structure of ammonia-oxidising bacteria during secondary succession of calcareous grasslands. Environmental Microbiology, 2: 99-110.
  80. Kowalchuk GA, Stienstra AW, Heilig GHJ, Stephen JR, Woldendorp JW (2000) Composition of communities of ammonium-oxidising bacteria in wet, slightly acid grassland soils using 16S rDNA-analysis. FEMS Microbiology Ecology, 31: 207-215.
  81. Chang Y-J, Stephen JR, Richter AP, Venosa AD, Brüggemann J, Macnaughton SJ, Kowalchuk G, Haines JR, White DC(2000) Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method. Journal of Microbiological Methods, 40: 19-31.
  82. Bruns MA, Stephen JR, Kowalchuk GA, Prosser JI, Paul EA (1999) Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in never-tilled, tilled, and successional soils. Applied and Environmental Microbiology, 65: 2994-3000.
  83. Ivanova IA, Stephen JR, Chang Y-J, Brüggemann J, Long PE, McKinley JP, Kowalchuk GA, White DC, Macnaughton SJ (2000) A survey of 16S rRNA and amoA genes related to autotrophic ammonia-oxidizing bacteria of the ß-subdivision of the class proteobacteria in contaminated groundwater. Canadian Journal of Microbiology, 46: 1012-1020.
  84. Brüggemann J, Stephen JR, Chang Y-J, Macnaughton SJ, Kowalchuk GA, Kline E, White DC (2000) Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy. Journal of Microbiological Methods, 40: 111-123.
  85. SengeløvG, Kowalchuk GA, Sørensen S (2000) Influence of fungal-bacterial interactions on bacterial conjugation in the residuesphere. FEMS Microbiology Ecology, 31: 39-45.
  86. McCaig AE, Phillips CJ, Stephen JR, Kowalchuk GA, Harvey M, Herbert RA, Embley TM, Prosser JI (1999) Nitrogen cycling and community structure of ß-subgroup ammonia oxidising bacteria within polluted, marine fish-farm sediments. Applied and Environmental Microbiology, 65: 213-220.
  87. Kowalchuk GA (1999) New perspectives towards analyzing fungal communities in terrestrial ecosystems. Current Opinions in Biotechnology, 10: 247-251.
  88. Kowalchuk GA, Naoumenko ZS, Derikx PJL, Felske A, Stephen JR, Arkhipchenko IA (1999) Molecular analysis of ammonia-oxidizing bacteria of the b subdivision of the class Proteobacteria in compost and composted materials. Applied and Environmental Microbiology, 65: 396-403.
  89. Stephen JR, Chang Y-J, Macnaughton SJ, Kowalchuk GA, Leung KT, Flemming CA, White DC (1999) Effect of toxic metals on indigenous soil ß-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria. Applied and Environmental Microbiology, 65: 95-101.
  90. Kowalchuk GA, Bodelier PLE, Heilig GHJ, Stephen JR, Laanbroek HJ(1998) Community analysis of ammonia-oxidising bacteria, in relation to oxygen-availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation. FEMS Microbiology Ecology, 27: 339-350.
  91. Speksnijder AGCL, Kowalchuk GA, Roest K, Laanbroek HJ (1998) Recovery of a  Nitrosomonas-like 16S rDNA sequence group from freshwater habitats. Systematic and Applied Microbiology, 21: 321-330.
  92. Stephen JR, Kowalchuk, GA, Bruns M-AV, McCaig AE, Phillips CJ, Embley TM, Prosser JI (1998) Analysis of ß-subgroup ammonia oxidizer populations in soils by DGGE analysis and hierarchical phylogenetic probing. Applied and Environmental Microbiology,64: 2958-2965.
  93. Kowalchuk GA, Gerards S, Woldendorp JW (1997) Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by Denaturing Gradient Gel Electrophoresis (DGGE) of specifically amplified 18S-rDNA Applied and Environmental Microbiology,63:3858-3865.
  94. Kowalchuk GA, Stephen LR, De Boer W, Prosser JI, Embley TM, Woldendorp, JW(1997) Analysis of ß-proteobacteria ammonia-oxidizing bacteria in coastal sand dunes using denaturing gradient gel electrophoresis and sequencing of PCR amplified 16S rDNA fragments. Applied and Environmental Microbiology, 63:1489-1497.
  95. Kowalchuk GA, Gregg-Jolly LA, Ornston, LN(1995) Nucleotide sequences transferred by gene conversion in the bacterium Acinetobacter calcoaceticus. Gene, 153: 111-115.
  96. Kowalchuk GA, Hartnett GB, Benson A, Ornston LN (1994) Contrasting patterns of evolutionary divergence within the Acinetobacter calcoaceticus pca operon. Gene, 146: 23-30.
  97. Shanley MS, Harrison A, Parales RE, Kowalchuk GA, Mitchell DJ, Ornston, LN (1994) Unusual G+C content and codon usage in catIJF, a segment of the ben-cat supraoperonic cluster in the Acinetobacter calcoaceticus chromosome. Gene, 138: 59-63.

 

 

 

Book chapters and other publications:

 

  1. Galende MA, Epelde L, Gómez-Sagasti MT, Barrutia O, Hernández A, Becerril JM, Kowalchuk GA, Garbisu C (2013) Stimulation of rhizosphere microbial communities during chemophytostabilization of a Pb-Zn mine, In “Microbial ecology of the rhizosphere”, Frans de Bruijn (ed.) DOI:10.1002/9781118297674.ch95 ISBN: 9781118297674 Publisher: John Wiley & Sons, Inc., pp.1013-1022
  2. Drigo BA, van Veen JA, Kowalchuk GA (2012) Tracking plant-derived carbon through rhizosphere microbial communities. In “Microbial ecology of the rhizosphere,” Frans de Bruijn (ed.) In press.
  3. Kielak A, Kowalchuk GA (2011) Targeting major soil-borne bacterial lineages using large-insert metagenomic approaches. In “Handbook of Molecular Microbial Ecology II:  Metagenomics in Different Habitats”, de Bruijn (Ed.) Wiley/Blackwell. pp. 135-142.
  4. Kowalchuk GA, Yergeau E, Leveau JHJ, Sessitsch A, Bailey MJ (2009) Plant-associated Microbial Communities. In, “Environmental Molecular Microbiology”, (Eds) Lui W-T, Jansson, J. Caister Academic Press, Norfolk, UK. pp. 131-148.
  5. Kowalchuk GA (2008) Moleculaire ontdekkingsreis naar micro-organismen in de bodem. In: Natuurkundige Voordrachten: Neiuwe reeks No. 86. Drukkerij Vis Offset, Alphen aan den Rijn. pp91-102.   
  6. Kowalchuk GA, Austin JJ, Gooding PS, Stephen JR (2007) Valid Recovery of Nucleic Acid Sequence Information from High Contamination Risk Samples – Ancient DNA and Environmental DNA. In: Mitchelson KR, (ed) New High Throughput Technologies for DNA Sequencing and Genomics. Chapter 13, Elsevier, Amsterdam.
  7. Kowalchuk GA (2007) Microbial diversity underground: do we need to protect the Earth’s greatest source of biodiversity? In: Forgotten Kingdoms. Publication of the IUCN Netherlands Committee.
  8. Kowalchuk GA, Drigo B, Yergeau E, van Veen JA. 2006. Molecular approaches to assess the structure of bacterial and fungal communities in soil – the use of rRNA and other gene markers. In: Nannipieri P, Smalla K (eds) Nucleic acids and Proteins in Soil, Springer, Heidelberg. Pp. 159-188.
  9. Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD (eds) 2004. Molecular Microbial Ecology Manual, 2nd edition. Kluwer Academic Publishers, Dordrecht, The Netherlands.
  10. Bruinsma M, Kowalchuk GA, Van Veen JA (2002) Effects of genetically modified plants on soil ecosystems. Ponsen and Looijen BV, Wageningen, The Netherlands.
  11. Stephen JR, Kowalchuk GA (2002) Ribotyping methods for assessment of in situ microbial community structure. In: Encyclopedia of Environmental Microbiology, Volume 5, pp. 2728-2741. Gabrielle Bitton (Ed.) John Wiley & Sons, New York, USA.
  12. Macnaughton SJ, Stephen JR, Chang Y-J,Davis GA, Kowalchuk GA, Gan Y-D, Brüggemann J, White DC(2001) A combined phospholipid and 16S rDNA PCR-DGGE analysis to study bioremediative communities in situ. In: Molecular Environmental Microbiology: Protocols and Applications. P. Rochelle (Ed). Horizon Scientific Press. pp. 141-160.
  13. Brüggemann J, Chang Y-J, Kowalchuk GA, Macnaughton SJ, Itävaara M, Kline E, White DC, Stephen JR. 2000. Dispelling the myths: How well do multiple competitive PCR products from 16S rDNA reflect the structures of microbial communities? Mutation detection Technical Note 2525 and Bioradiations, 104: 32 - 34, Bio-Rad Laboratories, Hercules, CA, USA.
  14. Kowalchuk GA, Zwart G (2000) Focus on molecular ecology research: Molecular biology provides new tools for environmental research. INTECOL Newsletter. Autumn, 2000: 7-8. 
  15. Kowalchuk GA (1999) Fungal Community Analysis using Denaturing Gradient Gel Electrophoresis (DGGE). In: Molecular microbial ecology manual (Akkermans ADL, van Elsas JD, de Bruijn FJ, Eds.), 3.4.6. pp. 1-16. Kluwer Academic Publishers, Dordrecht, the Netherlands.

 

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