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George A. Kowalchuk PhD

Personal Page: Prof dr George A. Kowalchuk PhD

  • E g.kowalchuk@nioo.knaw.nl
  • T +31 (0)317-473 478
  • M

    +31 (0)6 22 546556
Curriculum Vitae

 

 

 

 

Gradated PhD students
 
  1. Anna Kielak. January 18th, 2010. Metagenomic analysis of two important, but difficult to culture, soil-borne bacterial phyla: Acidobacteria and Verrucomicrobia. Vrije Universiteit Amsterdam, Ecogenomics program (Promoter) ), primary work location – Heteren.      
  2. Barbara Drigo. January 19th, 2009. Effects of elevated atmospheric Carbon Dioxide concentrations on the functional diversity of microbial communities in soil and feedbacks to plant disease incidences in natural ecosystems (January, 2004 - December, 2007) Leiden University, NWO-ALW (2nd Promoter), primary work location – Heteren.
  3. Etienne Yergeau. June 27th, 2008. Effects of global warming on microbial community structure and function in Antarctic terrestrial environments (June, 2004 - June, 2008) Vrije Universiteit Amsterdam, NWO – NAAP (Promoter) primary work location – Heteren.
  4. Francisco de Souza. October 10th, 2005. Biology, ecology and evolution of the family Gigasporaceae, arbuscular mycorrhizal fungi (Glomeromycota) (February 2001 – February, 2005). Leiden University, (2nd Promoter), primary work location – Heteren.   
 
 
Current PhD Students
 
  1. Ronald van Doorn. Detection of Plant Pathogens with novel micro-array assay platforms (2005 - 2009) Free University of Amsterdam, Bsik (Promoter), primary work location – Plant Research International, Wageningen. Defense expected 09/2011.
  2. Remy Hillekens. Effects of genetically modified crops on beneficial soil fungi: Community structure and function of fungal decomposers (July, 2007 - July, 2011) Free University of Amsterdam, NWO – ERGO (Promoter), primary work location – Wageningen.
  3. Annelein Meisner. Plant-microbe interactions in the rhizosphere of invasive exotic plants (March, 2007 – March, 2011) vici grant of Wim van der Putten (2nd promoter), primary work location – Wageningen.
  4. Erik Verbruggen. Effects of genetically modified crops on beneficial soil fungi: AMF community structure and function (May, 2007 - May, 2011) Free University of Amsterdam, NWO – ERGO (2nd promoter), primary work location – VU-Amsterdam.
  5. Mitja Remus-Emsermann. The ecology of bacterial individuality (July 2007 – July 2011). Free University of Amsterdam, vidi-grant of Johan Leveau (Promoter), primary work location – Wageningen.
  6. James Weedon. Nitrogen availability in a warmer world: linking microbial N transformations at the genetic level and plant responses at the community level. (2008-2012): NWO – Open competition P.I. = R. Aerts (2nd promoter), primary work location – VU-Amsterdam.
  7. Sarah Jennings. Crossing the frontiers of microbial ecology: Microscale patterns of microbial diversity. (January, 2009 – January, 2012). Free University of Amsterdam, NWO-vici grant (Promoter), primary work location – Wageningen.
  8. Alexandra Wolf. Crossing the frontiers of microbial ecology: Effects of microscale soil structure on microbial diversity patterns. (March, 2009 – March, 2012). Free University of Amsterdam, NWO-vici grant (Promoter), primary work location – Wageningen.

 

Date of birth                         : June 10th, 1966
Nationality                            : Dutch / American
Country of residence         : The Netherlands
Ph.D.                                     : 25/06/1993 (Yale University)
Number of current PhD students: 8
 
Current research topics and interests:
 
Environmental genomics of ecologically relevant micro-organisms; Molecular community analysis of bacterial and fungal communities; Relationships between microbial community shifts and vegetation development; Soil-borne microbial diversity; Effects of genetically modified plants on soil communities; Rhizosphere ecology; Roles of plant-microbe interactions in C and N cycling; polar microbial ecology.
 
 
Professor George A. Kowalchuk leads a multifaceted research program with emphasis on environmental and rhizosphere microbiology within the department of Plant Microorganism Interactions of the Netherlands Institute of Ecology. He also holds a professor’s chair at the Free University of Amsterdam within the Institute of Ecological Sciences, titled plant-microbe interactions. His research foci include environmental genomics of ecologically relevant micro-organisms, rhizosphere ecology, molecular community analysis of bacterial and fungal communities, microbial diversity in the rhizosphere, interactions between aboveground and belowground biota, effects of genetically modified plants on soil communities, and roles of plant-microbe interactions in C and N cycling. Much of this work is related to the development and application of the new molecular and genomics approaches for understanding not only the diversity but also the functions of the largely unexplored soil microbial communities. Within the personal Vici grant “Crossing the frontiers of microbial ecology”, Professor Kowalchuk’s research team seeks to unravel the fundamental patterns of microbial diversity, by applying emerging genomics toolboxes to the study of microbial diversity at scales from the individual microbe to the globe. Professor Kowalchuk is a founding editor and co-editor-in-chief of the flagship journal of the International Society for Microbial Ecology, The ISME Journal, launched in 2007 by The Nature Publishing Group. He also serves as editor-in-chief of the Molecular Microbial Ecology Manual, and sits on the editor boards of the journals Environmental Microbiology, Applied and Environmental Microbiology, FEMS Microbiology Ecology, and The Journal of Genomic Standards.
 
 
Professional appointments and education:
 
-  02/2005-present: 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-present: 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           

Co-Operation

National collaboration
Within NIOO-KNAW:
Departments on Terrestrial Ecology
 
Other national collaborations include:
P. Klinkhamer and E. van der Meyden (both Leiden University), J.D. van Elsas (Univesity of Groningen, C. C. Schoen, A. Speksnijder & P Bonants (PRI, Wageningen), J. Raaijmakers (Wageningen University), R. Aerts, M. van der Heijden, & N. van Straalen (Free University, Amsterdam); E. Smit & M Rutgers (RIVM); Peter de Ruyter (WUR)
 
Current International co-operation
Gary A. Andersen (Lawrence Berkeley National Laboratory, Berkeley, CA, USA) M.J. Bailey & A. Whiteley (CEH, Oxford, UK); M. Carnol (Liège University, Belgium); Stephane Declerck, de l'Université catholique de Louvain (MUCL);  L. Vinolas & R. Vallejo (Catalonyan University, Spain); J. Zhou (Oklahoma University, USA); J.R. Stephen (Australian Genome Research Facility, Adelaide Australia); Steven Wakeline & Maureen O’Çallaghan (AgResearch, Christchurch, New Zealand); Eske Willerslev (University of Copenhagen); Bill Sloan, Chris Quince (University of Glasgow)
 

Selected Publications

 
1.      Kuramae EE, 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. In press.
2.      Gilbert JA, et al ., and Kowalchuk GA (2011) The Grand Challenge of the Earth Microbiome Project. Science. Submitted
3.      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.
4.      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.
5.      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.
6.      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.
7.      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.
8.      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.
9.      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.
10.   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.
11.   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
12.   Gamper HA, van der Heijden MGA, Kowalchuk GA (2010) Molecular trait indicators: moving beyond phylogeny in arbuscular mycorrhizal ecology. New Phylogist 185: 67-82.
13.   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.
14.   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.
15.   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.
16.   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.
17.   Mello A, Miozzi L, Vizzini A, Napoli C, Kowalchuk GA, Bonfante P (2010) Bacterial and fungal communities associated to Tuber magnatum-productive niches. Plant Biosystems, 144: 323–332.
18.   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.
19.   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.
20.   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.
21.   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.
22.   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.
23.   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.
24.   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.
25.   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.
26.   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.
27.   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.
28.   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.
29.   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.
30.   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.
31.   Kowalchuk GA, Heidelberg JF, Bailey MJ (2007) The ISME Journal: Multidisciplinary Journal of Microbial Ecology. The ISME Journal, 1: 1-3.      
32.   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.
33.   Nelson KE, Methe´ BM, Kowalchuk GA (2007) Microbial Environmental Genomics. Microbial Ecology, 53: 367-368.
34.   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.   
35.   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.
36.   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.
37.   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.
38.   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.
39.   De Boer W, Kowalchuk GA, van Veen JA (2006) `Root-Food` and the rhizosphere microbial community composition. New Phytologist, 170: 3-6.  
40.   Kowalchuk GA, Nelson KE, Bailey MJ (2006) Introducing the ‘New’ Microbial Ecology. Microbial Ecology, 51: 1-3.
41.   De Souza FA,Smit E, Kowalchuk GA, Declerck S (2005) Morphological ontogenetic and molecular characterization of Scutellospora reticulata (Glomeromycota). Mycological Research, 109: 697-706 .
42.   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.
43.   Kowalchuk GA (2004)International group emphasizes microbial environmental genomics. ASM NEWS 70 (11): 507-508.
44.   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.
45.   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.
46.   Kowalchuk GA, Bruinsma M, Van Veen JA (2003) Assessing Soil Ecosystem Responses to GM Plants. Trends in Ecology & Evolution, 18: 403-410.
47.   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.
48.   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.
49.   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.
50.   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.
51.   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.
52.   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.
53.   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.
54.   Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: A model for molecular microbial ecology. Annual Review of Microbiology, 55: 485-529.
55.   De Boer W, Kowalchuk GA (2001) Nitrification in acid soils: microorganisms and mechanisms. Soil Biology and Biochemistry, 33:853-866.
56.   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.
57.   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.   
58.   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.
59.   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.
60.   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.
61.   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.
62.   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.
63.   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.
64.   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.
65.   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.
66.   SengeløvG, Kowalchuk GA, Sørensen S (2000) Influence of fungal-bacterial interactions on bacterial conjugation in the residuesphere. FEMS Microbiology Ecology, 31: 39-45.
67.   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.
68.   Kowalchuk GA (1999) New perspectives towards analyzing fungal communities in terrestrial ecosystems. Current Opinions in Biotechnology, 10: 247-251.
69.   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.
70.   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.
71.   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.
72.   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.
73.   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.
74.   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.
75.   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.
76.   Kowalchuk GA, Gregg-Jolly LA, Ornston, LN (1995) Nucleotide sequences transferred by gene conversion in the bacterium Acinetobacter calcoaceticus. Gene, 153: 111-115.
77.   Kowalchuk GA, Hartnett GB, Benson A, Ornston LN (1994) Contrasting patterns of evolutionary divergence within the Acinetobacter calcoaceticus pca operon. Gene, 146: 23-30.
78.   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.      Kielak A, Kowalchuk GA (2010) Targeting major soil-borne bacterial lineages using large-insert metagenomic approaches. In “Handbook of Molecular Microbial Ecology: Metagenomics and Complementary Approaches”, de Bruijn (Ed.) Wiley/Blackwell. In Press.
2.      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.
3.      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.
4.      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.
5.      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.
6.      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.
7.      Bruisma M, Kowalchuk GA, Van Veen JA (2002) Effects of genetically modified plants on soil ecosystems. Ponsen and Looijen BV, Wageningen, The Netherlands.
8.      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.
9.      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.
10.   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.
11.   Kowalchuk GA, Zwart G (2000) Focus on molecular ecology research: Molecular biology provides new tools for environmental research. INTECOL Newsletter. Autumn, 2000: 7-8. 
12.   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.
g.kowalchuk

FUNCTION & DEPARTMENT:
Senior researcher
Microbial Ecology
 

 
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