Hofman J, Bezchlebová J, Dušek L, Doležal L, Holoubek I, Anděl P, et al. Novel approach to monitoring of the soil biological quality. Environ Int. 2003;28:771–8.
Article
CAS
PubMed
Google Scholar
Gkarmiri K, Finlay R, Alstrom S, Thomas E, Cubeta M, Hogberg N. Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica. BMC Genomics. 2015;16:630.
Article
PubMed
PubMed Central
Google Scholar
Nazir R, Warmink JA, Boersma H, Van Elsas JD. Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats. Fems Microbiol Ecol. 2010;71:169–85.
Article
CAS
PubMed
Google Scholar
Wargo MJ, Hogan DA. Fungal-bacterial interactions: a mixed bag of mingling microbes. Curr Opin Microbiol. 2006;9:359–64.
Article
CAS
PubMed
Google Scholar
Benoit I, van den Esker MH, Patyshakuliyeva A, Mattern DJ, Blei F, Zhou M, et al. Bacillus subtilis attachment to Aspergillus niger hyphae results in mutually altered metabolism. Environ Microbiol. 2015;17:2099–113.
Article
CAS
PubMed
Google Scholar
Chapelle E, Mendes R, Bakker PAHM, Raaijmakers JM. Fungal invasion of the rhizosphere microbiome. ISME J. 2015: doi:10.1038/ismej.2015.82.
Mathioni SM, Patel N, Riddick B, Sweigard JA, Czymmek KJ, Caplan JL, et al. Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes. PLoS One. 2013;8:e76487.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mela F, Fritsche K, de Boer W, van Veen JA, de Graaff LH, van den Berg M, et al. Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger. ISME J. 2011;5:1494–504.
Article
CAS
PubMed
PubMed Central
Google Scholar
Massart S, Perazzolli M, Höfte M, Pertot I, Jijakli MH. Impact of the omic technologies for understanding the modes of action of biological control agents against plant pathogens. BioControl. 2015;60:725–46.
Article
CAS
Google Scholar
Neupane S, Finlay RD, Alström S, Elfstrand M, Högberg N. Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani. Environ Microbiol Rep. 2015;7:123–7.
Article
CAS
PubMed
Google Scholar
Baumgartner K, Coetzee MP, Hoffmeister D. Secrets of the subterranean pathosystem of Armillaria. Mol Plant Pathol. 2011;12:515–34.
Article
PubMed
Google Scholar
Travadon R, Smith ME, Fujiyoshi P, Douhan GW, Rizzo DM, Baumgartner K. Inferring dispersal patterns of the generalist root fungus Armillaria mellea. New Phytol. 2012;193:959–69.
Article
PubMed
Google Scholar
Perazzolli M, Bampi F, Faccin S, Moser M, De Luca F, Ciccotti AM, et al. Armillaria mellea induces a set of defense genes in grapevine roots and one of them codifies a protein with antifungal activity. Mol Plant Microbe Interact. 2010;23:485–96.
Article
CAS
PubMed
Google Scholar
Aguin O, Mansilla JP, Sainz MJ. In vitro selection of an effective fungicide against Armillaria mellea and control of white root rot of grapevine in the field. Pest Manag Sci. 2006;62:223–8.
Article
CAS
PubMed
Google Scholar
Longa CMO, Pertot I, Tosi S. Ecophysiological requirements and survival of a Trichoderma atroviride isolate with biocontrol potential. J Basic Microbiol. 2008;48:269–77.
Article
CAS
PubMed
Google Scholar
Pellegrini A, Corneo PE, Camin F, Ziller L, Tosi S, Pertot I. Studying trophic interactions between a plant pathogen and two different antagonistic microorganisms using a 13C-labeled compound and isotope ratio mass spectrometry. Rapid Commun Mass Spectrom. 2012;26:510–6.
Article
CAS
PubMed
Google Scholar
Lorito M, Woo SL, Harman GE, Monte E. Translational research on Trichoderma: from ‘omics to the field. Annu Rev Phytopathol. 2010;48:395–417.
Article
CAS
PubMed
Google Scholar
Barret M, Frey-Klett P, Boutin M, Guillerm-Erckelboudt AY, Martin F, Guillot L, et al. The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescens Pf29Arp. New Phytol. 2009;181:435–47.
Article
CAS
PubMed
Google Scholar
Tarkka MT, Sarniguet A, Frey-Klett P. Inter-kingdom encounters: recent advances in molecular bacterium-fungus interactions. Curr Genet. 2009;55:233–43.
Article
CAS
PubMed
Google Scholar
Perazzolli M, Antonielli L, Storari M, Puopolo G, Pancher M, Giovannini O, et al. Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides. Appl Environ Microbiol. 2014;80:3585–96.
Article
PubMed
PubMed Central
Google Scholar
Savazzini F, Longa CMO, Pertot I. Impact of the biocontrol agent Trichoderma atroviride SC1 on soil microbial communities of a vineyard in northern Italy. Soil Biol Biochem. 2009;41:1457–65.
Article
CAS
Google Scholar
Leibniz Institute DSMZ - German Collection of Microorganisms and cell Culture. www.dsmz.de. Accessed 01 Sept 2013.
ATTC Collection. www.lgcstandards-atcc.org. Accessed 01 Sept 2013.
CBS Collection. www.cbs.knaw.nl. Accessed 01 Sept 2013.
Ellis RJ. Artificial soil microcosms: a tool for studying microbial autecology under controlled conditions. J Microbiol Methods. 2004;56:287–90.
Article
PubMed
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
FASTQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc. Accessed 1 Jan 2014.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
Google Scholar
Sibthorp C, Wu H, Cowley G, Wong PW, Palaima P, Morozov I, et al. Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters. BMC Genomics. 2013;14:847.
Article
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
Google Scholar
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Article
CAS
PubMed
Google Scholar
Jung JY, Lee SH, Jin HM, Hahn Y, Madsen EL, Jeon CO. Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation. Int J Food Microbiol. 2013;163:171–9.
Article
CAS
PubMed
Google Scholar
Johansson H, Dhaygude K, Lindstrom S, Helantera H, Sundstrom L, Trontti K. A metatranscriptomic approach to the identification of microbiota associated with the ant Formica exsecta. PLoS One. 2013;8:e79777.
Article
PubMed
PubMed Central
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–8.
Article
CAS
PubMed
Google Scholar
Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G. High throughput sequencing methods and analysis for microbiome research. J Microbiol Methods. 2013;95:401–14.
Article
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed
PubMed Central
Google Scholar
Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. TM4 microarray software suite. Methods Enzymol. 2006;411:134–93.
Article
CAS
PubMed
Google Scholar
Falda M, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, et al. Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. BMC Bioinformatics. 2012;13:S14.
Article
PubMed
PubMed Central
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000;25:25–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
UniProt. http://www.uniprot.org/. Accessed 01 Jan 2016.
Maere S, Heymans K, Kuiper M. BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005;21:3448–9.
Article
CAS
PubMed
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, et al. SGD: saccharomyces genome database. Nucleic Acids Res. 1998;26:73–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saccharomyces cerevisiae S288c. http://fungi.ensembl.org/Saccharomyces_cerevisiae/Info/Index. Accessed 01 Sept 2014.
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35:W182–5.
Article
PubMed
PubMed Central
Google Scholar
KAAS: KEGG Automatic Annotation Server. http://www.genome.jp/tools/kaas. Accessed 01 Jan 2016.
Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. iPath2.0: interactive pathway explorer. Nucleic Acids Res. 2011;39:W412–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
iPath2.0: interactive pathway explorer. http://pathways.embl.de/. Accessed 01 Jan 2016.
T-Coffee Multiple Sequence Alignment. http://www.ebi.ac.uk/Tools/msa/tcoffee/. Accessed 01 Mar 2016.
Ruijter JM, Ramakers C, Hoogaars WM, Karlen Y, Bakker O, van den Hoff MJ, et al. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009;37:e45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007;8:R19.
Article
PubMed
PubMed Central
Google Scholar
Silver N, Best S, Jiang J, Thein S. Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR. BMC Mol Biol. 2006;7:33.
Article
PubMed
PubMed Central
Google Scholar
Lee K-B, De Backer P, Aono T, Liu C-T, Suzuki S, Suzuki T, et al. The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. BMC Genomics. 2008;9:271.
Article
PubMed
PubMed Central
Google Scholar
Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, Sekowska A, et al. From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology. 2009;155:1758–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, et al. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One. 2010;5:e10433.
Article
PubMed
PubMed Central
Google Scholar
Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GSA, Mavrodi DV, et al. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotech. 2005;23:873–8.
Article
CAS
Google Scholar
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, et al. Genome evolution in yeasts. Nature. 2004;430:35–44.
Article
PubMed
Google Scholar
Kumar S, Randhawa A, Ganesan K, Raghava GP, Mondal AK. Draft genome sequence of salt-tolerant yeast Debaryomyces hansenii var. hansenii MTCC 234. Eukaryot Cell. 2012;11:961–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, et al. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotech. 2007;25:319–26.
Article
CAS
Google Scholar
Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, et al. The genome sequence of Schizosaccharomyces pombe. Nature. 2002;415:871–80.
Article
CAS
PubMed
Google Scholar
Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotech. 2007;25:221–31.
Article
Google Scholar
van den Berg MA, Albang R, Albermann K, Badger JH, Daran J-M, M Driessen AJ, et al. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotech. 2008;26:1161–8.
Article
CAS
Google Scholar
Ma L-J, van der Does HC, Borkovich KA, Coleman JJ, Daboussi M-J, Di Pietro A, et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010;464:367–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kubicek C, Herrera-Estrella A, Seidl-Seiboth V, Martinez D, Druzhinina I, Thon M, et al. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol. 2011;12:R40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Collins C, Keane TM, Turner DJ, O’Keeffe G, Fitzpatrick DA, Doyle S. Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system. J Proteome Res. 2013;12:2552–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, Malerba G, et al. Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol. 2010;152:1787–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perazzolli M, Moretto M, Fontana P, Ferrarini A, Velasco R, Moser C, et al. Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes. BMC Genomics. 2012;13:660.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tyc O, Wolf AB, Garbeva P. The effect of phylogenetically different bacteria on the fitness of Pseudomonas fluorescens in sand microcosms. PLoS One. 2015;10:e0119838.
Article
PubMed
PubMed Central
Google Scholar
Stout JD. The role of protozoa in nutrient cycling and energy flow. In: Alexander M, editor. Advances in microbial ecology, vol. 5. Boston: Springer US; 1980. p. 1–50.
Chapter
Google Scholar
Leonhartsberger S, Korsa I, Bock A. The molecular biology of formate metabolism in enterobacteria. J Mol Microbiol Biotechnol. 2002;4:269–76.
CAS
PubMed
Google Scholar
Turnbull GA, Morgan JA, Whipps JM, Saunders JR. The role of bacterial motility in the survival and spread of Pseudomonas fluorescens in soil and in the attachment and colonisation of wheat roots. Fems Microbiol Ecol. 2001;36:21–31.
Article
CAS
PubMed
Google Scholar
Hibbing ME, Fuqua C, Parsek MR, Peterson SB. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol. 2010;8:15–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pal KK, McSpadden GB. Biological control of plant pathogens. Plant Health Instr. 2006;10:1094–117.
Google Scholar
Deveau A, Barret M, Diedhiou A, Leveau J, de Boer W, Martin F, et al. Pairwise transcriptomic analysis of the interactions between the ectomycorrhizal fungus Laccaria bicolor s238n and three beneficial, neutral and antagonistic soil bacteria. Microb Ecol. 2015;69:146–59.
Article
PubMed
Google Scholar
Atanasova L, Crom SL, Gruber S, Coulpier F, Seidl-Seiboth V, Kubicek CP, et al. Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC Genomics. 2013;14:121.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seidl V, Song L, Lindquist E, Gruber S, Koptchinskiy A, Zeilinger S, et al. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. BMC Genomics. 2009;10:567.
Article
PubMed
PubMed Central
Google Scholar
Gebendorfer KM, Drazic A, Le Y, Gundlach J, Bepperling A, Kastenmuller A, et al. Identification of a hypochlorite-specific transcription factor from Escherichia coli. J Biol Chem. 2012;287:6892–903.
Article
CAS
PubMed
PubMed Central
Google Scholar
Braun BR, Kadosh D, Johnson AD. NRG1, a repressor of filamentous growth in C. albicans, is down‐regulated during filament induction. EMBO J. 2001;20:4753–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Park W, Padmanabhan P, Padmanabhan S, Zylstra GJ, Madsen EL. nahR, encoding a LysR-type transcriptional regulator, is highly conserved among naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNAb. Microbiology. 2002;148:2319–29.
Article
CAS
PubMed
Google Scholar
Reithner B, Ibarra-Laclette E, Mach RL, Herrera-Estrella A. Identification of mycoparasitism-related genes in Trichoderma atroviride. Appl Environ Microbiol. 2011;77:4361–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Viterbo A, Ramot O, Chernin L, Chet I. Significance of lytic enzymes from Trichoderma spp. in the biocontrol of fungal plant pathogens. Antonie Van Leeuwenhoek. 2002;81:549–56.
Article
CAS
PubMed
Google Scholar
Steindorff AS, Ramada MHS, Coelho ASG, Miller RNG, Pappas GJ, Ulhoa CJ, et al. Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum. BMC Genomics. 2014;15:1–14.
Article
Google Scholar
Mukherjee PK, Horwitz BA, Kenerley CM. Secondary metabolism in Trichoderma – a genomic perspective. Microbiology. 2012;158:35–45.
Article
CAS
PubMed
Google Scholar
Zeilinger S, Gruber S, Bansal R, Mukherjee PK. Secondary metabolism in Trichoderma – Chemistry meets genomics. Fungal Biol Rev. 2016;30:74–90.
Article
Google Scholar
Azorhizobium caulinodans ORS 571. http://bacteria.ensembl.org/azorhizobium_caulinodans_ors_571/Info/Index. Accessed 01 Sept 2014.
Bacillus subtilis subtilis 168 http://bacteria.ensembl.org/Bacillus_subtilis_subsp_subtilis_str_168/Info/Index. Accessed 01 Sept 2014.
Cupriavidus metallidurans CH34. http://bacteria.ensembl.org/cupriavidus_metallidurans_ch34/Info/Index. Accessed 01 Sept 2014.
Pseudomonas protegens Pf-5. http://bacteria.ensembl.org/pseudomonas_protegens_pf_5/Info/Index. Accessed 01 Sept 2014.
Debaryomyces hansenii CBS767. http://genome.jgi.doe.gov/Debha1/Debha1.home.html. Accessed 01 Sept 2014.
Pichia stipitis CBS6054. http://genome.jgi-psf.org/Picst3/Picst3.home.html. Accessed 01 Sept 2014.
Schizosaccharomyces pombe 972h. http://fungi.ensembl.org/Schizosaccharomyces_pombe/Info/Index. Accessed 01 Sept 2014.
Aspergillus niger CBS 513.88. http://fungi.ensembl.org/Aspergillus_niger/Info/Index. Accessed 01 Sept 2014.
Fusarium oxysporum lycopersici 4287. http://fungi.ensembl.org/Fusarium_oxysporum/Info/Index. Accessed 01 Sept 2014.
Penicillium chrysogenum Wisconsin54-125. http://genome.jgi.doe.gov/PenchWisc1_1/PenchWisc1_1.home.html. Accessed 01 Sept 2014.
Trichoderma atroviride IMI 206040. http://genome.jgi.doe.gov/Triat2/Triat2.home.html. Accessed 01 Sept 2014.
Armillaria mellea DSM 3731. http://genome.jgi.doe.gov/Armme1_1/Armme1_1.home.html. Accessed 01 Sept 2014.