Download

Full Text

See more details

X (1)

Facebook (1)

Mendeley (168)

73

CITATIONS

73 Total citations

16 Recent citations

n/a Field Citation Ratio

n/a Relative Citation Ratio

publications

0

supporting

0

mentioning

0

contrasting

0

Smart Citations

0

0

0

0

Citing PublicationsSupportingMentioningContrasting

View Citations

See how this article has been cited at scite.ai

scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.

• Adomas A, Eklund M, Johansson M, Asiegbu FO (2006) Identification and analysis of differentially expressed cDNAs during nonself-competitive interaction between Phlebiopsis gigantea and Heterobasidion parviporum. FEMS Microbiol Ecol 57:26–39
• Aegerter BJ, Gordon TR (2006) Rates of pitch canker induced seedling mortality among Pinus radiata families varying in levels of genetic resistance to Gibberella circinata (anamorph Fusarium circinatum). For Ecol Manag 235:14–17
• Alfano G, Ivey ML, Cakir C, Bos JI, Miller SA, Madden LV, Kamoun S, Hoitink HA (2007) Systemic modulation of gene expression in tomato by Trichoderma hamatum 382. Phytopathology 97:429–437
• Armengaud J (2013) Microbiology and proteomics, getting the best of both worlds! Environ Microbiol 15:12–23
• Bachmann B, van Lanen S, Baltz R (2014) Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? J Ind Microbiol Biotechnol 41:175–184
• Barret M, Frey-Klett P, Boutin M, Guillerm-Erckelboudt AY, Martin F, Guillot L, Sarniguet A (2009a) 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 181:435–447
• Barret M, Frey-Klett P, Guillerm-Erckelboudt AY, Boutin M, Guernec G, Sarniguet A (2009b) Effect of wheat roots infected with the pathogenic fungus Gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp. Mol Plant Microbe Interact 22:1611–1623
• Baysal Ö, Lai D, Xu HH, Siragusa M, Çalışkan M, Carimi F, da Silva JAT, Tör M (2013) A proteomic approach provides new insights into the control of soil-borne plant pathogens by Bacillus species. PLoS ONE 8:e53182
• Bernhardt J, Völker U, Völker A, Antelmann H, Schmid R, Mach H, Hecker M (1997) Specific and general stress proteins in Bacillus subtilis—a two-dimensional protein electrophoresis study. Microbiology 143:999–1017
• Brotman Y, Briff E, Viterbo A, Chet I (2008) Role of swollenin, an expansin-like protein from Trichoderma, in plant root colonization. Plant Physiol 147:779–789
• Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Lu TS, Schadt CW, Doktycz MJ, Pelletiera DA (2012) Twenty-one genome sequences from pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. J Bacteriol 194:5991–5993
• Buensanteai N, Yuen GY, Prathuangwong S (2008) The biocontrol bacterium Bacillus amyloliquefaciens KPS46 produces auxin, surfactin and extracellular proteins for enhanced growth of soybean plant. Thai J Agric Sci 41:111–116
• Challis GL (2008) Mining microbial genomes for new natural products and biosynthetic pathways. Microbiology 154:1555–1569
• Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R (2007) Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25:1007–1014
• Chen W, Yunsheng W, Dingjun L, Lin L, Qiming X, Qingming Z (2012) Draft genome sequence of Brevibacillus brevis strain X23, a biocontrol agent against bacterial wilt. J Bacteriol 194:6634–6635
• Cheng C-H, Yang C-A, Peng K-C (2012) Antagonism of Trichoderma harzianum ETS 323 on Botrytis cinerea mycelium in culture conditions. Phytopathology 102:1054–1063
• Czajkowski R, van der Wolfa JM (2012) Draft genome sequence of the biocontrol strain Serratia plymuthica A30, isolated from rotting potato tuber tissue. J Bacteriol 194:6999–7000
• Daly DS, Anderson KK, Panisko EA, Purvine SO, Fang R, Monroe ME, Baker SE (2008) Mixed-effects statistical model for comparative LC–MS proteomics studies. J Proteome Res 7:1209–1217
• Daval S, Lebreton L, Gazengel K, Boutin M, Guillerm-Erckelboudt AY, Sarniguet A (2011) The biocontrol bacterium Pseudomonas fluorescens Pf29Arp strain affects the pathogenesis-related gene expression of the take-all fungus Gaeumannomyces graminis var. tritici on wheat roots. Mol Plant Pathol 12:839–854
• De Las RJ, Aibar S, Roson B (2014) Gene expression analysis and profiling of microarrays data and RNA-sequencing data. In: Cifuentes A, Simó C, Virginia GC (eds) Comprehensive analytical chemistry, vol 63. Elsevier, Oxford, UK, pp 355–384
• Eyiwumi Olorunleke F, Phuong Kieu N, Höfte M (2015) Recent advances in pseudomonas biocontrol pp. In: Murillo J, Vinatzer B, Jackson R, Arnold D (eds) Bacteria-plant interactions: advanced research and future trends. Caister Academic Press, Wymondham, UK, pp 167–198
• Faraji M, Ahmadzadeh M, Behboudi K, Okhovvat SM, Ruocco M, Lorito M, Rezaei-Tavirani M, Zali H (2013) Study of proteome pattern of Pseudomonas fluorescens strain UTPF68 in interaction with Trichoderma atroviride strain P1 and tomato. J Paramed Sci 4:30–44
• Feng DX, Tasset C, Hanemian M, Barlet X, Hu J, Trémousaygue D, Deslandes L, Marco Y (2012) Biological control of bacterial wilt in Arabidopsis thaliana involves abscissic acid signalling. New Phytol 194:1035–1045
• Gil C, Monteoliva L (2014) Trends in microbial proteomics. J Proteomics 97:1–2
• Grevesse C, Lepoivre P, Jijakli MH (2003) Characterization of the exoglucanase-encoding gene PaEXG2 and study of its role in the biocontrol activity of Pichia anomala strain K. Phytopathology 93:1145–1152
• Grinyer J, McKay M, Herbert B, Nevalainen H (2004a) Fungal proteomics: mapping the mitochondrial proteins of a Trichoderma harzianum strain applied for biological control. Curr Genet 45:170–175
• Grinyer J, McKay M, Nevalainen H, Herbert B (2004b) Fungal proteomics: initial mapping of biological control strain Trichoderma harzianum. Curr Genet 45:163–169
• Grinyer J, Hunt S, McKay M, Herbert B, Nevalainen H (2005) Proteomic response of the biological control fungus Trichoderma atroviride to growth on the cell walls of Rhizoctonia solani. Curr Genet 47:381–388
• Grinyer J, Kautto L, Traini M, Willows R, Te’o J, Bergquist P, Nevalainen H (2007) Proteome mapping of the Trichoderma reesei 20S proteasome. Curr Genet 51:79–88
• Hammami W, Chain F, Michaud D, Belanger R (2010) Proteomic analysis of the metabolic adaptation of the biocontrol agent Pseudozyma flocculosa leading to glycolipid production. Proteome Sci 8:7
• Hao K, He P, Blom J, Rueckert C, Mao Z, Wu Y, He Y, Borriss R (2012) The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum Strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis. J Bacteriol 194:3264–3265
• Hassan KA, Johnson A, Shaffer BT, Ren Q, Kidarsa TA, Elbourne LDH, Hartney S, Duboy R, Goebel NC, Zabriskie TM, Paulsen IT, Lope JE (2010) Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences. Environ Microbiol 12:899–915
• Helsens K., Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L (2010) Ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics 10:1261–1264
• Hermosa RL, Woo S, Lorito M, Monte E (2010) Proteomic approaches to understand Trichoderma biocontrol mechanisms and plant interactions. Curr Proteomics 7:298–305
• Hershkovitz V, Ben-Dayan C, Raphael G, Pasmanik-Chor M, Liu J, Belausov E, Aly R, Wisniewski M, Droby S (2012) Global changes in gene expression of grapefruit peel tissue in response to the yeast biocontrol agent Metschnikowia fructicola. Mol Plant Pathol 13:338–349
• Hershkovitz V, Sela N, Taha-Salaime L, Liu J, Rafael G, Kessler C, Aly R, Levy M, Wisniewski M, Droby S (2013) De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel. BMC Genom 14:168
• Illakkiam D, Shankar M, Ponraj P, Rajendhran J, Gunasekaran P (2014) Genome sequencing of a mung bean plant growth promoting strain of P. aeruginosa with biocontrol ability. Int J Genomics. doi:10.1155/2014/123058
• Jiang F, Zheng X, Chen J (2009) Microarray analysis of gene expression profile induced by the biocontrol yeast Cryptococcus laurentii in cherry tomato fruit. Gene 430:12–16
• Jijakli MH, Lepoivre P (1998) Characterization of an exo-β-1,3-glucanase produced by Pichia anomala strain K, antagonist of Botrytis cinerea on apples. Phytopathology 88:335–343
• Kandasamy S, Loganathan K, Muthuraj R, Duraisamy S, Seetharaman S, Thiruvengadam R, Ponnusamy B, Ramasamy S (2009) Understanding the molecular basis of plant growth promotional effect of Pseudomonas fluorescens on rice through protein profiling. Proteome Sci 7:1–8
• Kanehisa M, Goto S, Kawashima S, Nakaya A (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30:42–46
• Kierul K, Voigt B, Albrecht D, Chen XH, Carvalhais LC, Borriss R (2015) Influence of root exudates on the extracellular proteome of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Microbiology 161:131–147
• Kim HJ, Park JY, Han SH, Lee JH, Rong X, McSpadden Gardener BB, Park SK, Kim YC (2011) Draft genome sequence of the biocontrol bacterium Chromobacterium sp. strain C-61. J Bacteriol 193:6803–6804
• Klaponski N, Selin C, Duke K, Spicer V, Fernando D, Belmonte M, de Kievit T (2014) The requirement for the LysR-type regulator PtrA for Pseudomonas chlororaphis PA23 biocontrol revealed through proteomic and phenotypic analysis. BMC Microbiol 14:94
• Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci. 5:216
• Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV (2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12:R40
• Kwasiborski A, Bajji M, Renaut J, Delaplace P, Jijakli MH (2014) Identification of metabolic pathways expressed by Pichia anomala Kh6 in the presence of the pathogen Botrytis cinerea on apple: new possible targets for biocontrol improvement. PLoS ONE 9:e91434
• Lee SY, Kim BY, Ahn JH, Song J, Seol YJ, Kim WG, Weon HY (2012) Draft genome sequence of the biocontrol bacterium Bacillus amyloliquefaciens strain M27. J Bacteriol 194:6934–6935
• Lefebvre F, Joly DL, Labbé C, Teichmann B, Linning R, Belzile F, Bakkeren G, Bélanger RR (2013) The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole-genome analysis. Plant Cell 25:1946–1959
• Lim CK, Hassan KA, Tetu SG, Loper JE, Paulsen IT (2012) The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5. PLoS ONE 7(6):e39139
• Lim JA, Lee DH, Kim BY, Heu S (2014) Draft genome sequence of Pantoea agglomerans R190, a producer of antibiotics against phytopathogens and foodborne pathogens. J Biotechnol 188:7–8
• Liu PG, Yang Q (2005) Identification of genes with a biocontrol function in Trichoderma harzianum mycelium using the expressed sequence tag approach. Res Microbiol 156:416–423
• Liu J, Zhou Q, Ibrahim M, Liu H, Jin G, Zhu B, Xie G (2012) Genome sequence of the biocontrol agent Microbacterium barkeri strain 2011-R4. J Bacteriol 194:6666–6667
• Loper JE, Hassan KA, Mavrodi DV, Davis EW, Lim CK, Shaffer BT, Elbourne LD, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, van de Mortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson LS III, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT (2012) Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet 8:e1002784
• Lorito M, Woo SL, Harman GE, Monte E (2010) Translational research on Trichoderma: from ‘omics to the field. Annu Rev Phytopathol 48:395–417
• Marra R, Ambrosino P, Carbone V, Vinale F, Woo S, Ruocco M, Ciliento R, Lanzuise S, Ferraioli S, Soriente I, Gigante S, Turrà D, Fogliano V, Scala F, Lorito M (2006) Study of the three-way interaction between Trichoderma atroviride, plant and fungal pathogens by using a proteomic approach. Curr Genet 50:307–321
• Martinez-Garcia P, Ruano-Rosa D, Schiliro E, Prieto P, Ramos C, Rodriguez-Palenzuela P, Mercado-Blanco J (2015) Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent against Verticillium dahliae. Stand Genomic Sci 10:10
• Massart S, Jijakli MH (2006) Identification of differentially expressed genes by cDNA-amplified fragment length polymorphism in the biocontrol agent Pichia anomala (strain Kh5). Phytopathology 96:80–86
• Massart S, Jijakli HM (2007) Use of molecular techniques to elucidate the mechanisms of action of fungal biocontrol agents: a review. J Microbiol Methods 69:229–241
• Massart S, Martinez-Medina M, Jijakli MH (2015) Biological control in the microbiome era: challenges and opportunities. Biol control 89: 98–108
• Mathimaran N, Srivastava R, Wiemken A, Sharma AK, Boller T (2012) Genome sequences of two plant growth-promoting fluorescent Pseudomonas strains, R62 and R81. J Bacteriol 194:3272–3273
• McGettigan PA (2013) Transcriptomics in the RNA-seq era. Curr Opin Chem Biol 17:4–11
• Mesuere B, Devreese B, Debyser G, Aerts M, Vandamme P, Dawyndt P (2012) Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples. J Proteome Res 11:5773–5780
• Mgbeahuruike AC, Kohler A, Asiegbu FO (2013) Expression analysis of the impact of culture filtrates from the biocontrol agent, Phlebiopsis gigantea on the conifer pathogen, Heterobasidion annosum s.s. transcriptome. Microb Ecol 66:669–681
• Monteiro V, Nascimento Silva R, Steindorff A, Costa F, Noronha E, Ricart C, Sousa M, Vainstein M, Ulhoa C (2010) New insights in Trichoderma harzianum antagonism of fungal plant pathogens by secreted protein analysis. Curr Microbiol 61:298–305
• Montero-Barrientos M, Hermosa R, Cardoza RE, Gutiérrez S, Monte E (2011) Functional analysis of the Trichoderma harzianum nox1 gene, encoding an NADPH oxidase, relates production of reactive oxygen species to specific biocontrol activity against Pythium ultimum. Appl Environ Microbiol 77:3009–3016
• Morán-Diez E, Hermosa R, Ambrosino P, Cardoza RE, Gutiérrez S, Lorito M, Monte E (2009) The ThPG1 endopolygalacturonase is required for the Trichoderma harzianum–plant beneficial interaction. Mol Plant Microbe Interact 22:1021–1031
• Morán-Diez E, Rubio B, Domínguez S, Hermosa R, Monte E, Nicolás C (2012) Transcriptomic response of Arabidopsis thaliana after 24 h incubation with the biocontrol fungus Trichoderma harzianum. J Plant Physiol 169:614–620
• Moretti M, Grunau A, Minerdi D, Gehrig P, Roschitzki B, Eberl L, Garibaldi A, Gullino ML, Riedel K (2010) A proteomics approach to study synergistic and antagonistic interactions of the fungal–bacterial consortium Fusarium oxysporum wild-type MSA 35. Proteomics 10:3292–3320
• Mukherjee PK, Horwitz BA, Herrera-Estrella A, Schmoll M, Kenerley CM (2013) Trichoderma research in the genome era. Annu Rev Phytopathol 51:105–129
• Niu B, Rueckert C, Blom J, Wang Q, Borriss R (2011) The genome of the plant growth-promoting rhizobacterium Paenibacillus polymyxa M-1 contains nine sites dedicated to nonribosomal synthesis of lipopeptides and polyketides. J Bacteriol 193:5862–5863
• Nookaew I, Papini M, Pornputtpong N, Scalcinati G, Fagerberg L, Uhlén M, Nielsen J (2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res 40:10084–10097
• Okubara PA, Call DR, Kwak YS, Skinner DZ (2010) Induction of defense gene homologues in wheat roots during interactions with Pseudomonas fluorescens. Biol Control 55:118–125
• Otto A, Bernhardt J, Hecker M, Becher D (2012) Global relative and absolute quantitation in microbial proteomics. Curr Opin Microbiol 15:364–372
• Otto A, Becher D, Schmidt F (2014) Quantitative proteomics in the field of microbiology. Proteomics 14:547–565
• Oudenhove L, Devreese B (2013) A review on recent developments in mass spectrometry instrumentation and quantitative tools advancing bacterial proteomics. Appl Microbiol Biotechnol 97:4749–4762
• Palmieri MC, Perazzolli M, Matafora V, Moretto M, Bachi A, Pertot I (2012) Proteomic analysis of grapevine resistance induced by Trichoderma harzianum T39 reveals specific defence pathways activated against downy mildew. J Exp Bot 63:6237–6251
• Park JY, Han SH, Lee JH, Han YS, Lee YS, Rong X, McSpadden Gardener BB, Park HS, Kim YC (2011) Draft genome sequence of the biocontrol bacterium Pseudomonas putida B001, an oligotrophic bacterium that induces systemic resistance to plant diseases. J Bacteriol 193:6795–6796
• Paul D, Dineshkumar N, Nair S (2006) Proteomics of a plant growth-promoting rhizobacterium, Pseudomonas fluorescens MSP-393, subjected to salt shock. World J Microbiol Biotechnol 22:369–374
• Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GSA, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS 3rd, Thomashow LS, Loper JE (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 23:873–878
• Perazzolli M, Moretto M, Fontana P, Ferrarini A, Velasco R, Moser C, Delledonne M, Pertot I (2012) Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes. BMC Genom 13:660
• Puopolo G, Cimmino A, Palmieri MC, Giovannini O, Evidente A, Pertot I (2014) Lysobacter capsici AZ78 produces cyclo(L-Pro-L-Tyr), a 2,5-diketopiperazine with toxic activity against sporangia of Phytophthora infestans and Plasmopara viticola. J Appl Microbiol 117:1168–1180
• Redondo-Nieto M, Barret M, Morrissey J, Germaine K, Martínez-Granero F, Barahona E, Navazo A, Sánchez-Contreras M, Moynihan JA, Muriel C, Dowling D, O’Gara F, Martín M, Rivilla R (2013) Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction. BMC Genom 14:54
• Reithner B, Ibarra-Laclette E, Mach RL, Herrera-Estrella A (2011) Identification of mycoparasitism-related genes in Trichoderma atroviride. Appl Environ Microbiol 77:4361–4370
• Rong X, Gurel FB, Meulia T, Gardener BBM (2012a) Draft genome sequences of the biocontrol bacterium Mitsuaria sp. strain H24L5A. J Bacteriol 194:734–735
• Rong X, Gurel FB, Meulia T, McSpadden Gardener BB (2012b) Draft genome sequences of the Pseudomonas fluorescens biocontrol strains Wayne1R and Wood1R. J Bacteriol 194:724–725
• Rubio M, Quijada NM, Pérez E, Domínguez S, Monte E, Hermosa R (2014) Identifying beneficial qualities of Trichoderma parareesei for plants. Appl Environ Microbiol 80:1864–1873
• Sánchez-Arreguín A, Pérez-Martínez AS, Herrera-Estrella A (2012) Proteomic analysis of Trichoderma atroviride reveals independent roles for transcription factors BLR-1 and BLR-2 in light and darkness. Eukaryot Cell 11:30–41
• Schmid R, Bernhardt J, Antelmann H, Völker A, Mach H, Völker U, Hecker M (1997) Identification of vegetative proteins for a two-dimensional protein index of Bacillus subtilis. Microbiology 143:991–998
• Segarra G, Casanova E, Bellido D, Odena MA, Oliveira E, Trillas I (2007) Proteome, salicylic acid, and jasmonic acid changes in cucumber plants inoculated with Trichoderma asperellum strain T34. Proteomics 7:3943–3952
• Seidl V, Marchetti M, Schandl R, Allmaier G, Kubicek CP (2006) Epl1, the major secreted protein of Hypocrea atroviridis on glucose, is a member of a strongly conserved protein family comprising plant defense response elicitors. FEBS J 273:4346–4359
• Seidl V, Song L, Lindquist E, Gruber S, Koptchinskiy A, Zeilinger S, Schmoll M, Martínez P, Sun J, Grigoriev I, Herrera-Estrella A, Baker SE, Kubicek CP (2009) Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. BMC Genom 10:567
• Sharma S, Aggarwal R, Yadav A, Gupta S (2014) Protein mapping of Chaetomium globosum, a potential biological control agent through proteomics approach. J Plant Biochem Biotechnol 23:284–292
• Shen X, Chen M, Hu H, Wang W, Peng H, Xu P, Zhang X (2012) Genome sequence of Pseudomonas chlororaphis GP72, a root-colonizing biocontrol strain. J Bacteriol 194:1269–1270
• Shentu XP, Liu WP, Zhan XH, Xu YP, Xu JF, Yu XP, Zhang CX (2014) Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions. PLoS ONE 9:e94203
• Shoresh M, Harman GE (2008a) The molecular basis of shoot responses of maize seedlings to Trichoderma harzianum T22 inoculation of the root: a proteomic approach. Plant Physiol 147:2147–2163
• Shoresh M, Harman GE (2008b) The relationship between increased growth and resistance induced in plants by root colonizing microbes. Plant Signal Behav 3:737–739
• Smits THM, Rezzonico F, Kamber T, Goesmann A, Ishimaru CA, Stockwell VO, Frey JE, Duffy B (2010) Genome sequence of the biocontrol agent Pantoea vagans strain C9-1. J Bacteriol 192:6486–6487
• Song JY, Kwak MJ, Lee KY, Kong HG, Kim BK, Kwon SK, Lee SW, Kim JF (2012) Draft genome sequence of the antifungal-producing plant-benefiting bacterium Burkholderia pyrrocinia CH-67. J Bacteriol 194:6649–6650
• Studholme DJ, Harris B, Le Cocq K, Winsbury R, Perera V, Ryder L, Ward JL, Beale MH, Thornton CR, Grant M (2013) Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics. Front Plant Sci. 4:258
• Suárez MB, Sanz L, Chamorro MI, Rey M, González FJ, Llobell A, Monte E (2005) Proteomic analysis of secreted proteins from Trichoderma harzianum: identification of a fungal cell wall-induced aspartic protease. Fungal Genet Biol 42:924–934
• Sun H, Paulin L, Alatalo E, Asiegbu FO (2011) Response of living tissues of Pinus sylvestris to the saprotrophic biocontrol fungus Phlebiopsis gigantea. Tree Physiol 31:438–451
• Takeuchi K, Noda N, Someya N (2014) Complete genome sequence of the biocontrol strain Pseudomonas protegens Cab57 discovered in Japan reveals strain-specific diversity of this species. PLoS ONE 9:e93683
• Tang J, Liu L, Huang X, Li Y, Chen Y, Chen J (2010) Proteomic analysis of Trichoderma atroviride mycelia stressed by organophosphate pesticide dichlorvos. Can J Microbiol 56:121–127
• Trushina N, Levin M, Mukherjee PK, Horwitz BA (2013) PacC and pH-dependent transcriptome of the mycotrophic fungus Trichoderma virens. BMC Genom 14:138
• Tseng SC, Liu SY, Yang HH, Lo CT, Peng KC (2008) Proteomic study of biocontrol mechanisms of Trichoderma harzianum ETS 323 in response to Rhizoctonia solani. J Agric Food Chem 56:6914–6922
• Ujor VC, Peiris DG, Monti M, Kang AS, Clements MO, Hedger JN (2012) Quantitative proteomic analysis of the response of the wood-rot fungus, Schizophyllum commune, to the biocontrol fungus, Trichoderma viride. Lett Appl Microbiol 54:336–343
• Vilanova L, Wisniewski M, Norelli J, Viñas I, Torres R, Usall J, Phillips J, Droby S, Teixidó N (2014) Transcriptomic profiling of apple in response to inoculation with a pathogen (Penicillium expansum) and a non-pathogen (Penicillium digitatum). Plant Mol Biol Rep 32:566–583
• Viterbo A, Harel M, Chet I (2004) Isolation of two aspartyl proteases from Trichoderma asperellum expressed during colonization of cucumber roots. FEMS Microbiol Lett 238:151–158
• Wilkins MR, Sanchez JC, Gooley AA, Appel RD, HumpherySmith I, Hochstrasser DF, Williams KL (1995) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50
• Wöhlbrand L, Trautwein K, Rabus R (2013) Proteomic tools for environmental microbiology—a roadmap from sample preparation to protein identification and quantification. Proteomics 13:2700–2730
• Wu DQ, Ye J, Ou HY, Wei X, Huang X, He YW, Xu Y (2011) Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18. BMC Genom 12:438
• Yang HH, Yang SL, Peng KC, Lo CT, Liu SY (2009) Induced proteome of Trichoderma harzianum by Botrytis cinerea. Mycol Res 113:924–932
• Zhang CX, Zhao X, Han F, Yang MF, Chen H, Chida T, Shen SH (2009) Comparative proteome analysis of two antagonist Bacillus subtilis strains. J Microbiol Biotechnol 19:351–357
• Zhang C, Zhang X, Shen S (2014) Proteome analysis for antifungal effects of Bacillus subtilis KB-1122 on Magnaporthe grisea P131. World J Microbiol Biotechnol 30:1763–1774