title: Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics.
abstract: Trichoderma hamatum strain GD12 is unique in that it can promote plant growth, activate biocontrol against pre- and post-emergence soil pathogens and can induce systemic resistance to foliar pathogens. This study extends previous work in lettuce to demonstrate that GD12 can confer beneficial agronomic traits to other plants, providing examples of plant growth promotion in the model dicot, Arabidopsis thaliana and induced foliar resistance to Magnaporthe oryzae in the model monocot rice. We further characterize the lettuce-T. hamatum interaction to show that bran extracts from GD12 and an N-acetyl-β-D-glucosamindase-deficient mutant differentially promote growth in a concentration dependent manner, and these differences correlate with differences in the small molecule secretome. We show that GD12 mycoparasitises a range of isolates of the pre-emergence soil pathogen Sclerotinia sclerotiorum and that this interaction induces a further increase in plant growth promotion above that conferred by GD12. To understand the genetic potential encoded by T. hamatum GD12 and to facilitate its use as a model beneficial organism to study plant growth promotion, induced systemic resistance and mycoparasitism we present de novo genome sequence data. We compare GD12 with other published Trichoderma genomes and show that T. hamatum GD12 contains unique genomic regions with the potential to encode novel bioactive metabolites that may contribute to GD12's agrochemically important traits.
authors.affiliation: Biosciences, Molecular Plant Pathology, College of Life and Environmental Sciences, University of Exeter Exeter, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Studholme
authors.forename: Beverley
authors.initials: B
authors.lastname: Harris
authors.forename: Kate
authors.initials: K
authors.lastname: Le Cocq
authors.forename: Rebecca
authors.initials: R
authors.lastname: Winsbury
authors.forename: Venura
authors.initials: V
authors.lastname: Perera
authors.forename: Lauren
authors.initials: L
authors.lastname: Ryder
authors.forename: Jane L
authors.initials: JL
authors.lastname: Ward
authors.forename: Michael H
authors.initials: MH
authors.lastname: Beale
authors.forename: Chris R
authors.initials: CR
authors.lastname: Thornton
authors.forename: Murray
authors.initials: M
authors.lastname: Grant
keywords: Trichoderma hamatum; comparative genomics; induced systemic resistance; plant growth promotion; secretome
references.citation: J Biol Chem. 2007 Feb 23;282(8):5608-16
references.pmid: 17182617
references.citation: Plant Signal Behav. 2009 Aug;4(8):757-9
references.pmid: 19820345
references.citation: Microbiology (Reading). 2012 Jan;158(Pt 1):84-97
references.pmid: 21835878
references.citation: Nature. 2012 Apr 11;484(7393):186-94
references.pmid: 22498624
references.citation: J Anim Sci. 2007 Aug;85(8):1962-70
references.pmid: 17468414
references.citation: Plant Physiol. 2009 Mar;149(3):1579-92
references.pmid: 19176721
references.citation: Front Plant Sci. 2012 May 29;3:108
references.pmid: 22661981
references.citation: Phytopathology. 2006 Feb;96(2):190-4
references.pmid: 18943924
references.citation: Microb Ecol. 1981 Mar;7(1):29-38
references.pmid: 24227317
references.citation: Plant Dis. 2003 Jan;87(1):4-10
references.pmid: 30812698
references.citation: J Biotechnol. 2001 Aug 23;89(2-3):247-55
references.pmid: 11500219
references.citation: Enzyme Res. 2011;2011:280696
references.pmid: 21912738
references.citation: Plant J. 2003 Oct;36(2):177-88
references.pmid: 14535883
references.citation: J Exp Bot. 2009;60(11):3279-95
references.pmid: 19564160
references.citation: Genome Biol. 2011;12(4):R40
references.pmid: 21501500
references.citation: Plant Cell. 2004 Aug;16(8):2117-27
references.pmid: 15258265
references.citation: Annu Rev Phytopathol. 2011;49:317-43
references.pmid: 21663438
references.citation: Nature. 2006 Nov 2;444(7115):97-101
references.pmid: 17080091
references.citation: Trends Microbiol. 2009 Apr;17(4):151-7
references.pmid: 19299132
references.citation: Mol Microbiol. 2008 May;68(4):838-47
references.pmid: 18430080
references.citation: Mycologia. 2006 Nov-Dec;98(6):838-49
references.pmid: 17486961
references.citation: J Biol Chem. 1992 Dec 25;267(36):26044-9
references.pmid: 1281482
references.citation: Appl Environ Microbiol. 2002 Aug;68(8):3956-64
references.pmid: 12147496
references.citation: Microbiology (Reading). 2012 Jan;158(Pt 1):147-154
references.pmid: 22096146
references.citation: J Mol Biol. 2004 Jul 16;340(4):783-95
references.pmid: 15223320
references.citation: Genes Dev. 1991 Mar;5(3):438-46
references.pmid: 2001843
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5602-7
references.pmid: 16565218
references.citation: Genetics. 1991 Jan;127(1):87-101
references.pmid: 2016048
references.citation: Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14558-63
references.pmid: 19666480
references.citation: Phytochemistry. 2011 Feb;72(2-3):223-9
references.pmid: 21145086
references.citation: J Nat Prod. 2009 Nov;72(11):2032-5
references.pmid: 19894739
references.citation: Phytochemistry. 2003 Mar;62(6):949-57
references.pmid: 12590122
references.citation: J Mol Biol. 2004 May 14;338(5):1027-36
references.pmid: 15111065
references.citation: Phytochemistry. 2006 Jul;67(14):1406-13
references.pmid: 16839576
references.citation: Microbiology (Reading). 2010 Oct;156(Pt 10):2887-2900
references.pmid: 20688823
references.citation: Mol Plant Pathol. 2011 May;12(4):341-54
references.pmid: 21453429
references.citation: Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13268-72
references.pmid: 17686990
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: Bioinformatics. 2005 Aug 15;21(16):3422-3
references.pmid: 15976072
references.citation: Plant Cell. 2007 Dec;19(12):3839-42
references.pmid: 18165326
references.citation: Plant Cell. 2010 Mar;22(3):973-90
references.pmid: 20348432
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19703-8
references.pmid: 18077404
references.citation: Annu Rev Phytopathol. 2010;48:395-417
references.pmid: 20455700
references.citation: Mol Plant Microbe Interact. 2004 Aug;17(8):895-908
references.pmid: 15305611
references.citation: Genetics. 2004 Dec;168(4):2197-206
references.pmid: 15611186
references.citation: Plant J. 2010 Aug;63(3):443-57
references.pmid: 20497374
references.citation: Plant Physiol. 2012 Dec;160(4):2173-88
references.pmid: 23073694
references.citation: Annu Rev Phytopathol. 2009;47:233-63
references.pmid: 19400631
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
references.pmid: 22127870
references.citation: Microb Ecol. 1993 Nov;26(3):277-85
references.pmid: 24190096
references.citation: Nat Rev Microbiol. 2011 Sep 16;9(10):749-59
references.pmid: 21921934
references.citation: Nat Rev Microbiol. 2004 Jan;2(1):43-56
references.pmid: 15035008
references.citation: Microbiology (Reading). 2012 Jan;158(Pt 1):155-165
references.pmid: 22075027
references.citation: Phytopathology. 2010 Jul;100(7):682-8
references.pmid: 20528186
references.citation: Nat Biotechnol. 2008 May;26(5):553-60
references.pmid: 18454138
references.citation: Trends Ecol Evol. 2004 Oct;19(10):535-44
references.pmid: 16701319
references.citation: Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13909-14
references.pmid: 19667182
references.citation: Environ Sci Technol. 2012 Dec 4;46(23):12864-72
references.pmid: 23136826
references.citation: Annu Rev Phytopathol. 2010;48:21-43
references.pmid: 20192757
references.citation: Science. 2009 May 8;324(5928):750-2
references.pmid: 19423816
references.citation: Environ Microbiol. 2005 May;7(5):737-49
references.pmid: 15819855
references.citation: Mol Plant Microbe Interact. 2006 Aug;19(8):838-53
references.pmid: 16903350
references.citation: BMC Genomics. 2013 Feb 22;14:121
references.pmid: 23432824
references.citation: Science. 2010 Aug 20;329(5994):953-5
references.pmid: 20724636
references.citation: Plant J. 2002 Jan;29(1):11-21
references.pmid: 12060223
references.citation: Int Microbiol. 2004 Dec;7(4):249-60
references.pmid: 15666245
references.citation: Plant Biol (Stuttg). 2009 Jan;11(1):90-6
references.pmid: 19121118