Natural rice rhizospheric microbes suppress rice blast infections

BackgroundThe natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. In rice (Oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen Magnaporthe oryzae. Capitalizing on the abilities of naturally occurring rice soil bacteria to reduce M. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to blast disease.ResultsNaturally occurring root-associated rhizospheric bacteria were isolated from California field grown rice plants (M-104), eleven of which were taxonomically identified by16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Bacterial isolates were tested for biocontrol activity against the devastating foliar rice fungal pathogen, M. oryzae pathovar 70–15. In vitro, a Pseudomonas isolate, EA105, displayed antibiosis through reducing appressoria formation by nearly 90% as well as directly inhibiting fungal growth by 76%. Although hydrogen cyanide (HCN) is a volatile commonly produced by biocontrol pseudomonads, the activity of EA105 seems to be independent of its HCN production. During in planta experiments, EA105 reduced the number of blast lesions formed by 33% and Pantoea agglomerans isolate, EA106 by 46%. Our data also show both EA105 and EA106 trigger jasmonic acid (JA) and ethylene (ET) dependent induced systemic resistance (ISR) response in rice.ConclusionsOut of 11 bacteria isolated from rice soil, pseudomonad EA105 most effectively inhibited the growth and appressoria formation of M. oryzae through a mechanism that is independent of cyanide production. In addition to direct antagonism, EA105 also appears to trigger ISR in rice plants through a mechanism that is dependent on JA and ET signaling, ultimately resulting in fewer blast lesions. The application of native bacteria as biocontrol agents in combination with current disease protection strategies could aid in global food security.

[1]  C. Keel,et al.  Characterization of the hcnABC Gene Cluster Encoding Hydrogen Cyanide Synthase and Anaerobic Regulation by ANR in the Strictly Aerobic Biocontrol Agent Pseudomonas fluorescens CHA0 , 1998, Journal of bacteriology.

[2]  A. J. Jones,et al.  New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras , 2006, Applied and Environmental Microbiology.

[3]  M. Madigan,et al.  Genetic transfer by conjugation in the thermophilic green sulfur bacterium Chlorobium tepidum , 1995, Journal of bacteriology.

[4]  Cedric E. Ginestet.  ggplot2: Elegant Graphics for Data Analysis , 2011 .

[5]  P. Vidhyasekaran,et al.  Evaluation of a Powder Formulation of Pseudomonas fluorescens Pf1 for Control of Rice Sheath Blight , 1999 .

[6]  R. Terauchi,et al.  Multiple Translocation of the AVR-Pita Effector Gene among Chromosomes of the Rice Blast Fungus Magnaporthe oryzae and Related Species , 2011, PLoS pathogens.

[7]  S. Gnanamanickam,et al.  Biological control of Setaria blast (Magnaporthe grisea) with bacterial strains , 2008 .

[8]  J. Sørensen,et al.  Structure, production characteristics and fungal antagonism of tensin – a new antifungal cyclic lipopeptide from Pseudomonas fluorescens strain 96.578 , 2000, Journal of applied microbiology.

[9]  C. R. Howell.  Control of rhizoctonia solani on cotton seedlings with Pseudomonas fluorescens and with an antibiotic produced by the bacterium. , 1979 .

[10]  C. R. Howell.  Suppression of Pythium ultimum-induced damping-off of cotton seedlings by Pseudomonas fluorescens and its antibiotic, pyoluteorin. , 1980 .

[11]  C. Keel,et al.  Role of Gluconic Acid Production in the Regulation of Biocontrol Traits of Pseudomonas fluorescens CHA0 , 2009, Applied and Environmental Microbiology.

[12]  J. Zlosnik,et al.  Methods for assaying cyanide in bacterial culture supernatant , 2004, Letters in Applied Microbiology.

[13]  H. Bais,et al.  Root-Secreted Malic Acid Recruits Beneficial Soil Bacteria1[C][W][OA] , 2008, Plant Physiology.

[14]  A. Pietro,et al.  Role of new bacterial surfactins in the antifungal interaction between Bacillus amyloliquefaciens and Fusarium oxysporum , 2012 .

[15]  G. S. Khush,et al.  Breeding Rice for Resistance to Pests , 1992 .

[16]  M. Shimada,et al.  Mechanisms regulating caste differentiation in an aphid social system , 2010, Communicative & integrative biology.

[17]  Lauren Hale,et al.  Characterisation of Pseudomonas chlororaphis subsp. aurantiaca strain Pa40 with the ability to control wheat sharp eyespot disease , 2013 .

[18]  C. Pieterse,et al.  Rhizobacteria-mediated Induced Systemic Resistance: Triggering, Signalling and Expression , 2004, European Journal of Plant Pathology.

[19]  T. Dubois,et al.  Structure, biosynthesis, and properties of kurstakins, nonribosomal lipopeptides from Bacillus spp. , 2012, Applied Microbiology and Biotechnology.

[20]  D. Scheel,et al.  Bacterial volatiles induce systemic resistance in Arabidopsis (vol 134, pg 1017, 2004) , 2005 .

[21]  C. Pieterse,et al.  Plant immune responses triggered by beneficial microbes. , 2008, Current opinion in plant biology.

[22]  J. G. Hancock,et al.  Disease-Suppressive Soil and Root-Colonizing Bacteria , 1982, Science.

[23]  B. Lugtenberg,et al.  Plant-growth-promoting rhizobacteria. , 2009, Annual review of microbiology.

[24]  E. Oakeley,et al.  Tissue-Adapted Invasion Strategies of the Rice Blast Fungus Magnaporthe oryzae[W] , 2010, Plant Cell.

[25]  C. Keel,et al.  Cyanide production by Pseudomonas fluorescens helps suppress black root rot of tobacco under gnotobiotic conditions , 1989, The EMBO journal.

[26]  Sridhara G. Kunjeti,et al.  The rhizobacterial elicitor acetoin induces systemic resistance in Arabidopsis thaliana , 2010, Communicative & integrative biology.

[27]  H. Hoitink,et al.  BIOCONTROL WITHIN THE CONTEXT OF SOIL MICROBIAL COMMUNITIES: A Substrate-Dependent Phenomenon. , 1999, Annual review of phytopathology.

[28]  L. Overbeek,et al.  Exploration of hitherto‐uncultured bacteria from the rhizosphere , 2009 .

[29]  C. Berry,et al.  Characterization of the Pseudomonas sp. DF41 quorum sensing locus and its role in fungal antagonism , 2014 .

[30]  C. R. Howell,et al.  Production of ammonia by Enterobacter cloacae and its possible role in the biological control of Pythium preemergence damping-off by the bacterium , 1988 .

[31]  T. Fujimura,et al.  Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice[W] , 2006, Plant Physiology.

[32]  L. C. Loon.  Plant responses to plant growth-promoting rhizobacteria , 2007, European Journal of Plant Pathology.

[33]  Chanhui Lee,et al.  Identification of rice genes induced in a rice blast-resistant mutant. , 2004, Molecules and cells.

[34]  J. Caplan,et al.  Microbe-Associated Molecular Patterns-Triggered Root Responses Mediate Beneficial Rhizobacterial Recruitment in Arabidopsis1[C][W][OA] , 2012, Plant Physiology.

[35]  C. Kusonwiriyawong,et al.  Screening of potential bacterial antagonists for control of sheath blight in rice and development of suitable bacterial formulations for effective application , 1999, Australasian Plant Pathology.

[36]  A. Price,et al.  Identification of rice blast disease-suppressing bacterial strains from the rhizosphere of rice grown in Pakistan. , 2009 .

[37]  A. Prabhu,et al.  Leaf blast (Magnaporthe oryzae) suppression and growth promotion by rhizobacteria on aerobic rice in Brazil , 2011 .

[38]  R. Ramarathnam,et al.  The role of antibiosis and induced systemic resistance, mediated by strains of Pseudomonas chlororaphis, Bacillus cereus and B. amyloliquefaciens, in controlling blackleg disease of canola , 2011, BioControl.

[39]  K. Vasumathi,et al.  Development of a powder formulation of Pseudomonas fluorescens for control of rice blast. , 1997 .

[40]  M. Yamasaki,et al.  Biological control for rice blast disease by employing detachment action with gelatinolytic bacteria , 2010 .

[41]  A. Kornberg,et al.  Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[42]  S. Gnanamanickam,et al.  Biological Control of Rice Blast byPseudomonas fluorescensStrainPf7–14: Evaluation of a Marker Gene and Formulations , 1998 .

[43]  J. A. Buso,et al.  BMC Plant Biology , 2003 .

[44]  H. Bais,et al.  Cyanogenic Pseudomonads Influence Multitrophic Interactions in the Rhizosphere , 2008, PloS one.

[45]  L. Thomashow,et al.  Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici , 1988, Journal of bacteriology.

[46]  S. Babu,et al.  Induction of systemic resistance in rice against sheath blight disease by Pseudomonas fluorescens , 2001 .

[47]  C. Pieterse,et al.  Transcription factor MYC2 is involved in priming for enhanced defense during rhizobacteria-induced systemic resistance in Arabidopsis thaliana. , 2008, The New phytologist.

[48]  S. Scheu,et al.  Secondary Metabolites of Pseudomonas fluorescens CHA0 Drive Complex Non-Trophic Interactions with Bacterivorous Nematodes , 2011, Microbial Ecology.

[49]  G. Défago,et al.  Naturally occurring fluorescent pseudomonads involved in suppression of black root rot of tobacco , 1986 .

[50]  M. Farag,et al.  Bacterial volatiles promote growth in Arabidopsis , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[51]  S. Chisholm,et al.  Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response , 2022 .

[52]  S. Gnanamanickam,et al.  Short Communication: Induction of systemic resistance and salicylic acid accumulation in Oryza sativa, L. in the biological suppression of rice blast caused by treatments with Pseudomonas spp. , 1998 .

[53]  J. Meis,et al.  In vitro activity of isavuconazole against 208 Aspergillus flavus isolates in comparison with 7 other antifungal agents: assessment according to the methodology of the European Committee on Antimicrobial Susceptibility Testing. , 2011, Diagnostic microbiology and infectious disease.

[54]  M. Megias,et al.  Use of two PGPR strains in the integrated management of blast disease in rice (Oryza sativa) in Southern Spain , 2009 .

[55]  T. Mew,et al.  Biological Control of Blast Disease of Rice (Oryza sativa L.) with Antagonistic Bacteria and Its Mediation by a Pseudomonas Antibiotic , 1992 .

[56]  James R. Cole,et al.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..

[57]  J. Beringer.  R factor transfer in Rhizobium leguminosarum. , 1974, Journal of general microbiology.

[58]  E. Boutet,et al.  Induced systemic resistance in Arabidopsis thaliana in response to root inoculation with Pseudomonas fluorescens CHA0. , 2003, Molecular plant-microbe interactions : MPMI.

[59]  R. Wiwattanapatapee,et al.  Floating pellets containing bacterial antagonist for control sheath blight of rice: formulations, viability and bacterial release studies. , 2004, Journal of controlled release : official journal of the Controlled Release Society.

[60]  M. Silby,et al.  Pseudomonas genomes: diverse and adaptable. , 2011, FEMS microbiology reviews.

[61]  R. Danti,et al.  Biocontrol of cypress canker by the phenazine producer Pseudomonas chlororaphis subsp. aureofaciens strain M71 , 2011 .

[62]  G. Pessi,et al.  Transcriptional Control of the Hydrogen Cyanide Biosynthetic Genes hcnABC by the Anaerobic Regulator ANR and the Quorum-Sensing Regulators LasR and RhlR inPseudomonas aeruginosa , 2000, Journal of bacteriology.

[63]  G. Bertani,et al.  STUDIES ON LYSOGENESIS I , 1951, Journal of bacteriology.

[64]  J. Sørensen,et al.  Viscosinamide, a new cyclic depsipeptide with surfactant and antifungal properties produced by Pseudomonas fluorescens DR54 , 1999, Journal of applied microbiology.

[65]  J. Caplan,et al.  Rhizobacteria Bacillus subtilis restricts foliar pathogen entry through stomata. , 2012, The Plant journal : for cell and molecular biology.

[66]  Dieter Haas,et al.  Mechanism, regulation, and ecological role of bacterial cyanide biosynthesis , 2000, Archives of Microbiology.

[67]  C. Pieterse,et al.  Jasmonate signaling in plant interactions with resistance-inducing beneficial microbes. , 2009, Phytochemistry.

[68]  W. Fernando,et al.  Identification and use of potential bacterial organic antifungal volatiles in biocontrol , 2005 .

[69]  Joaquima Messeguer,et al.  The Arabidopsis AtNPR1 inversely modulates defense responses against fungal, bacterial, or viral pathogens while conferring hypersensitivity to abiotic stresses in transgenic rice. , 2008, Molecular plant-microbe interactions : MPMI.

[70]  Dieter Haas,et al.  Regulation of antibiotic production in root-colonizing Peudomonas spp. and relevance for biological control of plant disease. , 2003, Annual review of phytopathology.

[71]  N. Someya,et al.  Potential of Serratia marcescens strain B2 for biological control of rice sheath blight , 2005 .

[72]  Birgit Piechulla,et al.  Bacterial volatiles and their action potential , 2009, Applied Microbiology and Biotechnology.

[73]  L. Thomashow,et al.  Frequency of Antibiotic-Producing Pseudomonas spp. in Natural Environments , 1997, Applied and environmental microbiology.

[74]  Paul Teng,et al.  Rice blast disease , 1996 .

[75]  Pari Skamnioti,et al.  Against the grain: safeguarding rice from rice blast disease. , 2009, Trends in biotechnology.

[76]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[77]  R. Peer,et al.  Induced resistance and phytoalexin accumulation in biological control of Fusarium wilt of carnation by Pseudomonas sp. strain WCS417r , 1991 .

[78]  N. Talbot,et al.  Under pressure: investigating the biology of plant infection by Magnaporthe oryzae , 2009, Nature Reviews Microbiology.

[79]  Xiuzhu Dong,et al.  Characterization of a novel plant growth-promoting bacteria strain Delftia tsuruhatensis HR4 both as a diazotroph and a potential biocontrol agent against various plant pathogens. , 2005, Systematic and applied microbiology.

[80]  Md. Wasim Aktar,et al.  Impact of pesticides use in agriculture: their benefits and hazards , 2009, Interdisciplinary toxicology.

[81]  P. Bakker,et al.  Pseudomonas fluorescens WCS374r-Induced Systemic Resistance in Rice against Magnaporthe oryzae Is Based on Pseudobactin-Mediated Priming for a Salicylic Acid-Repressible Multifaceted Defense Response1[C][OA] , 2008, Plant Physiology.

[82]  A. Osbourn,et al.  The rice leaf blast pathogen undergoes developmental processes typical of root-infecting fungi , 2004, Nature.

[83]  Haihua Wang,et al.  Constitutive expression of rice WRKY30 gene increases the endogenous jasmonic acid accumulation, PR gene expression and resistance to fungal pathogens in rice , 2012, Planta.