Omics sciences potential on bioprospecting of biological control microbial agents: the case of the Mexican agro-biotechnology
Abstract
At present, studies of biological control agents of microbial origin (BCA-M) have mainly focused on their taxonomic characterization, through the use of conventional molecular markers, and the in vitro evaluation of modes of action, or under greenhouse conditions, but limitedly under field conditions. Furthermore, recent bioprospecting studies of BCA of microbial origin mainly focus on Trichoderma, Paecilomyces, Beauveria, Pseudomonas, and Bacillus. Even when the research developed in Mexico on this topic has been active during the last years, the development and innovation of greater variety of registered and currently commercialized biopesticides need to be improved. In this context, the use of cut-edge techniques in the era of omics sciences (genomics, transcriptomics, and metabolomics) focused on the correct taxonomic affiliation of BCA-M, as well as their modes of action and ecology in agroecosystems, will expand the bioprospecting and extensive use of these BCA in a more efficient, biosafety, and cost-effective manner. In the framework of the international celebration of plant health, this review critically analyzes the knowledge status of the aspects that limit the bioprospecting and extensive use of BCA-M, mainly in Mexico, from the application of omics sciences for the identification, selection, and study of action mechanisms of those agents until the dissemination and socialization of the generated scientific knowledge. The foregoing is intended to promote reflection on this field of knowledge and encourage the new generation BCA-M with a holistic and systemic vision for the benefit of sustainable and resilient agriculture.
Keywords
Full Text:
PDFReferences
Agrawal P, Khate S, Gupta M, Sain N and Mohanty D. 2017. RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. Nucleic Acids Research 45(W1): W80–W88. https://doi.org/10.1093/nar/gkx408
Aguilar-Marcelino L, Mendoza-de-Gives P, Al-Ani LKT, López-Arellano ME, Gómez-Rodríguez O, Villar-Luna E and Reyes-Guerrero DE. 2020. Using molecular techniques applied to beneficial microorganisms as biotechnological tools for controlling agricultural plant pathogens and pest. Pp: 333–349. In: Sharma V, Salwan R, and Al-Ani LKT (eds). Molecular Aspects of Plant Beneficial Microbes in Agriculture. https://doi.org/10.1016/b978-0-12-818469-1.00027-4 425p.
Anders S, Pyl PT and Huber W. 2015. HTSeq--a Python framework to work with highthroughput sequencing data. Bioinformatics 31(2):166–169. https://doi.org/10.1093/bioinformatics/btu638
Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham The RAST Server: rapid annotations using subsystems technology.ac.uk/projects/fastq http://www.bioinformatics.babraham.ac.uk/projects/fastqc (Consulta, Mayo, 2020).
Ansari MZ, Yadav G, Gokhale RS and Mohanty D. 2004. NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic acids research 32(2): W405–W413. https://doi.org/10.1093/nar/gkh359
Antipov D, Korobeynikov A, McLean JS and Pevzner PA. 2016. HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads. Bioinformatics 32(7):1009–1015, https://doi.org/10.1093/bioinformatics/btv688
Arredondo-Bernal HC y Rodríguez-del Bosque LA. 2015. Casos de control biológico en México. Editorial Colegio de Postgraduados. Vol. 2. Texcoco, México. 413 p.
Ayala-Zermeño MA, Gallou A, Berlanga-Padilla AM, Serna-Domínguez MG, Arredondo-Bernal HC and Montesinos-Matías R. 2015. Characterization of entomopathogenic fungi used in the biological control programme of Diaphorina citri in Mexico. Biocontrol Science and Technology 25(10): 1192-1207. https://doi.org/10.1080/09583157.2015.1041878
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A and Zagnitko O. 2008. The RAST Server: Rapid annotations using subsystems technology. BMC Genomics 9(75): 1-15. https://doi.org/10.1186/1471-2164-9-75
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA and Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology: a journal of computational molecular cell biology 19(5): 455-477. https://doi.org/10.1089/cmb.2012.0021
Benton HP, Wong DM, Trauger SA and Siuzdak G. 2008. XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Analitical Chemistry 80(16): 6382–6389. https://doi.org/10.1021/ac800795f
Bernal JS and Quezada JR. 1999. Perspectivas y desafíos para el control biológico en México. Vedalia 6: 3-14.
Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH and Weber T. 2019. AntiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Research 47(1): W81-W87. https://doi.org/10.1093/nar/gkz310
Bolger AM, Lohse M and Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics 30(15): 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
Borodovsky M and Lomsadze A. 2011. Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES. Current protocols in bioinformatics 35(1): 4.6.1-4.6.10. https://doi.org/10.1002/0471250953.bi0406s35
Bray NL, Pimentel H, Melsted P and Pachter L. 2016. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology 34: 525-527. https://doi.org/10.1038/nbt.3519
Burketova L, Trda L, Ott PG and Valentova O. 2015. Bio-based resistance inducers for sustainable plant protection against pathogens. Biotechnology Advances 33(6):994-1004. https://doi.org/10.1016/j.biotechadv.2015.01.004
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K and Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421. https://doi.org/10.1186/1471-2105-10-421
Carrión G y Desgarennes D. 2012. Efecto de Paecilomyces lilacinus en nemátodos de vida libre asociados a la rizósfera de papas cultivadas en la región del Cofre de Perote, Veracruz, México. Revista Mexicana de Fitopatología 30(1): 86-90. http://www.scielo.org.mx/pdf/rmfi/v30n1/v30n1a9.pdf
Chaudhuri RR, Loman NJ, Snyder LAS, Bailey CM, Stekel DJ and Pallen MJ. 2008. xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Research 36(1): D543–D546. https://doi.org/10.1093/nar/gkm928
Darling AC, Mau B, Blattner FR and Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome research 14:1394-1403. https://doi.org/10.1101/gr.2289704
De León SG y Mier T. 2010. Visión general de la producción y aplicación de bioplaguicidas en México. Sociedades Rurales, Producción y Medio Ambiente 10(20): 37-63. https://biblat.unam.mx/hevila/Sociedadesruralesproduccionymedioambiente/2010/vol10/no20/2.pdf
De los Santos?Villalobos S, Kremer J M, Parra?Cota, FI, Hayano?Kanashiro AC, García?Ortega LF, Gunturu SK, Tiedje JM, He SY, Peña?Cabriales JJ. 2018. Draft genome of the fungicidal biological control agent Burkholderia anthina strain XXVI. Archives of Microbiology 200:803–810. https://doi.org/10.1007/s00203-018-1490-6
De los Santos-Villalobos S, Parra-Cota FI, Herrera-Sepúlveda A, Valenzuela-Aragón B y Estrada-Mora JC. 2018. Colmena: colección de microorganismos edáficos y endófitos nativos, para contribuir a la seguridad alimentaria nacional. Revista Mexicana de Ciencias Agrícolas 9(1): 191-202. https://doi.org/10.29312/remexca.v9i1.858
De los Santos-Villalobos S, Robles-Montoya RI, Parra-Cota FI, Larsen J, Lozano P and Tiedje JM. 2019. Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico. International Journal of Systematic and Evolutionary Microbiology 69(12): 3939-3945. https://doi.org/10.1099/ijsem.0.003711
Delcher AL, Bratke KA, Powers EC and Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6): 673–679. https://doi.org/10.1093/bioinformatics/btm009
Delgado Ortiz JC, Beltrán Beache M, Cerna Chávez E, Aguirre Uribe LA, Landero Flores J, Rodríguez Pagaza Y y Ochoa Fuentes YM. 2019. Candidatus Liberibacter solanacearum patógeno vascular de solanáceas: Diagnóstico y control. TIP Revista Especializada en Ciencias Químico-Biológicas 22: 1-12. https://doi.org/10.22201/fesz.23958723e.2019.0.177
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S and Gingeras TR 2013. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29(1): 15-21. https://doi.org/10.1093/bioinformatics/bts635
Duke KA, Becker MG, Girard LJ, Millar JL, Fernando WGD, Belmonte MF and De Kievit TR. 2017. The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks. BMC Genomics 18: 1-16. https://doi.org/10.1186/s12864-017-3848-6
Ehling-Schulzn M, Lereclus D and Koehler TM. 2019. The Bacillus cereus Group: Bacillus species with pathogenic potential. Microbiology Spectrum 7(3): GPP3-0032. https://doi.org/10.1128/microbiolspec.GPP3-0032-2018
Espinas NA, Saze H and Saijo Y. 2016. Epigenetic Control of Defense Signaling and Priming in Plants. Frontiers in Plant Science 7: 1201-1201. https://doi.org/10.3389/fpls.2016.01201
Espinosa-Victoria D, López-Reyes L, Carcaño-Montiel MG and Serret-López M. 2020. The Burkholderia genus: between mutualism and pathogenicity. Mexican Journal of Phytopathology 38(3): 337-359. https://doi.org/10.18781/R.MEX.FIT.2004-5
FAO. 2018. El futuro de la alimentación y la agricultura: Vías alternativas hacia el 2050. Versión resumida. Rome. 64 pp. http://www.fao.org/3/CA1553ES/ca1553es.pdf (Consulta, Mayo 2020).
Franco-Navarro F, Cid del Prado-Vera I y Romero-Tejeda, ML. 2013. Aislamiento y Potencial Parasítico de un Aislamiento Nativo de Pochonia chlamydosporia en Contra de Nacobbus aberrans en Frijol. Revista Mexicana de Fitopatología 30(2): 101-114. http://www.scielo.org.mx/pdf/rmfi/v30n2/v30n2a1.pdf
Fukushima A and Kusano M. 2013. Recent progress in the development of metabolome databases for plant systems biology. Frontier in Plant Science 4: 73. http://dx.doi.org/10.3389/fpls.2013.00073
Galindo E, Serrano-Carreón L, Gutiérrez CR, Allende R, Balderas K, Patiño M, Trejo M, Wong MA, Rayo E, Isauro D and Jurado C. 2013. The challenges of introducing a new biofungicide to the market: A case study. Electronic Journal of Biotechnology 16(3): 5-5. http://dx.doi.org/10.2225/vol16-issue3-fulltext-6
Galindo E, Serrano-Carreón L, Gutiérrez CR, Balderas-Ruíz KB, Muñoz-Celaya AL, Mezo-Villalobos M y Arroyo-Colín J. 2015. Desarrollo histórico y los retos tecnológicos y legales para comercializar Fungifree AB®, el primer biofungicida 100% mexicano. Revista Especializada en Ciencias Químico-Biológicas 18(1): 52-60. https://doi.org/10.1016/j.recqb.2015.05.005
Gallou A, Serna-Domínguez MG, Berlanga-Padilla AM, Ayala-Zermeño MA, Mellín-Rosas MA, Montesinos-Matías R and Arredondo-Bernal HC. 2016. Species clarification of Isaria isolates used as biocontrol agents against Diaphorina citri (Hemiptera: Liviidae) in Mexico. Fungal biology 120(3): 414-423. https://doi.org/10.1016/j.funbio.2015.11.009
García-Juárez HS, Ortiz-García CF, Salgado-García S, Valdez-Balero A, Silva-Rojas HV, and Ovalle-Saenz WR. 2016. Immunodetection of the Leifsopnia Xyli ssp. xyli bacteria in commercial clones of Saccharum spp. in Tabasco, Mexico. Agro Productividad 9(3): 3-9. https://www.colpos.mx/wb_pdf/Agroproductividad/2016/AGROPRODUCTIVIDAD_III_2016.pdf
García-Nevárez G and Hidalgo-Jaminson E. 2019. Efficacy of indigenous and commercial Simplicillium and Lecanicillium strains for controlling Hemileia vastatrix. Mexican Journal of Phytopathology 37(2): 237-250. https://doi.org/10.18781/R.MEX.FIT.1810-4
García-Núñez HG, Martínez-Campos AR, Hermosa-Prieto MR; Monte-Vázquez E, Aguilar-Ortigoza CJ and González-Esquivel CE. 2017. Morphological and molecular characterization of native isolates of Trichoderma and its potential biocontrol against Phytophthora infestans. Revista Mexicana de Fitopatología 35(1): 58-79. https://doi.org/10.18781/R.MEX.FIT.1605-4
Gill HK and Garg H. 2014. Pesticides: environmental impacts and management strategies. In: Larramendy ML and Soloneski S (eds.). Pesticides-toxic aspects. IntechOpen. http://dx.doi.org/10.5772/57399
Gómez-De La Cruz I, Pérez-Portilla E, Escamilla-Prado E, Martínez-Bolaños M, Carrión-Villarnovo GLL and Hernández-Leal TI. 2017. Selection in vitro of mycoparasites with potential for biological control on Coffee Leaf Rust (Hemileia vastatrix). Revista Mexicana de Fitopatología 36(1): 172-183. https://doi.org/10.18781/R.MEX.FIT.1708-1
Granado J, Felix G and Boller T. 1995. Perception of fungal sterols in plants-Subnanomolar concentrations of ergosterol elicits extracellular alkalinisation in tomato cells. Plant Physiology 107: 485–490. https://doi.org/10.1104/pp.107.2.485
Guerrero PVM, Blanco PAC, Guigón LC, Tamayo UCJ, Molina CFJ, Berlanga RDI, Carvajal ME and Ávila QGD. 2011. Competencia por nutrientes; modo de acción de Candida oleophila contra Penicillium expansum y Botrytis cinerea. Revista Mexicana de Fitopatología 29 (2): 90-97. http://www.scielo.org.mx/pdf/rmfi/v29n2/v29n2a1.pdf
Gupta R and Bar M. 2020. Plant Immunity, Priming, and Systemic Resistance as Mechanisms for Trichoderma spp. Biocontrol. Pp: 81-110. In: Sharma A. and Sharma P. (eds) Trichoderma. Rhizosphere Biology. Springer, Singapore. https://doi.org/10.1007/978-981-15-3321-1_5
Gurevich A, Saveliev V, Vyahhi N and Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8): 1072-1075. http://dx.doi.org/10.1093/bioinformatics/btt086
Hassan MM, Farid MA and Gaber A. 2019. Rapid identification of Trichoderma koningiopsis and Trichoderma longibrachiatum using sequence-characterized amplified region markers. Egyptian Journal of Biological Pest Control 29 (13): 1-8. https://doi.org/10.1186/s41938-019-0113-0
Illa C, Pérez AA, Torassa M and Pérez MA. 2020. Effect of biocontrol and promotion of peanut growth by inoculating Trichoderma harzianum and Bacillus subtilis under controlled conditions and field. Mexican Journal of Phytopathology 38(1): 119-131. https://doi.org/10.18781/R.MEX.FIT.1910-6
Instituto Nacional de Estadística y Geografía (INEGI). 2017. Encuesta Nacional Agropecuaria 2017 MEX-INEGI.EEC2.05-ENA-2017. https://www.inegi.org.mx/rnm/index.php/catalog/498 (Consulta, Mayo, 2020).
Jagadeesan B, Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S, Vossen JVD, Tang S, Katase M, McClure P, Kimura B, Chai LC, Chapman J and Grant K. 2019. The Use of Next Generation Sequencing for Improving Food Safety: Translation into practice. Food Microbiology 79: 96–115. https://doi.org/10.1016/j.fm.2018.11.005
Jhonson AD, Handsaker RE, Pulit SL, Nizzari MM, O’Donell CJ and andde Bakker PIW. 2008. SNAO: a web based tool for identification and annotation of proxy SNPs using hadmap. Bioinformatics 24(24): 2938-2939. https://doi.org/10.1093/bioinformatics/btn564
Jiménez-Delgadillo R, Valdés-Rodríguez SE, Olalde-Portugal V, Abraham-Juárez R and García-Hernández JL. 2018. Effect of pH and temperature on the growth and antagonistic activity of Bacillus subtilis on Rhizoctonia solani. Revista Mexicana de Fitopatología 36(2): 256-275. https://doi.org/10.18781/R.MEX.FIT.1711-3
Kanehisa M, Goto S, Kawashima S, Okuno Y and Hattori M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Research 32: 277-280. https://doi.org/10.1093/nar/gkh063
Kang D, Kim J, Choi JN, Liu KH and Lee CH. 2011. Chemotaxonomy of Trichoderma spp. using mass spectrometry-based metabolite profiling. Journal of Microbiology and Biotechnology 21(1): 5-13. https://doi.org/10.4014/jmb.1008.08018
Keller O, Kollmar M, Stanke M and Waack S. 2011. A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics 27(6): 757–763. https://doi.org/10.1093/bioinformatics/btr010.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R and Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14(4):1-13. https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-4-r36
Köhl J, Kolnaar R and Ravensberg WJ. 2019. Mode of action of microbial biological control agents against plant diseases: relevance beyond efficacy. Frontier in Plant Science 10: 845. https://doi.org/10.3389/fpls.2019.00845
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH and Phillipy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27: 722–736. https://doi.org/10.1101/gr.215087.116
Ku’c J. 1982. Induced immunity to plant disease. BioScience 32(11): 854–860. https://doi.org/10.2307/1309008
Lagunes-Castro MS, López Monteon A, Ramos Ligonio A, Trigos A, Salinas A y Espinoza C. 2015. Actividad antibacteriana de extractos metanol:cloroformo de hongos fitopatógenos. Revista Mexicana de Fitopatología 33(1): 87-94. http://www.scielo.org.mx/pdf/rmfi/v33n1/2007-8080-rmfi-33-01-00087.pdf
Lamdan NL, Shalaby S, Ziv T, Kenerley CM and Horwitz BA. 2015. Secretome of Trichoderma interacting with maize roots: role in induced systemic resistance. Molecular Cell Proteomics 14(4): 1054-1063. https://doi.org/10.1074/mcp.M114.046607
Langmead B and Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357-359. https://www.nature.com/articles/nmeth.1923
Ley-López N, Márquez-Zequera I, Carrillo-Fasio JA, León-Félix J, Cruz-Lachica I, García-Estrada RS and Allende-Molar R. 2018. Effect of biocontrol and germinative inhibition of Bacillus spp. on zoospores of Phytophthora capsici. Revista Mexicana de Fitopatología 36(2): 215-232. https://doi.org/10.18781/r.mex.fit.1711-2
Li B and Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMCBioinformatics 12: 323. https://doi.org/10.1186/1471-2105-12-323
Li H and Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14): 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
Li H. 2011. ImprovingSNP discovery by base alignment quality. Bioinformatics 27(8): 1157-1158. https://doi.org/10.1093/bioinformatics/btr076
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K and Wang J. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15): 1966-1967. https://doi.org/10.1093/bioinformatics/btp336
Liu W, Liu J, Ning Y, Ding B, Wang X, Wang Z and Wan GL. 2013. Recent progress in understanding PAMP- and effector-triggered immunity against the rice blast fungus Magnaporthe oryzae. Molecular Plant 6(3): 605–620. https://doi.org/10.1093/mp/sst015
Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M, Sun Y, Wang L and Shao Z. 2015. Genomic insights into the taxonomic status of the Bacillus cereus group. Scientific Reports 5: 14082. https://doi.org/10.1038/srep14082
Lloyd N, Johnson DL and Herderich MJ. 2015. Metabolomics approaches for resolving and harnessing chemical diversity in grapes, yeast and wine. Australian Journal of Grape Wine Research 21(S1): 723–740. https://doi.org/10.1111/ajgw.12202
Love MI, Huber W and Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15: 550. http://dx.doi.org/10.1186/s13059-014-0550-8
Lozano-Alejo N, Guzmán-Plazola RA, Zavaleta-Mejía E, Aguilar-Rincón VH y Ayala-Escobar V. 2015. Etiología y evaluación de alternativas de control de la Marchitez del chile de árbol (Capsicum annuum L.) en La Vega de Metzitlán, Hidalgo, México. Revista Mexicana de Fitopatología 33(1): 31-53. http://www.scielo.org.mx/pdf/rmfi/v33n1/2007-8080-rmfi-33-01-00031.pdf
Luo R, Liu B, XieY, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW and Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short read de novo assembler. Gigascience 1(1): 18. https://doi.org/10.1186/2047-217X-1-18
Macedo CA, Martínez HA y Lara RJ. 2012. Rizobacterias aisladas del trópico húmedo con actividad antagónica sobre Colletotrichum gloeosporioides, evaluación cuantitativa e identificación molecular. Revista Mexicana de Fitopatología 30(1): 11-30. http://www.scielo.org.mx/pdf/rmfi/v30n1/v30n1a2.pdf
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1): 10–12. https://doi.org/10.14806/ej.17.1.200
Mauch-Mani B, Baccelli I, Luna E and Flors V. 2017. Defense Priming: An Adaptive Part of Induced Resistance. Annual Review of Plant Biology 68: 485–512. https://doi.org/10.1146/annurev-arplant-042916-041132
Mazrou YSA, Makhlouf AH, Elseehy MM, Awad MF and Hassan MM. 2020. Antagonistic activity and molecular characterization of biological control agent Trichoderma harzianum from Saudi Arabia. Egyptian Journal of Biological Pest Control 30(4): 1-8. https://doi.org/10.1186/s41938-020-0207-8
Meier-Kolthoff JP, Auch AF, Klenk HP and Göker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14(60): 1–14. https://doi.org/10.1186/1471-2105-14-60
Mejía-Bautista MA, Reyes-Ramírez A, Cristobal-Alejo J, Tun-Suárez JM, Borges-Gómez LC y Pacheco-Aguilar JR. 2016. Bacillus spp. in the control of wilt caused by Fusarium spp. in Capsicum chinense. Revista Mexicana de Fitopatología 34(3): 208-222. https://doi.org/10.18781/R.MEX.FIT.1603-1
Mhlongo MI, Piater LA, Madala NE, Labuschagne N and Dubery IA. 2018. The Chemistry of Plant-Microbe interactions in the rhizosphere and the potential for metabolomics to reveal signaling related to defense priming and Induced Systemic Resistance. Frontiers in Plant Science 9: 112. https://doi.org/10.3389/fpls.2018.00112
Mi H, Muruganujan A, Casagrande JT and Thomas PD. 2013. Large-scale gene function analysis with the PANTHER classification system. Nature Protocols 8: 1551-1566. https://doi.org/10.1038/nprot.2013.092
Michel-Aceves AC, Otero-Sánchez MA, Díaz-Castro A, Martínez-Rojero RD, Ariza-Flores R y Barrios-Ayala A. 2013. Biocontrol de la “Escoba de Bruja” del mango, con Trichoderma spp., en condiciones de campo. Revista Mexicana de Fitopatología 31(1): 1-12. http://www.scielo.org.mx/pdf/rmfi/v31n1/v31n1a1.pdf
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, López R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJA, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD and Finn R. 2015. The InterPro protein families datábase: the classification resource after 15 years. Nucleic Acids Research 43(D1): 1-9. https://doi.org/10.1093/nar/gku1243
Moriuchi R, Dohra H, Kanesaki Y and Ogawa N. 2019. Complete Genome Sequence of Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses. Frontiers in Microbiology 10: 1–21. https://doi.org/10.3389/fmicb.2019.00133
Mousa WK and Raizada MN. 2016. Natural disease control in cereal grains. Pp:1-7. In: reference module in Food Science. https://doi.org/10.1016/B978-0-08-100596-5.00206-7
Naz S. 2014. Analytical protocols based on LC–MS, GC–MS and CE–MS for nontargeted metabolomics of biological tissues. Bioanalysis 6(12): 1657–1677. https://doi.org/10.4155/BIO.14.119
Ocegueda-Reyes MD, Casas-Solís J, Virgen-Calleros G, González-Eguiarte DR, López-Alcocer E and Olalde-Portugal V. 2020. Isolation, identification and characterization of antagonistic rhizobacteria to Sclerotium cepivorum. Mexican Journal of Phytopathology 38(1): 146-159. https://doi.org/10.18781/R.MEX.FIT.1911-2
ONU. 2018. La Agenda 2030 y los Objetivos de Desarrollo Sostenible: una oportunidad para América Latina y el Caribe (LC/G.2681-P/Rev.3), Santiago. https://repositorio.cepal.org/bitstream/handle/11362/40155/24/S1801141_es.pdf (Consulta, Junio 2020).
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P and Tyson GW. 2015 CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research 25: 1043 1055. https://doi.org/10.1101/gr.186072.114
Peng Y, Leung HCM, Yiu SM, Chin FYL and IDBA-UD. 2012. a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28(11): 1420-1428. https://doi.org/10.1093/bioinformatics/bts174
Pérez-Moreno L, Belmonte-Vargas JR, Núñez-Palenius HG, Guzmán-Mendoza R y Mendoza-Celedón B. 2015. Sensibilidad de especies de Sclerotinia spp. y Sclerotium cepivorum a agentes de control biológico y fungicidas. Revista Mexicana de Fitopatología 33(2): 256-267. http://www.scielo.org.mx/pdf/rmfi/v33n2/2007-8080-rmfi-33-02-00256.pdf
Pérez-Rojas F, León-Quispe J y Galindo-Cabello N. 2015. Actinomicetos Aislados del Compost y su Actividad Antagonista a Fitopatógenos de la papa (Solanum tuberosum spp. andigena Hawkes). Revista Mexicana de Fitopatología 33(2): 116-139. http://www.scielo.org.mx/pdf/rmfi/v33n2/2007-8080-rmfi-33-02-00116-en.pdf
Petersen TN, Brunak S, von Heijne G and Nielsen H. 2011. SignalP 4.0: Discriminating signal peptides from transmembrane regions. Natural Methods 8: 785–786. https://doi.org/10.1038/nmeth.1701
Pott DM, Osorio S and Vallarino JG. 2019. From central to specialized metabolism: an overview of some secondary compounds derived from the primary metabolism for their role in conferring nutritional and organoleptic characteristics to fruit. Frontiers in Plant Science 10: 835. https://doi.org/10.3389/fpls.2019.00835
Potter SC, Aurélien Luciani, Sean R Eddy, Youngmi Park, Rodrigo Lopez and Robert D Finn. 2018. HMMER web server: 2018 update. Nucleic Acids Research 46(W1): W200–W204. https://doi.org/10.1093/nar/gky448
Quinland A and Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformática 26(6): 841-2 https://doi.org/10.1093/bioinformatics/btq033
Raja HA, Miller AN, Pearce CJ and Oberlies NH. 2017. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. Journal of Natural Products 80(3): 756-770. https://doi.org/10.1021/acs.jnatprod.6b01085
Ramautar R, Somsen GW and de Jong GJ. 2016. CE–MS for metabolomics: developments and applications in the period 2014–2016. Electrophoresis 38(1): 1–13. https://doi.org/10.1002/elps.201600370
Richter M, Rosselló-Móra R, Oliver Glöckner F and Peplies J. 2016. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32(6): 929–931. https://doi.org/10.1093/bioinformatics/btv681
Rios-Velasco C, Caro-Cisneros JN, Berlanga-Reyes DI, Ruíz-Cisneros MF, Ornelas-Paz JJ, Salas-Marina MA, Villalobos-Pérez E and Guerrero-Prieto VM. 2016. Identification and antagonistic activity in vitro af Bacillus spp. and Trichoderma spp. isolates against common phytopathogenic fungi. Revista Mexicana de Fitopatología 34(1): 84-99. https://doi.org/10.18781/R.MEX.FIT.1507-1
Rodríguez-Millán KA, Monreal Vargas CT, Huerta Díaz J, Soria Colunga JC y Jarquín Gálvez R. 2013. Aporte de microorganismos benéficos por la incorporación al suelo de residuos deshidratados de col (Brassica oleracea var capitata) y su efecto en el pH. Revista Mexicana de Fitopatología 31(1):29-44. http://www.scielo.org.mx/pdf/rmfi/v31n1/v31n1a4.pdf
Rodríguez-Romero VM, Villanueva-Arce R, Trejo-Raya AB and Bautista-Baños S. 2019. Chitosan and Pseudomonas fluorescens extracts for Alternaria alternata control in tomato (Solanum lycopersicum). Mexican Journal of Phytopathology 37(2): 202-219. https://doi.org/10.18781/R.MEX.FIT.1812-2
Rollano-Peñaloza OM y Mollinedo-Portugal P. 2017. Análisis bioinformático de Arn-Seq con una perspectiva para Bolivia. Revista Boliviana de Química 4(2): 50-55. http://www.scielo.org.bo/pdf/rbq/v34n2/v34n2_a02.pdf
Roser M. 2019. Pesticides. University of Oxford. https://ourworldindata.org/pesticides (Consulta, Mayo de 2020).
Ruiz-Cisneros MF, Ornelas-Paz JJ, Olivas-Orozco GI, Acosta-Muñiz CH, Sepúlveda-Ahumada DR, Pérez-Corral DA, Rios-Velasco C, Salas-Marina MA and Fernández-Pavía SP. 2018. Efect of Trichoderma spp. and phytopathogenic fungi on plant growth and tomato fruit quality. Revista Mexicana de Fitopatología 36(3): 444-456. https://doi.org/10.18781/R.MEX.FIT.1804-5
Ruiz-Cisneros MF, Rios-Velasco C, Berlanga-Reyes DI, Ornelas-Paz JJ, Acosta-Muñiz CH, Romo-Chacón A, Zamudio-Flores PB, Pérez-Corral DA, Salas-Marina MÁ, Ibarra-Rendón JE and Fernández-Pavía SP. 2017. Incidence and causal agents of root diseases and its antagonists in apple orchards of Chihuahua, México. Revista Mexicana de Fitopatología 35(3): 437-462. https://doi.org/10.18781/R.MEX.FIT.1704-3
Samaniego-Gaxiola JA, Pedroza-Sandoval A, Chew-Madinaveitia Y and Gaytán-Mascorro A. 2019. Reductive disinfestation, soil desiccation and Trichoderma harzianum to control Phymatotrichopsis omnivora in pecan tree nursery. Mexican Journal of Phytopathology 37(2): 287-303. https://doi.org/10.18781/R.MEX.FIT.1808-7
Serret-López M, Aranda-Ocampo S, Espinosa-Victoria D, Ortiz-Martínez LE and Ramírez-Razo K. 2021. Polyphasic characterization of Burkholderia gladioli isolated from onion and evaluation of its potential pathogenicity for other crops. Mexican Journal of Phytopathology 39(1): 1-20. https://doi.org/10.18781/R.MEX.FIT.2007-2
Schmieder R and Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27(6): 863-864. https://doi.org/10.1093/bioinformatics/btr026
Schwamborn K. 2012. Imaging mass spectrometry in biomarker discovery and validation. Journal of Proteomics 75(16): 4990–4998. https://doi.org/10.1016/j.jprot.2012.06.015
Sentausa E and Fournier PE. 2013. Advantages and limitations of genomics in prokaryotic taxonomy. Clinical microbiology and infection. European Society of Clinical Microbiology and Infectious Diseases 19(9): 790-795. https://doi.org/10.1111/1469-0691.12181
Serrano-Carreón L, Balderas K, Wong MA, Rosas DR y Galindo-Fentanes EG. 2010. Biofungicidas para el control de la antracnosis del mango: Logrando frutos de alta calidad internacional para mercados exigentes. Claridades Agropecuarias 208: 28-37. https://info.aserca.gob.mx/claridades/revistas/208/ca208-28.pdf
Shen Z, Ruan Y and Chao X. 2015. Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression. Biology and Fertility Soils 51: 553–562. https://doi.org/10.1007/s00374-015-1002-7
Skinnider MA, Merwin NJ, Johnston CW and Magarvey NA. 2017. PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. Nucleic Acids Research 45(W1): W49–W54. https://doi.org/10.1093/nar/gkx320
Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, Xu W and Su Z. 2017. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic acids research 45(W1): W122–W129. https://doi.org/10.1093/nar/gkx382
Tlapal-Bolaños B, González Hernández H, Zavaleta Mejía E, Sánchez García P, Mora Aguilera G, Nava Díaz C, Del Real Laborde JI y Rubio Cortes R. 2014. Colonización de Trichoderma y Bacillus en plántulas de Agave tequilana Weber, var. Azul y el efecto sobre la fisiología de la planta y densidad de Fusarium. Revista Mexicana de Fitopatología 32(1): 62-74. http://www.scielo.org.mx/pdf/rmfi/v32n1/v32n1a6.pdf
Trapnell C, Pachter L and Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9): 1105-1111. https://doi.org/10.1093/bioinformatics/btp120
Trinidad-Cruz JR, Quiñones-Aguilar EE, Rincón-Enríquez G, López-Pérez L y Hernández-Cuevas LV. 2017. Mycorrhization of Agave cupreata: Biocontrol of Fusarium oxysporum and plant growth promotion. Revista Mexicana de Fitopatología 35(2): 151-169. https://doi.org/10.18781/R.MEX.FIT.1607-5
Uc-Arguelles AK, Perez-Moreno J, Ayala-EscobaR V y Zavaleta-Mejia E. 2017. Antagonismo de Saccharicola sp. contra fitopatógenos de la raíz de chile jalapeño (Capsicum annuum). Revista Mexicana de Fitopatología 35(2):263-283. http://dx.doi.org/10.18781/R.MEX.FIT.1611-6
Valenzuela-Aragon B, Parra-Cota FI, Santoyo G Arellano-Wattenbarger GL and de los Santos-Villalobos S. 2019. Plant-assisted selection: a promising alternative for in vivo identification of wheat (Triticum turgidum L. subsp. Durum) growth promoting bacteria. Plant Soil 435: 367–384. https://doi.org/10.1007/s11104-018-03901-1
Valenzuela-Ruiz V, Gálvez-Gamboa GT, Villa-Rodríguez ED, Parra-Cota FI, Santoyo G and de los Santos-Villalobos S. 2020. Lipopeptides produced by biological control agents of the genus Bacillus: a review of analytical tools used for their study. Revista Mexicana de Ciencias Agrícolas 11(2): 419-432. https://doi.org/10.29312/remexca.v11i2.2191
Valenzuela-Ruiz V, Robles-Montoya R, Parra-Cota FI, Santoyo G, Orozco-Mosqueda, Ma. Del Carmen, Rodríguez-Ramírez R and de los Santos-Villalobos S. 2019. Draft genome sequence of Bacillus paralicheniformis TRQ65, a biological control agent and plant growth-promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere in the Yaqui Valley, Mexico. 3 Biotech 9:436. https://doi.org/10.1007/s13205-019-1972-5
Van Heel AJ, de Jong A, Song C, Viel JH, Kok J and Kuipers OP. 2018. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Research 46(W1): W278-W281. https://doi.org/10.1093/nar/gky383
Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC and Pati A. 2015. Microbial species delineation using whole genome sequences. Nucleic Acids Research 43(14): 6761–6771. https://doi.org/10.1093/nar/gkv657
Vatsa P, Chiltz A, Luini E, Vandelle E, Pugin A and Roblin G. 2011. Cytosolic calcium rises and related events in ergosterol-treated Nicotiana cells. Plant Physiology and Biochemestry 49(7): 764-773. https://doi.org/10.1016/j.plaphy.2011.04.002
Villa-Rodríguez E, Parra-Cota F, Castro-Longoria E, López-Cervantes J and de los Santos-Villalobos S. 2019. Bacillus subtilis TE3: A promising biological control agent against Bipolaris sorokiniana, the causal agent of spot blotch in wheat (Triticum turgidum L. subsp. durum). Biological control 132: 135-143. https://doi.org/10.1016/j.biocontrol.2019.02.012
Villarreal-Delgado MF, Villa-Rodríguez ED, Cira-Chávez LA, Estrada-Alvarado MI, Parra-Cota FI and De los Santos-Villalobos S. 2017. The genus Bacillus as a biological control agent and its implications in the agricultural biosecurity. Mexican Journal of Phytopathology 36(1): 95-130.
Vinale F, Manganiello G, Nigro M, Mazzei P, Piccolo A, Pascale A, Ruocco M, Marra R, Lombardi N, Lanzuise S, Varlese R, Cavallo P, Lorito M and Woo SL. 2014. A novel fungal metabolite with beneficial properties for agricultural applications. Molecules 19(7): 9760-9772. https://doi.org/10.3390/molecules19079760
Weber T, Rausch C, Lopez P, Hoof I, Gaykova V, Huson DH and Wohlleben W. 2009. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. Journal of Biotechnology 140(1-2): 13–17. https://doi.org/10.1016/j.jbiotec.2009.01.007
Woo SL, Ruocco M, Vinale F, Nigro M, Marra R, Lombardi N, Pascale A, Lanzuise S, Manganiello G and Lorito M. 2014. Trichoderma-based products and their widespread use in agricultura. Open Mycology Journal 8: 71–126. https://doi.org/10.2174/1874437001408010071
Worley B and Powers R. 2013. Multivariate analysis in metabolomics. Current Metabolomics 1(1):92–107. https://doi.org/10.2174/2213235X11301010092
Wu TD and Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26(7): 873-881. https://doi.org/10.1093/bioinformatics/btq057
Xi W, Gao Y, Cheng Z, Chen C, Han M, Yang P, Xiong G and Ning K. 2019. Using QC-Blind for Quality Control and Contamination Screening of Bacteria DNA Sequencing Data Without Reference Genome. Frontiers in Microbiology 10: 1–15. https://doi.org/10.3389/fmicb.2019.01560
Xu Y, Chen H, Zhon X and Cai X. 2012. Induction of hypersensitive response and nonhost resistance by a Cladosporium fulvum elicitor CfHNNI1 is dose-dependent and negatively regulated by salicylic acid. Journal of Integrative Agriculture 11(10): 1665–1674. https://doi.org/10.1016/S2095-3119(12)60169-5
Yoon SH, Ha SM, Lim J, Kwon S and Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 110: 1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Zerbino DR and Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821–829. https://doi.org/10.1101/gr.074492.107
Zhang W, Fraiture M, Kolb D, Löffelhardt B, Desaki Y and Boutrot FF. 2013. Arabidopsis receptor-like protein30 and receptor-like kinase suppressor of BIR1-1/EVERSHED mediate innate immunity to necrotrophic fungi. Plant Cell 25(10): 4227–4241. https://doi.org/10.1105/tpc.113.117010
DOI: http://dx.doi.org/10.18781/R.MEX.FIT.2009-3
Refbacks
- There are currently no refbacks.