3 Biotech

, 9:436 | Cite as

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

  • Valeria Valenzuela-Ruiz
  • Rosa Icela Robles-Montoya
  • Fannie Isela Parra-Cota
  • Gustavo Santoyo
  • Ma. del Carmen Orozco-Mosqueda
  • Roberto Rodríguez-Ramírez
  • Sergio de los Santos-VillalobosEmail author
Genome Reports


The strain denominated TRQ65 was isolated from wheat (Triticum turgidum subsp. durum) commercial fields in the Yaqui Valley, Mexico. Here, we report its draft genome sequence, which presented ~ 4.5 million bp and 45.5% G + C content. Based on the cutoff values on species delimitation established for average nucleotide identity (> 95 to 96%), genome-to-genome distance calculator (> 70%), and the reference sequence alignment-based phylogeny builder method, TRQ65 was strongly affiliated to Bacillus paralicheniformis. The rapid annotation using subsystem technology server revealed that TRQ65 contains genes related to osmotic, and oxidative stress response, as well as auxin biosynthesis (plant growth promotion traits). In addition, antiSMASH and BAGEL revealed the presence of genes involved in lipopeptides and antibiotic biosynthesis. The function of those annotated genes was validated at a metabolic level, observing that strain TRQ65 was able to tolerate saline (91.0%), and water (155.0%) stress conditions, besides producing 28.8 ± 0.9 µg/mL indoles. In addition, strain TRQ65 showed growth inhibition (1.6 ± 0.4 cm inhibition zone) against the causal agent of wheat spot blotch, Bipolaris sorokiniana. Finally, plant–microbe interactions assays confirm the ability of strain TRQ65 to regulate wheat growth, showing a significant increment in shoot height (26%), root length (40%), shoot dry weight (48%), stem diameter (55%), and biovolume index (246%). These findings provide insights for future agricultural studies of this strain.


Plant growth-promoting rhizobacteria Biocontrol agent Average nucleotide identity Genome to genome distance calculator Biofertilizer 



This study was supported by the CONACyT Project 257246 “Interacción trigo x microorganismos promotores del crecimiento vegetal: identificando genes con potencial agro-biotecnológico”, and the Instituto Tecnológico de Sonora (ITSON) Project PROFAPI 2019-0094 “Identificación de genes asociados al control biológico y promoción del crecimiento vegetal en el genoma de Bacillus sp. TRQ65”. In addition, we thank Abraham Chaparro Encinas for his support in the bacterial DNA extraction. Valeria Valenzuela-Ruiz and Rosa Robles Montoya were supported by CONACYT fellowship number 712969 and 627262, respectively.

Author contributions

VV: conceptualization; data curation; formal analysis; investigation; methodology; visualization; writing—original draft; writing—review and editing. RIRM: conceptualization; data curation; formal analysis; investigation; methodology; visualization; writing—original draft. FP: conceptualization; formal analysis; investigation; methodology; visualization; writing—original draft; writing—review and editing. GS: visualization; writing—original draft; writing—review and editing. MCO: visualization; writing—original draft; writing—review and editing. RRR: visualization; writing—original draft; writing—review and editing. SS: conceptualization; data curation; formal analysis; funding acquisition; investigation; methodology; project administration; resources; software; supervision; validation; visualization; writing—original draft; writing—review and editing.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

13205_2019_1972_MOESM1_ESM.docx (25 kb)
Supplementary material 1 (DOCX 25 kb)


  1. Agriculture Solution AGSOL What is Bio-P™?. Accessed 30 June 2019
  2. Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Accessed 8 may 2019
  3. Aziz RK, Bartels D, Best A et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:1–15. CrossRefGoogle Scholar
  4. Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. CrossRefPubMedPubMedCentralGoogle Scholar
  5. Barra F, Roscetto E, Soriano AA, Vollaro A, Postiglione I, Pierantoni GM (2015) Photodynamic and antibiotic therapy in combination to fight biofilms and resistant surface bacterial infections. Int J Mol Sci 16:20417–20430. CrossRefPubMedPubMedCentralGoogle Scholar
  6. Berendsen R, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Bertels F, Silander OK, Pachkov M, Rainey PB, Van Nimwegen E (2014) Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol 31:1077–1088. CrossRefPubMedPubMedCentralGoogle Scholar
  8. BioAgro Chemical, BIO X TERRA BS (2019a) Accessed 30 June 2019
  9. BioAgro Chemical, BIO X TERRA BT (2019b) Accessed 30 June 2019
  10. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. CrossRefPubMedPubMedCentralGoogle Scholar
  11. Botanicare, Hydroguard® (2012) Accessed 30 June 2019
  12. Chun J, Oren A, Ventosa A et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. CrossRefPubMedGoogle Scholar
  13. Cohn F (1872) Untersuchungen Über Bakterien. Beitrage zur Biologie Pflanz 1:127–1224. Scholar
  14. Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14(7):1394–1403. CrossRefPubMedPubMedCentralGoogle Scholar
  15. de los Santos Villalobos S, Parra Cota F, Herrea Sepulveda A, Valenzuela Aragon B, Estrada Mora JC (2018) Colmena: colección de microorganismos edáficos y endófitos nativos, para contribuir a la seguridad alimentaria nacional. Rev Mexicana Cienc Agric 9(1):191–202. CrossRefGoogle Scholar
  16. de los Santos-Villalobos S, Robles RI, Parra Cota FI, Larsen J, Lozano P, Tiedje MJ (2019) Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico. Int J Syst Evol Microbiol. CrossRefPubMedGoogle Scholar
  17. Diaz-Rodriguez A, Parra-Cota FI, Santoyo G, de los Santos-Villalobos S (2019) Chlorothalonil tolerance of indole producing bacteria associated to wheat (Triticum turgidum L.) rhizosphere in the Yaqui Valley, Mexico. Ecotoxicology 28:569–577. CrossRefPubMedGoogle Scholar
  18. Fan B, Blom J, Klenk HP, Borriss R (2017) Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis form an “operational group B. amyloliquefaciens” within the B. subtilis species complex. Front Microbiol 8:22. CrossRefPubMedPubMedCentralGoogle Scholar
  19. García Meléndez M, Zárate Camargo G, Meza Contreras JJ, Herrera Sepúlveda A, Parra Cota FI, de los Santos Villalobos S (2017) Abiotic stress tolerance of microorganisms associated with oregano (Origanum vulgare L.) in the Yaqui Valley. Sonora. Open Agric J 2(1):260–265. CrossRefGoogle Scholar
  20. Kashyap BK, Solanki MK, Pandey AK, Prabha S, Kumar P, Kumari B (2019) Bacillus as plant growth promoting rhizobacteria (PGPR): a promising green agriculture technology. In: Ansari R, Mahmood I (eds) Plant health under biotic stress, 1st edn. Springer, Singapore, pp 219–236CrossRefGoogle Scholar
  21. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. CrossRefPubMedPubMedCentralGoogle Scholar
  22. McSpadden Gardener BB (2004) Ecology of Bacillus and Paenibacillus spp. in agricultural systems. Phytopathology 94(11):1252–1258. CrossRefPubMedGoogle Scholar
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:1–14. CrossRefGoogle Scholar
  24. Obeidat M (2017) Isolation and characterization of extremely halotolerant Bacillus species from Dead Sea black mud and determination of their antimicrobial and hydrolytic activities. Afr J Microbiol Res 11(32):1303–1314. CrossRefGoogle Scholar
  25. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T et al (2013) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. CrossRefPubMedPubMedCentralGoogle Scholar
  26. Palacio-Rodríguez R, Coria-Arellano JL, López-Bucio J, Sánchez-Salas J, Muro-Pérez G, Castañeda-Gaytán G, Sáenz-Mata J (2017) Halophilic rhizobacteria from Distichlis spicata promote growth and improve salt tolerance in heterologous plant hosts. Symbiosis 73(3):179–189. CrossRefGoogle Scholar
  27. Parte AC (2018) LPSN—list of prokaryotic names with standing in nomenclature ( 20 years on. Int J Syst Evol Microbiol 68:1825–1829. CrossRefGoogle Scholar
  28. Raaijmakers JM, De Bruijn I, Nybroe O, Ongena M (2010) Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics. FEMS Microbiol Rev 34(6):1037–1062. CrossRefPubMedGoogle Scholar
  29. Rahman A, Sitepu IR, Tang SY, Hashidoko Y (2010) Salkowski’s reagent test as a primary screening index for functionalities of rhizobacteria isolated from wild dipterocarp saplings growing naturally on medium-strongly acidic tropical peat soil. Biosci Biotechnol Biochem 74(11):2202–2208. CrossRefPubMedGoogle Scholar
  30. Rajabi Agereh S, Kiani F, Khavazi K, Rouhipour H, Khormali F (2019) An environmentally friendly soil improvement technology for sand and dust storms control. Environ Health Eng Manag 6(1):63–71. CrossRefGoogle Scholar
  31. Robles-Montoya RI, Parra Cota FI, de los Santos Villalobos S (2019) Draft genome sequence of Bacillus megaterium TRQ8, a plant growth‐promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere in the Yaqui Valley, Mexico. 3 Biotech 9:201. CrossRefPubMedGoogle Scholar
  32. Rooney AP, Price NP, Ehrhardt C, Swezey JL, Bannan JD (2009) Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. Int J Syst Evol Microbiol 59(10):2420–2436. CrossRefGoogle Scholar
  33. Tejera-Hernández B, Rojas-Badía MM, Heydrich-Pérez M (2011) Potencialidades del género Bacillus en la promoción del crecimiento vegetal y el control de hongos fitopatógenos. Rev CENIC Cienc Biol 42(3):131–138.
  34. Thilagar G, Bagyaraj DJ, Podile AR, Vaikuntapu PR (2016) Bacillus sonorensis, a novel plant growth promoting rhizobacterium in improving growth, nutrition and yield of chilly (Capsicum annuum L.). Proc Natl Acad Sci 88:813–818. CrossRefGoogle Scholar
  35. Tiwari S, Prasad V, Lata C (2019) Bacillus: Plant growth promoting bacteria for sustainable agriculture and environment. In: Shankar Singh J, Singh DP (eds) New and future developments in microbial biotechnology and bioengineering. Elsevier, Lucknow, pp 43–55. CrossRefGoogle Scholar
  36. Trabelsi D, Mhamdi R (2013) Microbial inoculants and their impact on soil microbial communities: a review. Biomed Res Int 2013:1–11. CrossRefGoogle Scholar
  37. Valenzuela-Aragon B, Parra-Cota F, Santoyo G, Arellano G, de los Santos-Villalobos S (2018) 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. CrossRefGoogle Scholar
  38. Valenzuela-Ruiz V, Ayala-Zepeda M, Arellano-Wattenbarger GL, Parra-Cota FI, García-Pereyra J, Aviña-Martínez GN, de los Santos-Villalobos S (2018) Microbial culture collections and their potential contribution to current and future food security. Rev Lat Rec Nat 14(1):18–25Google Scholar
  39. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A (2015) Microbial species delineation using whole genome sequences. Nucleic Acids Res 43(14):6761–6771. CrossRefPubMedPubMedCentralGoogle Scholar
  40. Vielva L, de Toro M, Lanza VF, de la Cruz F (2017) PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes. Bioinformatics 33(23):3796–3798. CrossRefPubMedGoogle Scholar
  41. Villa-Rodriguez E, Lugo-Enriquez C, de los Santos-Villalobos S (2016) First report of Cochliobolus sativus causing spot blotch on durum wheat (Triticum durum) in the Yaqui Valley, Mexico. Plant Dis 100:2329. CrossRefGoogle Scholar
  42. Villa-Rodríguez E, Parra-Cota F, Castro-Longoria E, López-Cervantes J, 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). Biol Control 132:135–143. CrossRefGoogle Scholar
  43. Villarreal-Delgado MF, Villa-Rodríguez ED, Cira-Chávez LA, Estrada-Alvarado MI, Parra-Cota FI, De los Santos-Villalobos S (2017) The genus Bacillus as a biological control agent and its implications in the agricultural biosecurity. Rev Mex Fitopatol 36(1):95–130. CrossRefGoogle Scholar
  44. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617. CrossRefPubMedPubMedCentralGoogle Scholar
  45. Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 110(10):1281–1286. CrossRefPubMedGoogle Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  • Valeria Valenzuela-Ruiz
    • 1
  • Rosa Icela Robles-Montoya
    • 1
  • Fannie Isela Parra-Cota
    • 2
  • Gustavo Santoyo
    • 3
  • Ma. del Carmen Orozco-Mosqueda
    • 4
  • Roberto Rodríguez-Ramírez
    • 1
  • Sergio de los Santos-Villalobos
    • 1
    Email author
  1. 1.Instituto Tecnológico de SonoraCiudad ObregónMexico
  2. 2.Campo Experimental Norman E. Borlaug, INIFAPCiudad ObregónMexico
  3. 3.Instituto de Investigaciones Químico BiológicasUniversidad Michoacana de San Nicolás de HidalgoMoreliaMexico
  4. 4.Facultad de Agrobiología “Presidente Juárez”Universidad Michoacana de San Nicolás de HidalgoUruapanMexico

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