1
|
Ayala Zepeda M, Valenzuela Ruiz V, Parra Cota FI, Chinchilla-Soto C, de la Cruz Torres E, Ibba MI, Estrada Alvarado MI, de los Santos Villalobos S. Genomic insights of a native bacterial consortium for wheat production sustainability. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100230. [PMID: 39026603 PMCID: PMC11256204 DOI: 10.1016/j.crmicr.2024.100230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Abstract
The use of plant growth-promoting bacteria as bioinoculants is a powerful tool to increase crop yield and quality and to improve nitrogen use efficiency (NUE) from fertilizers in plants. This study aimed to bioprospecting a native bacterial consortium (Bacillus cabrialesii subsp. cabrialesii TE3T, Priestia megaterium TRQ8, and Bacillus paralicheniformis TRQ65), through bioinformatic analysis, and to quantify the impact of its inoculation on NUE (measured through 15N-isotopic techniques), grain yield, and grain quality of durum wheat variety CIRNO C2008 grown under three doses of urea (0, 120, and 240 kg N ha-1) during two consecutive agricultural cycles in the Yaqui Valley, Mexico. The inoculation of the bacterial consortium (BC) to the wheat crop, at a total N concentration of 123-225 kg N ha-1 increased crop productivity and maintained grain quality, resulting in a yield increase of 1.1 ton ha-1 (6.0 vs. 7.1 ton ha-1, 0 kg N ha-1 added, 123 kg N ha-1 in the soil) and of 2.0 ton ha-1 (5.9 vs. 7.9 ton ha-1, 120 kg N ha-1 added, 104 kg N ha-1 in the soil) compared to the uninoculated controls at the same doses of N. The genomic bioinformatic analysis of the studied strains showed a great number of biofertilization-related genes regarding N and Fe acquisition, P assimilation, CO2 fixation, Fe, P, and K solubilization, with important roles in agroecosystems, as well as genes related to the production of siderophores and stress response. A positive effect of the BC on NUE at the studied initial N content (123 and 104 kg N ha-1) was not observed. Nevertheless, increases of 14 % and 12.5 % on NUE (whole plant) were observed when 120 kg N ha-1 was applied compared to when wheat was fully fertilized (240 kg N ha-1). This work represents a link between bioinformatic approaches of a native bacterial inoculant and the quantification of its impact on durum wheat.
Collapse
Affiliation(s)
- Marisol Ayala Zepeda
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora ITSON, Obregón, 85000, Mexico
| | - Valeria Valenzuela Ruiz
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora ITSON, Obregón, 85000, Mexico
| | - Fannie Isela Parra Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias INIFAP, Obregón, 85000, Mexico
| | - Cristina Chinchilla-Soto
- Centro de Investigación en Contaminación Ambiental, Universidad de Costa Rica UCR, San José, 11501-2060, Costa Rica
| | - Eulogio de la Cruz Torres
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares ININ, Ocoyoacac, 52750, Mexico
| | - María Itria Ibba
- Centro Internacional de Mejoramiento de Maíz y de Trigo CIMMYT, Texcoco, 56237, Mexico
| | - María Isabel Estrada Alvarado
- Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora ITSON, Obregón, 85000, Mexico
| | | |
Collapse
|
2
|
de Los Santos Villalobos S, Félix Pablos CM, Valenzuela Ruiz V, Parra Cota FI. Bacillus mexicanus sp. nov., a biological control bacterium isolated from the common bean ( Phaseolus vulgaris L.) crop in Sinaloa, Mexico. Int J Syst Evol Microbiol 2023; 73. [PMID: 37916690 DOI: 10.1099/ijsem.0.006110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Strain FSQ1T was isolated from the rhizosphere of the common bean (Phaseolus vulgaris L.) crop sampled in a commercial field located in the Gabriel Leyva Solano community, which belongs to the Guasave municipality (state of Sinaloa, Mexico). Based on its full-length 16S rRNA gene sequence, strain FSQ1T was assigned to the genus Bacillus (100 % similarity). This taxonomic affiliation was supported by its morphological and metabolic traits. Strain FSQ1T was a Gram-stain-positive bacterium with the following characteristics: rod-shaped cells, strictly aerobic, spore forming, catalase positive, reduced nitrate to nitrite, hydrolysed starch and casein, grew in the presence of lysozyme and 2 % NaCl, utilized citrate, grew at pH 6.0-8.0, produced acid from glucose, was unable to produce indoles from tryptophan, and presented biological control against Sclerotinia sclerotiorum. The whole-genome phylogenetic results showed that strain FSQ1T formed an individual clade in comparison with highly related Bacillus species. In addition, the maximum values for average nucleotide identity and from Genome-to-Genome Distance Calculator analysis were 91.57 and 44.20 %, respectively, with Bacillus spizizenii TU-B-10T. Analysis of its fatty acid content showed the ability of strain FSQ1T to produce fatty acids that are not present in closely related Bacillus species, such as C18 : 0 and C20 : 0. Thus, these results provide strong evidence that strain FSQ1T represents a novel species of the genus Bacillus, for which the name Bacillus mexicanus sp. nov. is proposed. The type strain is FSQ1T (CM-CNRG TB51T=LBPCV FSQ1T).
Collapse
Affiliation(s)
- Sergio de Los Santos Villalobos
- Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P.85000, Col. Centro, Ciudad 9 Obregón, Sonora, México
| | - Carmen María Félix Pablos
- Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P.85000, Col. Centro, Ciudad 9 Obregón, Sonora, México
| | - Valeria Valenzuela Ruiz
- Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P.85000, Col. Centro, Ciudad 9 Obregón, Sonora, México
| | - Fannie I Parra Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Km. 12, C. P. 85000, Cd., Obregón, Sonora, México
| |
Collapse
|
3
|
Makuwa SC, Motadi LR, Choene M, Liu Y, Serepa-Dlamini MH. Bacillus dicomae sp. nov., a new member of the Bacillus cereus group isolated from medicinal plant Dicoma anomala. Int J Syst Evol Microbiol 2023; 73. [PMID: 37877980 DOI: 10.1099/ijsem.0.006112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
A Gram-stain-positive, endospore-forming endophytic bacterial strain designated MHSD28T was isolated from surface-sterilized leaves of Dicoma anomala collected from Eisleben, Botlokwa, Limpopo Province, South Africa. The phenotypic and phylogenetic characteristics of strain MHSD28T were consistent with those of members within the Bacillus cereus group. Comparative analysis between this strain and its relatives confirmed that it belongs to this group and forms a monophyletic branch. The digital DNA-DNA hybridization values between strain MHSD28T and its relatives were lower than the 70 % threshold for species delineation. To further determine its phylogenetic position, multi-locus sequence analysis (MLSA) based on five concatenated housekeeping gene (gyrB, atpD, DnaK, rpoB and rpoD) sequences, phenotypic analysis, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) biotyper identification, fatty acid and polar lipid profile analyses were carried out. Phenotypic characterization, MLSA, whole genome sequence based analyses and MALDI-TOF results placed strain MHSD28T within the B. cereus group. The major fatty acids were iso-C15 : 0 and summed feature 3 and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The respiratory quinone was menaquinone-7. The cell-wall peptidoglycan structure included meso-diaminopimelic acid. Considering the above results, strain MHSD28T represents a novel species of the B. cereus group, for which the name Bacillus dicomae sp. nov. is proposed. The type strain is MHSD28T (=BD 2262T=LMG 32287T=CECT 30671T).
Collapse
Affiliation(s)
- Sephokoane Cindy Makuwa
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, PO Box 17011, Doornfontein, 2028, Johannesburg, South Africa
| | - Lesetja Raymond Motadi
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Kingsway Campus, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa
| | - Mpho Choene
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Kingsway Campus, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa
| | - Yang Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), State Key Laboratory of Applied Microbiology Southern China,, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, People's Republic of China
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, PO Box 17011, Doornfontein, 2028, Johannesburg, South Africa
| |
Collapse
|
4
|
Orozco-Mosqueda MDC, Kumar A, Babalola OO, Santoyo G. Rhizobiome Transplantation: A Novel Strategy beyond Single-Strain/Consortium Inoculation for Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2023; 12:3226. [PMID: 37765390 PMCID: PMC10535606 DOI: 10.3390/plants12183226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023]
Abstract
The growing human population has a greater demand for food; however, the care and preservation of nature as well as its resources must be considered when fulfilling this demand. An alternative employed in recent decades is the use and application of microbial inoculants, either individually or in consortium. The transplantation of rhizospheric microbiomes (rhizobiome) recently emerged as an additional proposal to protect crops from pathogens. In this review, rhizobiome transplantation was analyzed as an ecological alternative for increasing plant protection and crop production. The differences between single-strain/species inoculation and dual or consortium application were compared. Furthermore, the feasibility of the transplantation of other associated micro-communities, including phyllosphere and endosphere microbiomes, were evaluated. The current and future challenges surrounding rhizobiome transplantation were additionally discussed. In conclusion, rhizobiome transplantation emerges as an attractive alternative that goes beyond single/group inoculation of microbial agents; however, there is still a long way ahead before it can be applied in large-scale agriculture.
Collapse
Affiliation(s)
- Ma. del Carmen Orozco-Mosqueda
- Departamento de Ingeniería Bioquímica y Ambiental, Tecnológico Nacional de México en Celaya, Celaya 38010, Guanajuato, Mexico;
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho 2735, South Africa;
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Michoacan, Mexico
| |
Collapse
|
5
|
Figueroa-Brambila KM, Escalante-Beltrán A, Montoya-Martínez AC, Díaz-Rodríguez AM, López-Montoya ND, Parra-Cota FI, de Los Santos-Villalobos S. Bacillus cabrialesii: Five Years of Research on a Novel Species of Biological Control and Plant Growth-Promoting Bacteria. PLANTS (BASEL, SWITZERLAND) 2023; 12:2419. [PMID: 37446980 DOI: 10.3390/plants12132419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Bacillus cabrialesii is a novel bacterial species isolated from wheat (Triticum turgidum L. subsp. durum) plants in the Yaqui Valley, Mexico, by our research team. Over years of research studying this strain at the cutting-edge level, it has shown different mechanisms of action. B. cabrialesii is strongly reported as a plant-growth-promoting bacterium and a biological control agent on wheat crops. Knowing this, B. cabrialesii has been brought from lab to field as part of a bacterial consortium, not to mention that there are ongoing investigations into formulating a cost-effective bioinoculant to increase the yield and/or quality of wheat. Moreover, studies of this novel species as a biocontrol agent in other crops (pepper, tomato, cucumber, and potato) are being carried out, with preliminary results that make B. cabrialesii a promising biological control agent, inhibiting the growth of phytopathogens. However, research into this bacterium has not only been reported in our country; there are many studies around the world in which promising native Bacillus strains end up being identified as B. cabrialesii, which reaffirms the fact that this bacterial species can promote plant growth and combat phytopathogens, showing great agrobiotechnological potential.
Collapse
Affiliation(s)
- Karem Ma Figueroa-Brambila
- Laboratorio de Biotecnología del Recurso Microbiano, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora (ITSON), 5 de Febrero 818 Sur, Colonia Centro, Obregón 85000, Mexico
| | - Alina Escalante-Beltrán
- Laboratorio de Biotecnología del Recurso Microbiano, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora (ITSON), 5 de Febrero 818 Sur, Colonia Centro, Obregón 85000, Mexico
| | - Amelia Cristina Montoya-Martínez
- Laboratorio de Biotecnología del Recurso Microbiano, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora (ITSON), 5 de Febrero 818 Sur, Colonia Centro, Obregón 85000, Mexico
| | - Alondra María Díaz-Rodríguez
- Laboratorio de Biotecnología del Recurso Microbiano, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora (ITSON), 5 de Febrero 818 Sur, Colonia Centro, Obregón 85000, Mexico
| | - Naomi Dayanna López-Montoya
- Laboratorio de Biotecnología del Recurso Microbiano, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora (ITSON), 5 de Febrero 818 Sur, Colonia Centro, Obregón 85000, Mexico
| | - Fannie Isela Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional De Investigaciones Forestales, Agrícolas y Pecuarias, Norman E. Borlaug s/n, Col. Centro, Obregón 85000, Mexico
| | - Sergio de Los Santos-Villalobos
- Laboratorio de Biotecnología del Recurso Microbiano, Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora (ITSON), 5 de Febrero 818 Sur, Colonia Centro, Obregón 85000, Mexico
| |
Collapse
|
6
|
Valenzuela Ruiz V, Santoyo G, Gómez Godínez LJ, Cira Chávez LA, Parra Cota FI, de los Santos Villalobos S. Complete genome sequencing of Bacillus cabrialesii TE3 T: A plant growth-promoting and biological control agent isolated from wheat ( Triticum turgidum subsp. durum) in the Yaqui Valley. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100193. [PMID: 37293250 PMCID: PMC10245096 DOI: 10.1016/j.crmicr.2023.100193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
Bacillus cabrialesii TE3T is a strictly aerobic and Gram-stain-positive plant growth-promoting bacterium, motile and catalase-positive. In addition, strain TE3T was also recently described as a biological control agent. Here, we present the complete circularized genome of this type strain, as well as a whole genome analysis identifying genes of agricultural interest. Thus, a hybrid assembly method was performed using short-read sequencing through the Illumina MiSeq platform, and long-read sequencing through the MinION sequencing technology by Oxford Nanopore Technology (ONT). This assembly method showed a closed circular chromosome of 4,125,766 bp and 44.2% G + C content. The strain TE3T genome annotation, based on the RAST platform, presented 4,282 Coding DNA sequences (CDS) distributed in 335 subsystems, from which 4 CDS are related to the promotion of plant growth and 28 CDS to biological control. Also, Prokka (Rapid Prokaryotic Genome Annotation) predicted a total of 119 RNAs composed of 87 tRNAs, 31 rRNA, and 1 tmRNA; and the PGAP (Prokaryotic Genome Annotation Pipeline) predicted a total of 4,212 genes (3,991 CDS). Additionally, seven putative biosynthetic gene clusters were identified by antiSMASH, such as Fengycin, Bacilysin, Subtilosin A, Bacillibactin, Bacillaene, Surfactin, and Rizocticin A, which are related to antimicrobial and antifungal properties, whose gene presence was further supported by the Prokaryotic Genome Annotation Pipeline (PGAP) annotation. Thus, the complete genome of Bacillus cabrialesii TE3T showed promising bioactivities for the use of this type strain to bioformulate bacterial inoculants for sustainable agriculture.
Collapse
Affiliation(s)
- Valeria Valenzuela Ruiz
- Instituto Tecnológico de Sonora (ITSON), 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Cd. Obregón, Sonora, Mexico
| | - Gustavo Santoyo
- Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Av. Francisco J. Múgica s/n, Edif. B-3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico
| | - Lorena Jacqueline Gómez Godínez
- Centro Nacional de Recursos Genéticos. Instituto Nacional de Investigación Forestales, Agrícolas y Pecuarios. Boulevard de la Biodiversidad 400, Rancho las Cruces, C.P. 47600. Tepatitlán de Morelos, Jalisco, Mexico
| | - Luis A. Cira Chávez
- Instituto Tecnológico de Sonora (ITSON), 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Cd. Obregón, Sonora, Mexico
| | - Fannie I. Parra Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Norman E. Borlaug Km. 12, C. P. 85000, Cd. Obregón, Sonora, Mexico
| | | |
Collapse
|
7
|
de Los Santos-Villalobos S, Valenzuela-Ruiz V, Montoya-Martínez AC, Parra-Cota FI, Santoyo G, Larsen J. Bacillus cabrialesii subsp. cabrialesii subsp. nov. and Bacillus cabrialesii subsp. tritici subsp. nov., plant growth-promoting bacteria and biological control agents isolated from wheat ( Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico. Int J Syst Evol Microbiol 2023; 73. [PMID: 37185134 DOI: 10.1099/ijsem.0.005779] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Strain TSO2T, a plant growth-promoting rhizobacteria and biological control agent, was isolated from wheat rhizosphere sampled from the Yaqui Valley in Mexico. The strain was identified using a polyphasic approach. Based on its analysis of the full-length 16S rRNA gene, strain TSO2T was assigned to the genus
Bacillus
, which was supported by morphological and metabolic traits, such as Gram-positive staining, rod shape, spore formation, strictly aerobic metabolism, catalase-positive activity, starch, and casein hydrolysis, reduction of nitrate to nitrite, growth in presence of lysozyme and 2 % NaCl, citrate utilization, growth at pH 6.0, acid production from glucose and indole production from tryptophan. Additionally, strain TSO2T possesses swarming motility, presenting a featureless mat pattern that can cover the whole petri dish. The whole-genome phylogenetic relationship analysis elucidated that strain TSO2T is closely related to
Bacillus cabrialesii
TE3T. The maximum values for average nucleotide identity (ANI) and in silico DNA–DNA hybridization from the genome-to-genome distance calculator (GGDC) were 97 and 73.4 %, respectively, related to
Bacillus cabrialesii
TE3T, where both ANI and GGDC values were barely above the species delimitation threshold, but below the subspecies limit. Also, strain TSO2T showed the ability to produce a fatty acid (C18 : 0) that is not present in closely related
Bacillus
species. These results provide evidence that strain TSO2T is a novel subspecies of the species
Bacillus cabrialesii
, for which the name
Bacillus cabrialesii
subsp. tritici subsp. nov. is proposed. The type strain of
Bacillus cabrialesii
subsp. tritici subsp. nov. is TSO2T (CM-CNRG TB52T=LBPCV TSO2T). The description of this novel subspecies automatically creates the subspecies
Bacillus cabrialesii
subsp. cabrialesii subsp. nov. for which the type strain is TE3T (CM-CNRG TB54T=CCStamb A1T).
Collapse
Affiliation(s)
- Sergio de Los Santos-Villalobos
- Departamento de Ciencias Agronómicas y Veterinarias, Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora (ITSON), 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Cd. Obregón, Sonora, Mexico
| | - Valeria Valenzuela-Ruiz
- Departamento de Ciencias Agronómicas y Veterinarias, Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora (ITSON), 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Cd. Obregón, Sonora, Mexico
| | - Amelia C Montoya-Martínez
- Departamento de Ciencias Agronómicas y Veterinarias, Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora (ITSON), 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Cd. Obregón, Sonora, Mexico
| | - Fannie I Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Norman E. Borlaug Km. 12, C. P. 85000, Cd. Obregón, Sonora, Mexico
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Av. Francisco J. Múgica s/n, Edif. B-3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, México
| | - John Larsen
- Laboratorio Nacional de Innovación Ecotecnologica para la Sustentabilidad, Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma México (UNAM), Antigua Carretera a Pátzcuaro 8701, Col. San José de La Huerta, C.P. 58190, Morelia, Michoacán, México
| |
Collapse
|
8
|
Illuminating the signalomics of microbial biofilm on plant surfaces. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
9
|
Rojas-Padilla J, de-Bashan LE, Parra-Cota FI, Rocha-Estrada J, de los Santos-Villalobos S. Microencapsulation of Bacillus Strains for Improving Wheat ( Triticum turgidum Subsp. durum) Growth and Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212920. [PMID: 36365373 PMCID: PMC9657316 DOI: 10.3390/plants11212920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 05/14/2023]
Abstract
Bio-formulation technologies have a limited impact on agricultural productivity in developing countries, especially those based on plant growth-promoting rhizobacteria. Thus, calcium alginate microbeads were synthesized and used for the protection and delivery of three beneficial Bacillus strains for agricultural applications. The process of encapsulation had a high yield per gram for all bacteria and the microbeads protected the Bacillus strains, allowing their survival, after 12 months of storage at room temperature. Microbead analysis was carried out by observing the rate of swelling and biodegradation of the beads and the released-establishment of bacteria in the soil. These results showed that there is an increase of around 75% in bead swelling on average, which allows for larger pores, and the effective release and subsequent establishment of the bacteria in the soil. Biodegradation of microbeads in the soil was gradual: in the first week, they increased their weight (75%), which consistently results in the swelling ratio. The co-inoculation of the encapsulated strain TRQ8 with the other two encapsulated strains showed plant growth promotion. TRQ8 + TRQ65 and TRQ8 + TE3T bacteria showed increases in different biometric parameters of wheat plants, such as stem height, root length, dry weight, and chlorophyll content. Thus, here we demonstrated that the application of alginate microbeads containing the studied strains showed a positive effect on wheat plants.
Collapse
Affiliation(s)
- Jonathan Rojas-Padilla
- Instituto Tecnológico de Sonora, 5 de Febrero 818 sur, Ciudad Obregon 85000, Sonora, Mexico
| | - Luz Estela de-Bashan
- The Bashan Institute of Science, 1730 Post Oak Court, Auburn, AL 36830, USA
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Av. IPN 195, La Paz 23096, Baja California Sur, Mexico
- Department of Entomology and Plant Pathology, Auburn University, 301 Funches Hall, Auburn, AL 36849, USA
| | - Fannie Isela Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ciudad Obregon 85000, Sonora, Mexico
| | - Jorge Rocha-Estrada
- CONACyT Unidad Regional Hidalgo, Centro de Investigación en Alimentación y Desarrollo, Pachuca Ciudad del Conocimiento y la Cultura, San Agustín Tlaxiaca 42163, Hidalgo, Mexico
| | | |
Collapse
|
10
|
Chávez-Luzanía RA, Montoya-Martínez AC, Parra-Cota FI, de Los Santos-Villalobos S. Pangenomes-identified singletons for designing specific primers to identify bacterial strains in a plant growth-promoting consortium. Mol Biol Rep 2022; 49:10489-10498. [PMID: 36125674 DOI: 10.1007/s11033-022-07927-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND The use of plant growth-promoting microorganisms represents a sustainable way to increase agricultural yields and plant health. Thus, the identification and tracking of these microorganisms are determinants for validating their positive effects on crops. Pangenomes allow the identification of singletons that can be used to design specific primers for the detection of the studied strains. OBJECTIVE This study aimed to establish a strategy based on the use of whole-genome sequencing and pangenomes for designing and validating primer sets for detecting Bacillus cabrialesii TE3T, Priestia megaterium TRQ8, and Bacillus paralicheniformis TRQ65, a promising beneficial bacterial consortium for wheat. METHODS AND RESULTS The identification of singletons of TE3T, TRQ8, and TRQ65 was performed by pangenomes using the Kbase platform and subsequently analyzed using BLAST®. The identified DNA regions were used for primer design in AlleleID version 7. Primers were validated by multiplex PCR using pure template DNA from each studied strain, combinations of two or three DNA from these strains, and DNA from agricultural soil samples enriched (and not) with the bacterial consortium. Here, we report the first design of primers capable of detecting and identifying the beneficial strains TE3T, TRQ8, and TRQ65. CONCLUSIONS The use of pangenomes allowed the distinction of unique sequences that enables the design of primers for specific identification of the studied bacterial strains. This strategy can be widely used for the design of primer sets to detect other strains of interest for combating biopiracy, and commercial protection of biological products, among other applications.
Collapse
Affiliation(s)
| | | | - Fannie Isela Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones forestales, Agrícolas y Pecuarias, Norman E. Borlaug Km. 12, C.P. 85000, Ciudad Obregón, SON, México
| | | |
Collapse
|
11
|
Progress and Applications of Plant Growth-Promoting Bacteria in Salt Tolerance of Crops. Int J Mol Sci 2022; 23:ijms23137036. [PMID: 35806037 PMCID: PMC9266936 DOI: 10.3390/ijms23137036] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Saline soils are a major challenge in agriculture, and salinization is increasing worldwide due to climate change and destructive agricultural practices. Excessive amounts of salt in soils cause imbalances in ion distribution, physiological dehydration, and oxidative stress in plants. Breeding and genetic engineering methods to improve plant salt tolerance and the better use of saline soils are being explored; however, these approaches can take decades to accomplish. A shorter-term approach to improve plant salt tolerance is to be inoculated with bacteria with high salt tolerance or adjusting the balance of bacteria in the rhizosphere, including endosymbiotic bacteria (living in roots or forming a symbiont) and exosymbiotic bacteria (living on roots). Rhizosphere bacteria promote plant growth and alleviate salt stress by providing minerals (such as nitrogen, phosphate, and potassium) and hormones (including auxin, cytokinin, and abscisic acid) or by reducing ethylene production. Plant growth-promoting rhizosphere bacteria are a promising tool to restore agricultural lands and improve plant growth in saline soils. In this review, we summarize the mechanisms of plant growth-promoting bacteria under salt stress and their applications for improving plant salt tolerance to provide a theoretical basis for further use in agricultural systems.
Collapse
|
12
|
Carmen María FP, I PCF, Gustavo S, Ma del Carmen OM, Sergio DLSV. Draft genome sequence of Bacillus sp. strain FSQ1, a biological control agent against white mold in common bean (Phaseolus vulgaris L.). CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100138. [PMID: 35909597 PMCID: PMC9325907 DOI: 10.1016/j.crmicr.2022.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/30/2022] Open
Abstract
Bacillus sp. FSQ1 was isolated from the rhizosphere of the common bean (Phaseolus vulgaris L.). Bacillus sp. FSQ1 can inhibit the growth of Sclerotinia sclerotiorum. The draft genome of strain Bacillus sp. FSQ1 consists of 3598,499 bp; 925,913 bp N50; 2 L50; 33 contigs; 97 RNAs and 3908 predicted CDS. The GC content in the draft genome of Bacillus sp. FSQ1 is 43.0%. Based on genome mining, potential metabolites involved in the biocontrol activity of strain Bacillus sp. FSQ1 are rhizocticin A and bacillibactin.
Bacillus sp. strain FSQ1 was isolated from the common bean (Phaseolus vulgaris L.). The genome of this strain presented 3,598,499 bp; 43.0% G + C content; 925,913 bp N50; 2 L50; 33 contigs; 97 RNAs and 3,908 predicted coding DNA sequences (CDS) distributed in 315 subsystems. Based on genome mining, the biological control activity of strains FSQ1 could be associated with the biosynthesis of rhizocticin A and bacillibactin. Thus, this strain is a promising active ingredient for the formulation of biopesticides.
Collapse
|
13
|
María Fernanda Villarreal-Delgado, Parra-Cota FI, Cira-Chávez LA, Estrada-Alvarado MI, de los Santos-Villalobos S. Bacillus sp. FSQ1: a Promising Biological Control Agent Against Sclerotinia sclerotiorum, the Causal Agent of white Mold in Common Bean (Phaseolus vulgaris L.). BIOL BULL+ 2021. [DOI: 10.1134/s1062359021060182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
14
|
Ali M, Ali Q, Sohail MA, Ashraf MF, Saleem MH, Hussain S, Zhou L. Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective. Int J Mol Sci 2021; 22:ijms221810165. [PMID: 34576331 PMCID: PMC8465699 DOI: 10.3390/ijms221810165] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.
Collapse
Affiliation(s)
- Mohsin Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Q.A.); (L.Z.)
| | - Muhammad Aamir Sohail
- Center for Excellence in Molecular Plant Sciences, National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China;
| | | | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Punjab, Pakistan;
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- Correspondence: (Q.A.); (L.Z.)
| |
Collapse
|
15
|
COLMENA: A Culture Collection of Native Microorganisms for Harnessing the Agro-Biotechnological Potential in Soils and Contributing to Food Security. DIVERSITY 2021. [DOI: 10.3390/d13080337] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
COLMENA is a microbial culture collection dedicated to the characterization, classification, preservation, and transferal of native microorganisms isolated from various agro-systems and other ecosystems in Mexico. This collection aims to protect microbial diversity, reducing soil degradation, but also exploiting its agro-biotechnological potential. So far, COLMENA has isolated and cryopreserved soil microorganisms from different crops in two major agricultural regions in Mexico, the Yaqui Valley, Sonora, and the Fuerte Valley, Sinaloa. COLMENA has specialized in the identification and characterization of microbial strains with metabolic capacities related to the promotion of plant growth and the biocontrol of phytopathogens. Thus, COLMENA has identified several promising plant growth-promoting microbial (PGPM) strains due to their metabolic and genetic potentials and their beneficial effects in vivo and field trials. These findings demonstrate the biotechnological potential of these strains for their future use in profitable agricultural alternatives focused on enhancing global food security. To share the knowledge and results of the COLMENA team’s scientific research, a virtual platform was created, where the database of the studied and preserved microorganisms is available to professionals, researchers, agricultural workers, and anyone who is interested.
Collapse
|
16
|
Villa-Rodriguez E, Moreno-Ulloa A, Castro-Longoria E, Parra-Cota FI, de Los Santos-Villalobos S. Integrated omics approaches for deciphering antifungal metabolites produced by a novel Bacillus species, B. cabrialesii TE3 T, against the spot blotch disease of wheat (Triticum turgidum L. subsp. durum). Microbiol Res 2021; 251:126826. [PMID: 34298216 DOI: 10.1016/j.micres.2021.126826] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 07/01/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Bipolaris sorokiniana is an important biotic constraint for global wheat production, causing spot blotch disease. In this work, we present a comprehensive characterization of the cell-free culture filtrate (CF) and precipitated fraction (PF) of Bacillus cabrialesii TE3T showing an effective inhibition of spot blotch. Our results indicated that CF produced by B. cabrialesii TE3T inhibits the growth of B. sorokiniana through stable metabolites (after autoclaving and proteinase K treatment). Antifungal metabolites in CF and PF were explored by an integrated genomic-metabolomic approach. Genome-mining revealed that strain TE3T contains the biosynthetic potential to produce wide spectrum antifungal (surfactin, fengycin, and rhizocticin A) and antibacterial metabolites (bacillaene, bacilysin, bacillibactin, and subtilosin A), and through bioactivity-guided LC-ESI-MS/MS approach we determined that a lipopeptide complex of surfactin and fengycin homologs was responsible for antifungal activity exhibited by B. cabrialesii TE3T against the studied phytopathogen. In addition, our results demonstrate that i) a lipopeptide complex inhibits B. sorokiniana by disrupting its cytoplasmatic membrane and ii) reduced spot blotch disease by 93 %. These findings show the potential application of metabolites produced by strain TE3T against B. sorokiniana and provide the first insight into antifungal metabolites produced by the novel Bacillus species, Bacillus cabrialesii.
Collapse
Affiliation(s)
- Eber Villa-Rodriguez
- Departamento de Ciencias Agronómicas y Veterinarias, Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, Mexico
| | - Aldo Moreno-Ulloa
- Laboratorio MS2, Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Ensenada, Mexico
| | - Ernestina Castro-Longoria
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Ensenada, Mexico
| | - Fannie I Parra-Cota
- Campo Experimental Norman E. Borlaug- INIFAP, Norman E. Borlaug Km. 12, C.P. 85000, Ciudad Obregón, Sonora, Mexico
| | - Sergio de Los Santos-Villalobos
- Departamento de Ciencias Agronómicas y Veterinarias, Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, Mexico.
| |
Collapse
|
17
|
Sarr M, Diouf FS, Lo CI, Tidjani Alou M, Alibar S, Million M, Sokhna C, Fenollar F. Taxonogenomics description of Bacillus marasmi sp. nov., a new species isolated from the stool sample. New Microbes New Infect 2021; 42:100906. [PMID: 34188938 PMCID: PMC8220230 DOI: 10.1016/j.nmni.2021.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/05/2022] Open
Abstract
Using the culturomics method, two strains were isolated, identified, and characterised following the taxonogenomics concept. Bacillus marasmi sp. nov. strain Marseille-P3556 (= CSURP3556) is isolated from a 13-month-old girl living in Niger. The phylogenetic tree, phenotypic criteria, and genomic analysis described here clearly show that this bacterium is different from previously known bacterial species withstanding in nomenclature and new members of Bacillus genus.
Collapse
Affiliation(s)
- M Sarr
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F S Diouf
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C I Lo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - M Tidjani Alou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - S Alibar
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Million
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - C Sokhna
- IHU-Méditerranée Infection, Marseille, France.,Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - F Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| |
Collapse
|
18
|
Zhang D, Xu H, Gao J, Portieles R, Du L, Gao X, Borroto Nordelo C, Borrás-Hidalgo O. Endophytic Bacillus altitudinis Strain Uses Different Novelty Molecular Pathways to Enhance Plant Growth. Front Microbiol 2021; 12:692313. [PMID: 34248918 PMCID: PMC8268155 DOI: 10.3389/fmicb.2021.692313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/26/2021] [Indexed: 11/15/2022] Open
Abstract
The identification and use of endophytic bacteria capable of triggering plant growth is an important aim in sustainable agriculture. In nature, plants live in alliance with multiple plant growth-promoting endophytic microorganisms. In the current study, we isolated and identified a new endophytic bacterium from a wild plant species Glyceria chinensis (Keng). The bacterium was designated as a Bacillus altitudinis strain using 16S rDNA sequencing. The endophytic B. altitudinis had a notable influence on plant growth. The results of our assays revealed that the endophytic B. altitudinis raised the growth of different plant species. Remarkably, we found transcriptional changes in plants treated with the bacterium. Genes such as maturase K, tetratricopeptide repeat-like superfamily protein, LOB domain-containing protein, and BTB/POZ/TAZ domain-containing protein were highly expressed. In addition, we identified for the first time an induction in the endophytic bacterium of the major facilitator superfamily transporter and DNA gyrase subunit B genes during interaction with the plant. These new findings show that endophytic B. altitudinis could be used as a favourable candidate source to enhance plant growth in sustainable agriculture.
Collapse
Affiliation(s)
- Dening Zhang
- Joint R&D Center of Biotechnology, Retda, Yota Bio-Engineering Co., Ltd., Rizhao, China
| | - Hongli Xu
- Joint R&D Center of Biotechnology, Retda, Yota Bio-Engineering Co., Ltd., Rizhao, China
| | - Jingyao Gao
- Joint R&D Center of Biotechnology, Retda, Yota Bio-Engineering Co., Ltd., Rizhao, China
| | - Roxana Portieles
- Joint R&D Center of Biotechnology, Retda, Yota Bio-Engineering Co., Ltd., Rizhao, China
| | - Lihua Du
- Joint R&D Center of Biotechnology, Retda, Yota Bio-Engineering Co., Ltd., Rizhao, China
| | - Xiangyou Gao
- Joint R&D Center of Biotechnology, Retda, Yota Bio-Engineering Co., Ltd., Rizhao, China
| | | | - Orlando Borrás-Hidalgo
- Joint R&D Center of Biotechnology, Retda, Yota Bio-Engineering Co., Ltd., Rizhao, China.,State Key Laboratory of Biobased Material and Green Papermaking, Shandong Provincial Key Lab of Microbial Engineering, Qilu University of Technology (Shandong Academy of Science), Jinan, China
| |
Collapse
|
19
|
Draft Genome Sequence of Bacillus sp. Strain IGA-FME-2, Isolated from the Bulk Soil of Soybean (Glycine max L.) in Northeast China. Microbiol Resour Announc 2021; 10:10/16/e00004-21. [PMID: 33888493 PMCID: PMC8063636 DOI: 10.1128/mra.00004-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Here, we present the draft genome of Bacillus sp. strain IGA-FME-2. This strain was isolated from the bulk soil of soybean (Glycine max L.). Its genome consists of 3,810 protein-coding genes, 44 tRNAs, two 16S rRNAs, and a single copy of 23S rRNA, with a GC content of 46.4%. Here, we present the draft genome of Bacillus sp. strain IGA-FME-2. This strain was isolated from the bulk soil of soybean (Glycine max L.). Its genome consists of 3,810 protein-coding genes, 44 tRNAs, two 16S rRNAs, and a single copy of 23S rRNA, with a GC content of 46.4%.
Collapse
|
20
|
Complete Genome Sequence of Bacillus sp. Strain IGA-FME-1, Isolated from the Bulk Soil of Maize ( Zea mays L.). Microbiol Resour Announc 2021; 10:10/13/e00192-21. [PMID: 33795345 PMCID: PMC8104053 DOI: 10.1128/mra.00192-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the complete genome of Bacillus sp. strain IGA-FME-1 (isolated from the bulk soil of maize [Zea mays L.]). This genome consists of 5,147,837 bp, 5,219 protein-coding genes, 112 tRNAs, thirteen 16S rRNAs, thirteen 23S rRNAs, and thirteen 5S rRNAs, with a G+C content of 38.2%. Here, we present the complete genome of Bacillus sp. strain IGA-FME-1 (isolated from the bulk soil of maize [Zea mays L.]). This genome consists of 5,147,837 bp, 5,219 protein-coding genes, 112 tRNAs, 13 16S rRNAs, 13 23S rRNAs, and 13 5S rRNAs, with a G+C content of 38.2%.
Collapse
|
21
|
Díaz-Rodríguez AM, Salcedo Gastelum LA, Félix Pablos CM, Parra-Cota FI, Santoyo G, Puente ML, Bhattacharya D, Mukherjee J, de los Santos-Villalobos S. The Current and Future Role of Microbial Culture Collections in Food Security Worldwide. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2020.614739] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Food security is the pillar of nutritional wellbeing for food availability, and is necessary to satisfy all physiological needs to thus maintain the general wellbeing of populations. However, global agricultural deficiencies occur due to rapid population growth, causing an increase in competition for resources; such as water, land, and energy, leading to the overexploitation of agro-ecosystems, and the inability to produce a suitable quantity of efficient food. Therefore, the development of sustainable agro-biotechnologies is vital to increase crop yield and quality, reducing the negative impacts caused by intensive non-sustainable agricultural practices. In this way, the genetic and metabolic diversity of soil and plant microbiota in agro-ecosystems are a current and promising alternative to ensure global food security. Microbial communities play an important role in the improvement of soil fertility and plant development by enhancing plant growth and health through several direct and/or indirect mechanisms. Thus, the bio-augmentation of beneficial microbes into agro-ecosystems not only generates an increase in food production but also mitigates the economic, social, and environmental issues of intensive non-sustainable agriculture. In this way, the isolation, characterization, and exploitation of preserved beneficial microbes in microbial culture collections (MCC) is crucial for the ex situ maintenance of native soil microbial ecology focused on driving sustainable food production. This review aims to provide a critical analysis of the current and future role of global MCC on sustainable food security, as providers of a large number of beneficial microbial strains with multiple metabolic and genetic traits.
Collapse
|
22
|
Bacillus rugosus sp. nov. producer of a diketopiperazine antimicrobial, isolated from marine sponge Spongia officinalis L. Antonie van Leeuwenhoek 2020; 113:1675-1687. [PMID: 32939598 DOI: 10.1007/s10482-020-01472-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
A novel Gram-positive and endospore-forming bacterium assigned as strain SPB7T which is also a new source of a cyclic diketopiperazine (3S,6S)-3,6-diisobutylpiperazine-2,5-dione is described. A polyphasic (biochemical, phenotypic and genotypic) approach was used to clarify the taxonomic affiliation of this strain. The partial and complete 16S rRNA gene sequences revealed that strain SPB7T is a member of the Bacillus genus [showing high similarity (> 98.70%) with Bacillus spizizenii NRRL B-23049T, Bacillus tequilensis KCTC 13622T, Bacillus inaquosorum KCTC 13429T and Bacillus cabrialesii TE3T]. The maximum values for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (GGDC, Formula 2) of strain SPB7T was obtained for twenty-five strains of Bacillus spizizenii (ANI 95.01-95.48% and GGDC 62.70-60.00%). The whole-genome phylogenetic relationship showed that SPB7T formed an individual and separated clade with the Bacillus spizizenii group. Principal cellular fatty acids identified in strain SPB7T were anteiso C15:0, anteiso C17:0, iso C15:0, iso C17:0, C16:0, C10:0 3OH and iso C17:1 ϖ10c. Polar lipid profile showed presence of diphosphotidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and five unknown lipids. Cells were rod shaped, catalase, oxidase-positive and motile. Growth occurred at 20-45 °C (optimal 35 °C), at pH 6.0-10.0 (optimal pH 8) and 0-10% (w/v) NaCl (optimal 2%). The phenotypic, biochemical, and genotypic traits of strain SPB7T strongly supported its taxonomic affiliation as a novel species of the Bacillus genus, for which the name Bacillus rugosus sp. nov. is proposed. The type strain is SPB7T (= NRRL B-65559T, = CICC 24827T, = MCC 4185T).
Collapse
|
23
|
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 2019; 9:436. [PMID: 31696041 DOI: 10.1007/s13205-019-1972-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/23/2019] [Indexed: 01/25/2023] Open
Abstract
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.
Collapse
|