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Rojas-Sánchez B, Castelán-Sánchez H, Garfias-Zamora EY, Santoyo G. Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System. Plants (Basel) 2024; 13:954. [PMID: 38611483 PMCID: PMC11013257 DOI: 10.3390/plants13070954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.
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Affiliation(s)
- Blanca Rojas-Sánchez
- Genomic Diversity Lab, Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolas de Hidalgo, Morelia 58030, Mexico; (B.R.-S.); (E.Y.G.-Z.)
| | - Hugo Castelán-Sánchez
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Esmeralda Y. Garfias-Zamora
- Genomic Diversity Lab, Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolas de Hidalgo, Morelia 58030, Mexico; (B.R.-S.); (E.Y.G.-Z.)
| | - Gustavo Santoyo
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
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Guzmán-Guzmán P, Valencia-Cantero E, Santoyo G. Plant growth-promoting bacteria potentiate antifungal and plant-beneficial responses of Trichoderma atroviride by upregulating its effector functions. PLoS One 2024; 19:e0301139. [PMID: 38517906 PMCID: PMC10959389 DOI: 10.1371/journal.pone.0301139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/08/2024] [Indexed: 03/24/2024] Open
Abstract
Trichoderma uses different molecules to establish communication during its interactions with other organisms, such as effector proteins. Effectors modulate plant physiology to colonize plant roots or improve Trichoderma's mycoparasitic capacity. In the soil, these fungi can establish relationships with plant growth-promoting bacteria (PGPBs), thus affecting their overall benefits on the plant or its fungal prey, and possibly, the role of effector proteins. The aim of this study was to determine the induction of Trichoderma atroviride gene expression coding for effector proteins during the interaction with different PGPBs, Arabidopsis or the phytopathogen Fusarium brachygibbosum, and to determine whether PGPBs potentiates the beneficial effects of T. atroviride. During the interaction with F. brachygibbosum and PGPBs, the effector coding genes epl1, tatrx2 and tacfem1 increased their expression, especially during the consortia with the bacteria. During the interaction of T. atroviride with the plant and PGPBs, the expression of epl1 and tatrx2 increased, mainly with the consortium formed with Pseudomonas fluorescens UM270, Bacillus velezensis AF12, or B. halotolerans AF23. Additionally, the consortium formed by T. atroviride and R. badensis SER3 stimulated A. thaliana PR1:GUS and LOX2:GUS for SA- and JA-mediated defence responses. Finally, the consortium of T. atroviride with SER3 was better at inhibiting pathogen growth, but the consortium of T. atroviride with UM270 was better at promoting Arabidopsis growth. These results showed that the biocontrol capacity and plant growth-promoting traits of Trichoderma spp. can be potentiated by PGPBs by stimulating its effector functions.
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Affiliation(s)
- Paulina Guzmán-Guzmán
- Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Eduardo Valencia-Cantero
- Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Gustavo Santoyo
- Institute of Chemical and Biological Research, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
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Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
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Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
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Afridi MS, Kumar A, Javed MA, Dubey A, de Medeiros FHV, Santoyo G. Harnessing root exudates for plant microbiome engineering and stress resistance in plants. Microbiol Res 2024; 279:127564. [PMID: 38071833 DOI: 10.1016/j.micres.2023.127564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico.
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Valencia-Marin MF, Chávez-Avila S, Guzmán-Guzmán P, Orozco-Mosqueda MDC, de Los Santos-Villalobos S, Glick BR, Santoyo G. Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health. Biotechnol Adv 2024; 70:108303. [PMID: 38128850 DOI: 10.1016/j.biotechadv.2023.108303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.
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Affiliation(s)
- María F Valencia-Marin
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Salvador Chávez-Avila
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Paulina Guzmán-Guzmán
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Ma Del Carmen Orozco-Mosqueda
- Departamento de Ingeniería Bioquímica y Ambiental, Tecnológico Nacional de México en Celaya, 38010 Celaya, Gto, Mexico
| | | | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico.
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Yadav P, Singh RP, Hashem A, Abd_Allah EF, Santoyo G, Kumar A, Gupta RK. Enhancing Biocrust Development and Plant Growth through Inoculation of Desiccation-Tolerant Cyanobacteria in Different Textured Soils. Microorganisms 2023; 11:2507. [PMID: 37894165 PMCID: PMC10609203 DOI: 10.3390/microorganisms11102507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/17/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
In recent years, there has been a burgeoning interest in the utilization of cyanobacteria for the purpose of land rehabilitation via enhancements in soil fertility, prevent erosion, and counter desertification. This study evaluated the ability of Nostoc calcicola BOT1, Scytonema sp. BOT2, and their consortia to form biocrusts on the substrate of coarse sand, fine sand, and loamy soil. A nutrient- and water-deficient substrate was inoculated with cyanobacteria to facilitate biocrust formation and evaluate their impact on agriculture. Cyanobacteria inoculation resulted in significant improvements in soil fertility, especially in coarse and fine sand, which initially had the lowest fertility. The findings of this investigation underscore that the consortium of cyanobacteria exhibited greater efficacy than individual strains in enhancing soil fertility and stimulating plant growth. The loamy soil treated with the consortium had the highest plant growth across all soil types, in contrast to the individual strains. The consortium of cyanobacteria showed promising results in promoting biocrust formation and fostering rice seedling growth in fine sand. This study provides empirical evidence supporting the potential utility of cyanobacterial consortia as a valuable tool for the rehabilitation of degraded land. Furthermore, the results indicate that cyanobacterial species can persist in soil environments even following prolonged periods of desiccation.
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Affiliation(s)
- Priya Yadav
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (P.Y.); (R.P.S.)
| | - Rahul Prasad Singh
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (P.Y.); (R.P.S.)
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.H.)
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (E.F.A.)
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico; (G.S.)
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201313, India
| | - Rajan Kumar Gupta
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (P.Y.); (R.P.S.)
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Oyedoh OP, Yang W, Dhanasekaran D, Santoyo G, Glick BR, Babalola OO. Rare rhizo-Actinomycetes: A new source of agroactive metabolites. Biotechnol Adv 2023; 67:108205. [PMID: 37356598 DOI: 10.1016/j.biotechadv.2023.108205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
Numerous biotic and abiotic stress in some geographical regions predisposed their agricultural matrix to challenges threatening plant productivity, health, and quality. In curbing these threats, different customary agrarian principles have been created through research and development, ranging from chemical inputs and genetic modification of crops to the recently trending smart agricultural technology. But the peculiarities associated with these methods have made agriculturists rely on plant rhizospheric microbiome services, particularly bacteria. Several bacterial resources like Proteobacteria, Firmicutes, Acidobacteria, and Actinomycetes (Streptomycetes) are prominent as bioinoculants or the application of their by-products in alleviating biotic/abiotic stress have been extensively studied, with a dearth in the application of rare Actinomycetes metabolites. Rare Actinomycetes are known for their colossal genome, containing well-preserved genes coding for prolific secondary metabolites with many agroactive functionalities that can revolutionize the agricultural industry. Therefore, the imperativeness of this review to express the occurrence and distributions of rare Actinomycetes diversity, plant and soil-associated habitats, successional track in the rhizosphere under diverse stress, and their agroactive metabolite characteristics and functionalities that can remediate the challenges associated with agricultural productivity.
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Affiliation(s)
- Oghoye Priscilla Oyedoh
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Wei Yang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dharumadurai Dhanasekaran
- Department of Microbiology, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biolόgicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Michoacán, Mexico
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
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Orozco-Mosqueda MDC, Kumar A, Babalola OO, Santoyo G. Rhizobiome Transplantation: A Novel Strategy beyond Single-Strain/Consortium Inoculation for Crop Improvement. Plants (Basel) 2023; 12:3226. [PMID: 37765390 PMCID: PMC10535606 DOI: 10.3390/plants12183226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Yadav P, Singh RP, Alodaini HA, Hatamleh AA, Santoyo G, Kumar A, Gupta RK. Impact of dehydration on the physiochemical properties of Nostoc calcicola BOT1 and its untargeted metabolic profiling through UHPLC-HRMS. Front Plant Sci 2023; 14:1147390. [PMID: 37426961 PMCID: PMC10327440 DOI: 10.3389/fpls.2023.1147390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023]
Abstract
The global population growth has led to a higher demand for food production, necessitating improvements in agricultural productivity. However, abiotic and biotic stresses pose significant challenges, reducing crop yields and impacting economic and social welfare. Drought, in particular, severely constrains agriculture, resulting in unproductive soil, reduced farmland, and jeopardized food security. Recently, the role of cyanobacteria from soil biocrusts in rehabilitating degraded land has gained attention due to their ability to enhance soil fertility and prevent erosion. The present study focused on Nostoc calcicola BOT1, an aquatic, diazotrophic cyanobacterial strain collected from an agricultural field at Banaras Hindu University, Varanasi, India. The aim was to investigate the effects of different dehydration treatments, specifically air drying (AD) and desiccator drying (DD) at various time intervals, on the physicochemical properties of N. calcicola BOT1. The impact of dehydration was assessed by analyzing the photosynthetic efficiency, pigments, biomolecules (carbohydrates, lipids, proteins, osmoprotectants), stress biomarkers, and non-enzymatic antioxidants. Furthermore, an analysis of the metabolic profiles of 96-hour DD and control mats was conducted using UHPLC-HRMS. Notably, there was a significant decrease in amino acid levels, while phenolic content, fatty acids, and lipids increased. These changes in metabolic activity during dehydration highlighted the presence of metabolite pools that contribute to the physiological and biochemical adjustments of N. calcicola BOT1, mitigating the impact of dehydration to some extent. Overall, present study demonstrated the accumulation of biochemical and non-enzymatic antioxidants in dehydrated mats, which could be utilized to stabilize unfavorable environmental conditions. Additionally, the strain N. calcicola BOT1 holds promise as a biofertilizer for semi-arid regions.
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Affiliation(s)
- Priya Yadav
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rahul Prasad Singh
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | | | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Ajay Kumar
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rajan Kumar Gupta
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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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. Curr Res Microb Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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11
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Sruthy KS, Shukla L, Kundu A, Singh SK, Abdulrahman Alodaini H, Hatamleh AA, Santoyo G, Kumar A. Effect of Microbial Consortium Constructed with Lignolytic Ascomycetes Fungi on Degradation of Rice Stubble. J Fungi (Basel) 2023; 9:jof9050567. [PMID: 37233278 DOI: 10.3390/jof9050567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/27/2023] Open
Abstract
Microbial degradation is an effective, eco-friendly and sustainable approach for management of the rice residue. After harvesting a rice crop, removal of stubble from the ground is a challenging task, that forces the farmers to burn the residue in-situ. Therefore, accelerated degradation using an eco-friendly alternative is a necessity. White rot fungi are the most explored group of microbes for accelerated degradation of lignin but they are very slow in growth. The present investigation focuses on degradation of rice stubble using a fungal consortium constructed with highly sporulating ascomycetes fungi, namely, Aspergillus terreus, Aspergillus fumigatus and Alternaria spp. All three species were successful at colonizing the rice stubble. Periodical HPLC analysis of rice stubble alkali extracts revealed that incubation with ligninolytic consortium released various lignin degradation products such as vanillin, vanillic acid, coniferyl alcohol, syringic acid and ferulic acid. The efficiency of the consortium was further studied at different dosages on paddy straw. Maximum lignin degradation was observed when the consortium was applied at 15% volume by weight of rice stubble. Maximum activity of different lignolytic enzymes such as lignin peroxidase, laccase and total phenols was also found with the same treatment. FTIR analysis also supported the observed results. Hence, the presently developed consortium for degrading rice stubble was found to be effective in both laboratory and field conditions. The developed consortium or its oxidative enzymes can be used alone or combined with other commercial cellulolytic consortia to manage the accumulating rice stubble effectively.
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Affiliation(s)
- Kallinkal Sobha Sruthy
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Livleen Shukla
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Aditi Kundu
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sandeep Kumar Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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).
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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
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13
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Kumar A, Santoyo G, White JF, Mishra VK. Special Issue “Microbial Endophytes: Functional Biology and Applications”: Editorial. Microorganisms 2023; 11:microorganisms11040918. [PMID: 37110341 PMCID: PMC10145780 DOI: 10.3390/microorganisms11040918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/12/2023] [Indexed: 04/05/2023] Open
Abstract
Plants harbour various microbial communities, including bacteria, fungi, actinomycetes, and nematodes, inside or outside their tissues [...]
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Affiliation(s)
- Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - James F. White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Virendra Kumar Mishra
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi 221005, India
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Fadiji AE, Yadav AN, Santoyo G, Babalola OO. Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview. Microbiol Res 2023; 271:127368. [PMID: 36965460 DOI: 10.1016/j.micres.2023.127368] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/07/2023] [Accepted: 03/19/2023] [Indexed: 03/27/2023]
Abstract
Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth and development. Abiotic stressors like drought and excessive heat are expected to occur more frequently in the future due to climate change, which would reduce the yields of important crops like maize, wheat, and rice which may jeopardize the food security of human populations. The plant microbiomes are a varied and taxonomically organized microbial community that is connected to plants. By supplying nutrients and water to plants, and regulating their physiology and metabolism, plant microbiota frequently helps plants develop and tolerate abiotic stresses, which can boost crop yield under abiotic stresses. In this present study, with emphasis on temperature, salt, and drought stress, we describe current findings on how abiotic stresses impact the plants, microbiomes, microbe-microbe interactions, and plant-microbe interactions as the way microorganisms affect the metabolism and physiology of the plant. We also explore crucial measures that must be taken in applying plant microbiomes in agriculture practices faced with abiotic stresses.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
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15
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Rojas-Solis D, Vences-Guzmán MÁ, Sohlenkamp C, Santoyo G. Cardiolipin synthesis in Pseudomonas fluorescens UM270 plays a relevant role in stimulating plant growth under salt stress. Microbiol Res 2023; 268:127295. [PMID: 36587534 DOI: 10.1016/j.micres.2022.127295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Membrane cardiolipin (CL) phospholipids play a fundamental role in the adaptation of bacteria to various environmental conditions, including saline stress. Here, we constructed deletion mutants of two CL synthetase genes, clsA (UM270 ∆clsA) and clsB (UM270 ∆clsB), in the rhizobacterium Pseudomonas fluorescens UM270, and evaluated their role in plant growth promotion under salt stress. UM270 ∆clsA and UM270 ∆clsB mutants showed a significant reduction in CL synthesis compared to the P. fluorescens UM270 wild-type (UM270 wt) strain (58% ∆clsA and 53% ∆clsB), and their growth rate was not affected, except when grown at 100 and 200 mM NaCl. Additionally, the root colonization capacity of both mutant strains was impaired compared with that of the wild type. Concomitant with the deletion of clsA and clsB genes, some physiological changes were observed in the UM270 ∆clsA and UM270 ∆clsB mutants, such as a reduction in indole acetic acid and biofilm production. By contrast, an increase in siderophore biosynthesis was observed. Further, inoculation of the UM270 wt strain in tomato plants (Solanum lycopersicum) grown under salt stress conditions (100 and 200 mM NaCl) resulted in an increase in root and shoot length, chlorophyll content, and dry weight. On the contrary, when each of the mutants were inoculated in tomato plants, a reduction in root length was observed when grown at 200 mM NaCl, but the shoot length, chlorophyll content, and total plant dry weight parameters were significantly reduced under normal or saline conditions (100 and 200 mM NaCl), compared to UM270 wt-inoculated plants. In conclusion, these results suggest that CL synthesis in P. fluorescens UM270 plays an important role in the promotion of tomato plant growth under normal conditions, but to a greater extent, under salt-stress conditions.
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Affiliation(s)
- Daniel Rojas-Solis
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | | | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico.
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16
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Orozco-Mosqueda MDC, Kumar A, Fadiji AE, Babalola OO, Puopolo G, Santoyo G. Agroecological Management of the Grey Mould Fungus Botrytis cinerea by Plant Growth-Promoting Bacteria. Plants (Basel) 2023; 12:637. [PMID: 36771719 PMCID: PMC9919678 DOI: 10.3390/plants12030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/21/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Botrytis cinerea is the causal agent of grey mould and one of the most important plant pathogens in the world because of the damage it causes to fruits and vegetables. Although the application of botrycides is one of the most common plant protection strategies used in the world, the application of plant-beneficial bacteria might replace botrycides facilitating agroecological production practices. Based on this, we reviewed the different stages of B. cinerea infection in plants and the biocontrol mechanisms exerted by plant-beneficial bacteria, including the well-known plant growth-promoting bacteria (PGPB). Some PGPB mechanisms to control grey mould disease include antibiosis, space occupation, nutrient uptake, ethylene modulation, and the induction of plant defence mechanisms. In addition, recent studies on the action of anti-Botrytis compounds produced by PGPB and how they damage the conidial and mycelial structures of the pathogen are reviewed. Likewise, the advantages of individual inoculations of PGPB versus those that require the joint action of antagonist agents (microbial consortia) are discussed. Finally, it should be emphasised that PGPB are an excellent option to prevent grey mould in different crops and their use should be expanded for environmentally friendly agricultural practices.
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Affiliation(s)
| | - Ajay Kumar
- Centre of Advanced study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Gerardo Puopolo
- Center Agriculture Food Environment (C3A), University of Trento, Via Edmund Mach 1, 38098 San Michele all’Adige, Italy
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mich, Mexico
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17
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Orozco-Mosqueda MDC, Santoyo G, Glick BR. Recent Advances in the Bacterial Phytohormone Modulation of Plant Growth. Plants (Basel) 2023; 12:606. [PMID: 36771689 PMCID: PMC9921776 DOI: 10.3390/plants12030606] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Phytohormones are regulators of plant growth and development, which under different types of stress can play a fundamental role in a plant's adaptation and survival. Some of these phytohormones such as cytokinin, gibberellin, salicylic acid, auxin, and ethylene are also produced by plant growth-promoting bacteria (PGPB). In addition, numerous volatile organic compounds are released by PGPB and, like bacterial phytohormones, modulate plant physiology and genetics. In the present work we review the basic functions of these bacterial phytohormones during their interaction with different plant species. Moreover, we discuss the most recent advances of the beneficial effects on plant growth of the phytohormones produced by PGPB. Finally, we review some aspects of the cross-link between phytohormone production and other plant growth promotion (PGP) mechanisms. This work highlights the most recent advances in the essential functions performed by bacterial phytohormones and their potential application in agricultural production.
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Affiliation(s)
- Ma. del Carmen Orozco-Mosqueda
- Departamento de Ingeniería Bioquímica y Ambiental, Tecnológico Nacional de México/I.T. Celaya, Celaya 38110, Guanajuato, Mexico
| | - Gustavo Santoyo
- Genomic Diversity Laboratory, Institute of Biological and Chemical Research, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Michoacan, Mexico
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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18
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Guzmán-Guzmán P, Kumar A, de los Santos-Villalobos S, Parra-Cota FI, Orozco-Mosqueda MDC, Fadiji AE, Hyder S, Babalola OO, Santoyo G. Trichoderma Species: Our Best Fungal Allies in the Biocontrol of Plant Diseases-A Review. Plants (Basel) 2023; 12:plants12030432. [PMID: 36771517 PMCID: PMC9921048 DOI: 10.3390/plants12030432] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 06/02/2023]
Abstract
Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due to plant pathogens infections and to increase plant food production globally, diminishing the necessity for chemical pesticides and fertilizers and offering a more sustainable and environmentally friendly option. Fungi from the genus Trichoderma are among the most used and studied microorganisms as BCA due to the variety of biocontrol traits, such as parasitism, antibiosis, secondary metabolites (SM) production, and plant defense system induction. Several Trichoderma species are well-known mycoparasites. However, some of those species can antagonize other organisms such as nematodes and plant pests, making this fungus a very versatile BCA. Trichoderma has been used in agriculture as part of innovative bioformulations, either just Trichoderma species or in combination with other plant-beneficial microbes, such as plant growth-promoting bacteria (PGPB). Here, we review the most recent literature regarding the biocontrol studies about six of the most used Trichoderma species, T. atroviride, T. harzianum, T. asperellum, T. virens, T. longibrachiatum, and T. viride, highlighting their biocontrol traits and the use of these fungal genera in Trichoderma-based formulations to control or prevent plant diseases, and their importance as a substitute for chemical pesticides and fertilizers.
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Affiliation(s)
- Paulina Guzmán-Guzmán
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Ajay Kumar
- Department of Postharvest Science, ARO, Volcani Center, Bet Dagan 50250, Israel
| | | | - Fannie I. Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Ciudad Obregón 85000, Mexico
| | | | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Sajjad Hyder
- Department of Botany, Government College Women University Sialkot, Sialkot 51310, Pakistan
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
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19
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Salmeron-Santiago IA, Martínez-Trujillo M, Valdez-Alarcón JJ, Pedraza-Santos ME, Santoyo G, López PA, Larsen J, Pozo MJ, Chávez-Bárcenas AT. Carbohydrate and lipid balances in the positive plant phenotypic response to arbuscular mycorrhiza: increase in sink strength. Physiol Plant 2023; 175:e13857. [PMID: 36648218 DOI: 10.1111/ppl.13857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
The exchange of phosphorus (P) and carbon (C) between plants and arbuscular mycorrhizal fungi (AMF) is a major determinant of their mutualistic symbiosis. We explored the C dynamics in tomato (Solanum lycorpersicum) inoculated or not with Rhizophagus irregularis to study their growth response under different NaH2 PO4 concentrations (Null P, 0 mM; Low P, 0.065 mM; High P, 1.3 mM). The percentage of AMF colonization was similar in plants under Null and Low P, but severely reduced under High P. However, the AMF mass biomarker 16:1ω5 revealed higher fungal accumulation in inoculated roots under Low P, while more AMF spores were produced in the Null P. Under High P, AMF biomass and spores were strongly reduced. Plant growth response to mycorrhiza was negative under Null P, showing reduction in height, biovolume index, and source leaf (SL) area. Under Low P, inoculated plants showed a positive response (e.g., increased SL area), while inoculated plants under High P were similar to non-inoculated plants. AMF promoted the accumulation of soluble sugars in the SL under all fertilization levels, whereas the soluble sugar level decreased in roots under Low P in inoculated plants. Transcriptional upregulation of SlLIN6 and SlSUS1, genes related to carbohydrate metabolism, was observed in inoculated roots under Null P and Low P, respectively. We conclude that P-limiting conditions that increase AMF colonization stimulate plant growth due to an increase in the source and sink strength. Our results suggest that C partitioning and allocation to different catabolic pathways in the host are influenced by AMF performance.
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Affiliation(s)
| | | | - Juan J Valdez-Alarcón
- Centro Multidisciplinario de Estudios en Biotecnología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Martha E Pedraza-Santos
- Facultad de Agrobiología "Presidente Juárez", Universidad Michoacana de San Nicolás de Hidalgo, Uruapan, Mexico
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Pedro A López
- Colegio de Postgraduados-Campus Puebla, San Pedro Cholula, Mexico
| | - John Larsen
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - María J Pozo
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Granada, Spain
| | - Ana T Chávez-Bárcenas
- Facultad de Agrobiología "Presidente Juárez", Universidad Michoacana de San Nicolás de Hidalgo, Uruapan, Mexico
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20
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Kumari M, Qureshi KA, Jaremko M, White J, Singh SK, Sharma VK, Singh KK, Santoyo G, Puopolo G, Kumar A. Deciphering the role of endophytic microbiome in postharvest diseases management of fruits: Opportunity areas in commercial up-scale production. Front Plant Sci 2022; 13:1026575. [PMID: 36466226 PMCID: PMC9716317 DOI: 10.3389/fpls.2022.1026575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
As endophytes are widely distributed in the plant's internal compartments and despite having enormous potential as a biocontrol agent against postharvest diseases of fruits, the fruit-endophyte-pathogen interactions have not been studied detail. Therefore, this review aims to briefly discuss the colonization patterns of endophytes and pathogens in the host tissue, the diversity and distribution patterns of endophytes in the carposphere of fruits, and host-endophyte-pathogen interactions and the molecular mechanism of the endophytic microbiome in postharvest disease management in fruits. Postharvest loss management is one of the major concerns of the current century. It is considered a critical challenge to food security for the rising global population. However, to manage the postharvest loss, still, a large population relies on chemical fungicides, which affect food quality and are hazardous to health and the surrounding environment. However, the scientific community has searched for alternatives for the last two decades. In this context, endophytic microorganisms have emerged as an economical, sustainable, and viable option to manage postharvest pathogens with integral colonization properties and eliciting a defense response against pathogens. This review extensively summarizes recent developments in endophytic interactions with harvested fruits and pathogens-the multiple biocontrol traits of endophytes and colonization and diversity patterns of endophytes. In addition, the upscale commercial production of endophytes for postharvest disease treatment is discussed.
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Affiliation(s)
- Madhuree Kumari
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kamal A. Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (R.S.R.C.), Division of Biological and Environmental Sciences and Engineering (B.E.S.E.), King Abdullah University of Science and Technology (K.A.U.S.T.), Thuwal, Saudi Arabia
| | - James White
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ, United States
| | - Sandeep Kumar Singh
- Division of Microbiology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Vijay Kumar Sharma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Gerardo Puopolo
- Center Agriculture Food Environment, University of Trento, Trentino, TN, Italy
| | - Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
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Fadiji AE, Orozco-Mosqueda MDC, Santos-Villalobos SDL, Santoyo G, Babalola OO. Recent Developments in the Application of Plant Growth-Promoting Drought Adaptive Rhizobacteria for Drought Mitigation. Plants (Basel) 2022; 11:plants11223090. [PMID: 36432820 PMCID: PMC9698351 DOI: 10.3390/plants11223090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 05/21/2023]
Abstract
Drought intensity that has increased as a result of human activity and global warming poses a serious danger to agricultural output. The demand for ecologically friendly solutions to ensure the security of the world's food supply has increased as a result. Plant growth-promoting rhizobacteria (PGPR) treatment may be advantageous in this situation. PGPR guarantees the survival of the plant during a drought through a variety of processes including osmotic adjustments, improved phytohormone synthesis, and antioxidant activity, among others and these mechanisms also promote the plant's development. In addition, new developments in omics technology have improved our understanding of PGPR, which makes it easier to investigate the genes involved in colonizing plant tissue. Therefore, this review addresses the mechanisms of PGPR in drought stress resistance to summarize the most current omics-based and molecular methodologies for exploring the function of drought-responsive genes. The study discusses a detailed mechanistic approach, PGPR-based bioinoculant design, and a potential roadmap for enhancing their efficacy in combating drought stress.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | | | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Correspondence: ; Tel.: +27-18-389-2568
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22
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Chávez-Moctezuma MP, Martínez-Cámara R, Hernández-Salmerón J, Moreno-Hagelsieb G, Santoyo G, Valencia-Cantero E. Comparative genomic and functional analysis of Arthrobacter sp. UMCV2 reveals the presence of luxR-related genes inducible by the biocompound N, N-dimethylhexadecilamine. Front Microbiol 2022; 13:1040932. [PMID: 36386619 PMCID: PMC9659744 DOI: 10.3389/fmicb.2022.1040932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/10/2022] [Indexed: 09/29/2023] Open
Abstract
Quorum sensing (QS) is a bacterial cell-cell communication system with genetically regulated mechanisms dependent on cell density. Canonical QS systems in gram-negative bacteria possess an autoinducer synthase (LuxI family) and a transcriptional regulator (LuxR family) that respond to an autoinducer molecule. In Gram-positive bacteria, the LuxR transcriptional regulators "solo" (not associated with a LuxI homolog) may play key roles in intracellular communication. Arthrobacter sp. UMCV2 is an actinobacterium that promotes plant growth by emitting the volatile organic compound N, N-dimethylhexadecylamine (DMHDA). This compound induces iron deficiency, defense responses in plants, and swarming motility in Arthrobacter sp. UMCV2. In this study, the draft genome of this bacterium was assembled and compared with the genomes of type strains of the Arthrobacter genus, finding that it does not belong to any previously described species. Genome explorations also revealed the presence of 16 luxR-related genes, but no luxI homologs were discovered. Eleven of these sequences possess the LuxR characteristic DNA-binding domain with a helix-turn-helix motif and were designated as auto-inducer-related regulators (AirR). Four sequences possessed LuxR analogous domains and were designated as auto-inducer analogous regulators (AiaR). When swarming motility was induced with DMHDA, eight airR genes and two aiaR genes were upregulated. These results indicate that the expression of multiple luxR-related genes is induced in actinobacteria, such as Arthrobacter sp. UMCV2, by the action of the bacterial biocompound DMHDA when QS behavior is produced.
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Affiliation(s)
| | - Ramiro Martínez-Cámara
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
- Tecnológico Nacional de México, Morelia, Michoacán, Mexico
| | | | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Eduardo Valencia-Cantero
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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Afridi MS, Javed MA, Ali S, De Medeiros FHV, Ali B, Salam A, Sumaira, Marc RA, Alkhalifah DHM, Selim S, Santoyo G. New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions. Front Plant Sci 2022; 13:899464. [PMID: 36186071 PMCID: PMC9524194 DOI: 10.3389/fpls.2022.899464] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 07/30/2023]
Abstract
Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.
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Affiliation(s)
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), São Paulo, Brazil
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sumaira
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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Flores A, Valencia-Marín MF, Chávez-Avila S, Ramírez-Díaz MI, de los Santos-Villalobos S, Meza-Carmen V, del Carmen Orozco-Mosqueda M, Santoyo G. Genome mining, phylogenetic, and functional analysis of arsenic (As) resistance operons in Bacillus strains, isolated from As-rich hot spring microbial mats. Microbiol Res 2022; 264:127158. [DOI: 10.1016/j.micres.2022.127158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 01/16/2023]
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Fadiji AE, Santoyo G, Yadav AN, Babalola OO. Efforts towards overcoming drought stress in crops: Revisiting the mechanisms employed by plant growth-promoting bacteria. Front Microbiol 2022; 13:962427. [PMID: 35966701 PMCID: PMC9372271 DOI: 10.3389/fmicb.2022.962427] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Globally, agriculture is under a lot of pressure due to rising population and corresponding increases in food demand. However, several variables, including improper mechanization, limited arable land, and the presence of several biotic and abiotic pressures, continually impact agricultural productivity. Drought is a notable destructive abiotic stress and may be the most serious challenge confronting sustainable agriculture, resulting in a significant crop output deficiency. Numerous morphological and physiological changes occur in plants as a result of drought stress. Hence, there is a need to create mitigation techniques since these changes might permanently harm the plant. Current methods used to reduce the effects of drought stress include the use of film farming, super-absorbent hydrogels, nanoparticles, biochar, and drought-resistant plant cultivars. However, most of these activities are money and labor-intensive, which offer limited plant improvement. The use of plant-growth-promoting bacteria (PGPB) has proven to be a preferred method that offers several indirect and direct advantages in drought mitigation. PGPB are critical biological elements which have favorable impacts on plants’ biochemical and physiological features, leading to improved sugar production, relative water content, leaf number, ascorbic acid levels, and photosynthetic pigment quantities. This present review revisited the impacts of PGPB in ameliorating the detrimental effects of drought stress on plants, explored the mechanism of action employed, as well as the major challenges encountered in their application for plant growth and development.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Eternal University, Baru Sahib, India
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- *Correspondence: Olubukola Oluranti Babalola,
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26
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Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
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Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
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Srivastava AK, Kashyap PL, Santoyo G, Newcombe G. Editorial: Plant Microbiome: Interactions, Mechanisms of Action, and Applications, Volume II. Front Microbiol 2022; 13:915684. [PMID: 35711786 PMCID: PMC9195422 DOI: 10.3389/fmicb.2022.915684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Alok Kumar Srivastava
- National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research (ICAR), Mau, India
| | - Prem Lal Kashyap
- Indian Institute of Wheat and Barley Research, Indian Council of Agricultural Research (ICAR), Karnal, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - George Newcombe
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, ID, United States
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Martínez BCS, Benavides LM, Santoyo G, Sánchez-Yáñez JM. Biorecovery of Agricultural Soil Impacted by Waste Motor Oil with Phaseolus vulgaris and Xanthobacter autotrophicus. Plants (Basel) 2022; 11:1419. [PMID: 35684191 PMCID: PMC9182674 DOI: 10.3390/plants11111419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/30/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Agricultural soil contamination by waste motor oil (WMO) is a worldwide environmental problem. The phytotoxicity of WMO hydrocarbons limits agricultural production; therefore, Mexican standard NOM-138-SEMARNAT/SSA1-2012 (NOM-138) establishes a maximum permissible limit of 4400 ppm for hydrocarbons in soil. The objectives of this study are to (a) biostimulate, (b) bioaugment, and (c) phytoremediate soil impacted by 60,000 ppm of WMO, to decrease it to a concentration lower than the maximum allowed by NOM-138. Soil contaminated with WMO was biostimulated, bioaugmented, and phytoremediated, and the response variables were WMO concentration, germination, phenology, and biomass of Phaseolus vulgaris. The experimental data were validated by Tukey HSD ANOVA. The maximum decrease in WMO was recorded in the soil biostimulated, bioaugmented, and phytoremediated by P. vulgaris from 60,000 ppm to 190 ppm, which was considerably lower than the maximum allowable limit of 4400 ppm of NOM-138 after five months. Biostimulation of WMO-impacted soil by detergent, mineral solution and bioaugmentation with Xanthobacter autotrophicus accelerated the reduction in WMO concentration, which allowed phytoremediation with P. vulgaris to oxidize aromatic hydrocarbons and recover WMO-impacted agricultural soil faster than other bioremediation strategies.
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29
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Amezquita Aviles CF, Coronel Acosta CB, De los Santos Villalobos S, Santoyo G, PARRA COTA FANNIEISELA. Characterization of native plant growth-promoting bacteria (PGPB) and their effect on the development of maize (Zea Mays L.). BIOTECNIA 2022. [DOI: 10.18633/biotecnia.v24i1.1353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Maize (Zea mays L.) is one of the most important cereals for Mexico and humanity. The Yaqui Valley -located in the northwest of Mexico- is one of the most important agricultural regions worldwide, it is characterized by an indiscriminate use of inorganic fertilizers for improving crop yields, leading to an increased environmental and economic cost of maize production. Here, a morphological, metabolic, and molecular characterization of native bacteria associated with maize rhizosphere was carried out, and then positive effects of bacterial inoculation to plants under greenhouse conditions were evaluated. The evaluated strains were taxonomically affiliated –based on the 16S rRNA gene- as Bacillus sp. (13B41), Advenella incenata (22A67), Pantoea dispersa (22B45), and Rhizobium pusense (31B11). All of these strains were able to synthesize indoles, produce siderophores, and solubilize phosphates. The individual inoculation of these strains to maize plants showed a significant increment (compared to un-inoculated plants) in height (35-40 %), shoot dry weight (244-289 %), root dry weight (99-137 %), and SPAD values (40- 47 %). The native bacteria associated with maize in the Yaqui Valley are a promising alternative to promote the growth of their host plant, and contribute to a sustainable maize production.
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30
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Chaparro-Encinas LA, Parra-Cota FI, Cruz-Mendívil A, Santoyo G, Peña-Cabriales JJ, Castro-Espinoza L, de Los Santos-Villalobos S. Transcriptional regulation of cell growth and reprogramming of systemic response in wheat (Triticum turgidum subsp. durum) seedlings by Bacillus paralicheniformis TRQ65. Planta 2022; 255:56. [PMID: 35106645 DOI: 10.1007/s00425-022-03837-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Bacillus paralicheniformis TRQ65 reprograms the gene expression patterns associated with systemic response to potentially facilitate its colonization and stimulate cell growth and plant biomass. Plant growth-promoting rhizobacteria (PGPR) carry out numerous mechanisms that enhance growth in seedlings, such as nutrient solubilization, phytohormone production, biocontrol activity, and regulation of induced systemic resistance (ISR) and acquired systemic resistance (ASR). Bacillus paralicheniformis TRQ65 is a biological and plant growth-promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere. In this study, we performed a transcriptomic analysis of wheat seedlings inoculated with the native rhizobacterium Bacillus paralicheniformis TRQ65 (1 × 107 cells∙g -1 of soil) at early development stages (GS15). A morphometrical assay was carried out to confirm growth promotion and after the cultivation period, TRQ65 was re-isolated to define inoculum persistence. Inoculated seedlings showed a significant (P < 0.05) increase in shoot length (93.48%) and dry weight in both shoot (117.02%) and root (48.33%) tissues; also, the strain persisted in the soil at 1.4 × 107 UFC∙g-1 of soil. A total of 228 differentially expressed genes (DEGs) (FDR < 0.05 and |log2 fold change|≥ 1.3) were observed in response to TRQ65 inoculation, of which 185 were down-regulated and 43 were up-regulated. The transcriptional patterns were characterized by the regulation of multidimensional cell growth (ROS, Ca+2 channel, and NADPH oxidases activity), suppression of defense mechanism (PR proteins, PDFs, ROS, transcription factors), induction of central stimuli receptors (RALF, WAK, MAPK), carbohydrate metabolism (invertase activity) and phytohormone-related transport (ABCG transporter and AAAP). These results suggest that B. paralicheniformis TRQ65 is a promising bioinoculant agent for increasing wheat growth and development by reprogramming ISR and ASR simultaneously, suppressing defense mechanisms and inducing central stimuli response.
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Affiliation(s)
- Luis A Chaparro-Encinas
- Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, México
- Universidad Autónoma Agraria Antonio Narro (UAAAN) Unidad Laguna, Periférico Raúl López Sánchez, Valle Verde, 27054, Torreón, Coahuila, México
| | - Fannie I Parra-Cota
- Campo Experimental Norman E. Borlaug-CIRNO. Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Norman E. Borlaug Km. 12, CP 85000, Valle del Yaqui, Ciudad Obregón, Sonora, México
| | - Abraham Cruz-Mendívil
- Cátedras CONACYT, Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación Para el Desarrollo Integral Regional (CIIDIR) Unidad Sinaloa, Guasave, Sinaloa, México
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Juan J Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Campus Guanajuato, Irapuato Guanajuato, México
| | - Luciano Castro-Espinoza
- Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, México
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Fadiji AE, Babalola OO, Santoyo G, Perazzolli M. The Potential Role of Microbial Biostimulants in the Amelioration of Climate Change-Associated Abiotic Stresses on Crops. Front Microbiol 2022; 12:829099. [PMID: 35095828 PMCID: PMC8795815 DOI: 10.3389/fmicb.2021.829099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/29/2021] [Indexed: 02/05/2023] Open
Abstract
Crop plants are more often exposed to abiotic stresses in the current age of fast-evolving climate change. This includes exposure to extreme and unpredictable changes in climatic conditions, phytosanitary hazards, and cultivation conditions, which results in drastic losses in worldwide agricultural productions. Plants coexist with microbial symbionts, some of which play key roles in the ecosystem and plant processes. The application of microbial biostimulants, which take advantage of symbiotic relationships, is a long-term strategy for improving plant productivity and performance, even in the face of climate change-associated stresses. Beneficial filamentous fungi, yeasts, and bacteria are examples of microbial biostimulants, which can boost the growth, yield, nutrition and stress tolerance in plants. This paper highlights recent information about the role of microbial biostimulants and their potential application in mitigating the abiotic stresses occurring on crop plants due to climate change. A critical evaluation for their efficient use under diverse climatic conditions is also made. Currently, accessible products generally improve cultural conditions, but their action mechanisms are mostly unknown, and their benefits are frequently inconsistent. Thus, further studies that could lead to the more precisely targeted products are discussed.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Michele Perazzolli
- Center Agriculture Food Environment (C3A), University of Trento, San Michele all’Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
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Jiménez-Mejía R, Medina-Estrada RI, Carballar-Hernández S, Orozco-Mosqueda MDC, Santoyo G, Loeza-Lara PD. Teamwork to Survive in Hostile Soils: Use of Plant Growth-Promoting Bacteria to Ameliorate Soil Salinity Stress in Crops. Microorganisms 2022; 10:150. [PMID: 35056599 PMCID: PMC8781547 DOI: 10.3390/microorganisms10010150] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/30/2022] Open
Abstract
Plants and their microbiomes, including plant growth-promoting bacteria (PGPB), can work as a team to reduce the adverse effects of different types of stress, including drought, heat, cold, and heavy metals stresses, as well as salinity in soils. These abiotic stresses are reviewed here, with an emphasis on salinity and its negative consequences on crops, due to their wide presence in cultivable soils around the world. Likewise, the factors that stimulate the salinity of soils and their impact on microbial diversity and plant physiology were also analyzed. In addition, the saline soils that exist in Mexico were analyzed as a case study. We also made some proposals for a more extensive use of bacterial bioinoculants in agriculture, particularly in developing countries. Finally, PGPB are highly relevant and extremely helpful in counteracting the toxic effects of soil salinity and improving crop growth and production; therefore, their use should be intensively promoted.
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Affiliation(s)
- Rafael Jiménez-Mejía
- Licenciatura en Genómica Alimentaria, Universidad de La Ciénega del Estado de Michoacán de Ocampo (UCEMICH), Sahuayo 59103, Mexico; (R.J.-M.); (R.I.M.-E.); (S.C.-H.)
| | - Ricardo I. Medina-Estrada
- Licenciatura en Genómica Alimentaria, Universidad de La Ciénega del Estado de Michoacán de Ocampo (UCEMICH), Sahuayo 59103, Mexico; (R.J.-M.); (R.I.M.-E.); (S.C.-H.)
| | - Santos Carballar-Hernández
- Licenciatura en Genómica Alimentaria, Universidad de La Ciénega del Estado de Michoacán de Ocampo (UCEMICH), Sahuayo 59103, Mexico; (R.J.-M.); (R.I.M.-E.); (S.C.-H.)
| | - Ma. del Carmen Orozco-Mosqueda
- Facultad de Agrobiología “Presidente Juárez”, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Uruapan 60170, Mexico;
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia 58030, Mexico;
| | - Pedro D. Loeza-Lara
- Licenciatura en Genómica Alimentaria, Universidad de La Ciénega del Estado de Michoacán de Ocampo (UCEMICH), Sahuayo 59103, Mexico; (R.J.-M.); (R.I.M.-E.); (S.C.-H.)
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Salmeron-Santiago IA, Martínez-Trujillo M, Valdez-Alarcón JJ, Pedraza-Santos ME, Santoyo G, Pozo MJ, Chávez-Bárcenas AT. An Updated Review on the Modulation of Carbon Partitioning and Allocation in Arbuscular Mycorrhizal Plants. Microorganisms 2021; 10:75. [PMID: 35056524 PMCID: PMC8781679 DOI: 10.3390/microorganisms10010075] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/29/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that supply mineral nutrients to the host plant in exchange for carbon derived from photosynthesis. Sucrose is the end-product of photosynthesis and the main compound used by plants to translocate photosynthates to non-photosynthetic tissues. AMF alter carbon distribution in plants by modifying the expression and activity of key enzymes of sucrose biosynthesis, transport, and/or catabolism. Since sucrose is essential for the maintenance of all metabolic and physiological processes, the modifications addressed by AMF can significantly affect plant development and stress responses. AMF also modulate plant lipid biosynthesis to acquire storage reserves, generate biomass, and fulfill its life cycle. In this review we address the most relevant aspects of the influence of AMF on sucrose and lipid metabolism in plants, including its effects on sucrose biosynthesis both in photosynthetic and heterotrophic tissues, and the influence of sucrose on lipid biosynthesis in the context of the symbiosis. We present a hypothetical model of carbon partitioning between plants and AMF in which the coordinated action of sucrose biosynthesis, transport, and catabolism plays a role in the generation of hexose gradients to supply carbon to AMF, and to control the amount of carbon assigned to the fungus.
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Affiliation(s)
| | | | - Juan J. Valdez-Alarcón
- Centro Multidisciplinario de Estudios en Biotecnología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58880, Mexico;
| | - Martha E. Pedraza-Santos
- Facultad de Agrobiología “Presidente Juárez”, Universidad Michoacana de San Nicolás de Hidalgo, Uruapan 60170, Mexico;
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico;
| | - María J. Pozo
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Ana T. Chávez-Bárcenas
- Facultad de Agrobiología “Presidente Juárez”, Universidad Michoacana de San Nicolás de Hidalgo, Uruapan 60170, Mexico;
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Chaparro-Encinas LA, Santoyo G, Peña-Cabriales JJ, Castro-Espinoza L, Parra-Cota FI, Santos-Villalobos SDL. Transcriptional Regulation of Metabolic and Cellular Processes in Durum Wheat (Triticum turgidum subsp. durum) in the Face of Temperature Increasing. Plants 2021; 10:plants10122792. [PMID: 34961263 PMCID: PMC8703274 DOI: 10.3390/plants10122792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 01/21/2023]
Abstract
The Yaqui Valley, Mexico, has been historically considered as an experimental field for semiarid regions worldwide since temperature is an important constraint affecting durum wheat cultivation. Here, we studied the transcriptional and morphometrical response of durum wheat at an increased temperature (+2 °C) for deciphering molecular mechanisms involved in the thermal adaptation by this crop. The morphometrical assay showed a significant decrease in almost all the evaluated traits (shoot/root length, biovolume index, and dry/shoot weight) except in the dry root weight and the root:shoot ratio. At the transcriptional level, 283 differentially expressed genes (DEGs) were obtained (False Discovery Rate (FDR) ≤ 0.05 and |log2 fold change| ≥ 1.3). From these, functional annotation with MapMan4 and a gene ontology (GO) enrichment analysis with GOSeq were carried out to obtain 27 GO terms significantly enriched (overrepresented FDR ≤ 0.05). Overrepresented and functionally annotated genes belonged to ontologies associated with photosynthetic acclimation, respiration, changes in carbon balance, lipid biosynthesis, the regulation of reactive oxygen species, and the acceleration of physiological progression. These findings are the first insight into the regulation of the mechanism influenced by a temperature increase in durum wheat.
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Affiliation(s)
- Luis Abraham Chaparro-Encinas
- Instituto Tecnológico de Sonora, 5 de Febrero 818 Sur, Ciudad Obregón 85000, Sonora, Mexico; (L.A.C.-E.); (L.C.-E.)
- Departamento de Fitomejoramiento, Universidad Autónoma Agraria Antonio Narro (UAAAN) Unidad Laguna, Periférico Raúl López Sánchez, Valle Verde, Torreón 27054, Coahuila, Mexico
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58000, Michoacán, Mexico;
| | - Juan José Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Libramiento Norte Carretera Irapuato León Kilómetro 9.6, Carr Panamericana Irapuato León, Irapuato 36821, Guanajuato, Mexico;
| | - Luciano Castro-Espinoza
- Instituto Tecnológico de Sonora, 5 de Febrero 818 Sur, Ciudad Obregón 85000, Sonora, Mexico; (L.A.C.-E.); (L.C.-E.)
| | - Fannie Isela Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Norman E. Borlaug Km. 12, Valle del Yaqui, Ciudad Obregón 85000, Sonora, Mexico
- Correspondence: (F.I.P.-C.); (S.d.l.S.-V.); Tel.: +52-(644)-410-0900 (ext. 2124) (S.d.l.S.-V.)
| | - Sergio de los Santos-Villalobos
- Instituto Tecnológico de Sonora, 5 de Febrero 818 Sur, Ciudad Obregón 85000, Sonora, Mexico; (L.A.C.-E.); (L.C.-E.)
- Correspondence: (F.I.P.-C.); (S.d.l.S.-V.); Tel.: +52-(644)-410-0900 (ext. 2124) (S.d.l.S.-V.)
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Abstract
Plant-microbiome interaction occurs at the rhizosphere, endosphere, and phyllosphere. Root exudates can favor the recruitment of a beneficial microbiome in the rhizosphere. Plant topology and phytochemistry influence the recruitment of the phyllosphere microbiome. Diverse plant strategies selectively recruit beneficial microbiomes. Multiple plant mechanisms displace potential pathogens from the rhizosphere. The beneficial microbiome helps plants to recruit other beneficial microbiota.
Background Research on beneficial mechanisms by plant-associated microbiomes, such as plant growth stimulation and protection from plant pathogens, has gained considerable attention over the past decades; however, the mechanisms used by plants to recruit their microbiome is largely unknown. Aim of Review Here, we review the latest studies that have begun to reveal plant strategies in selectively recruiting beneficial microbiomes, and how they manage to exclude potential pathogens. Key Scientific concepts of Review: We examine how plants attract beneficial microbiota from the main areas of interaction, such as the rhizosphere, endosphere, and phyllosphere, and demonstrate that such process occurs by producing root exudates, and recognizing molecules produced by the beneficial microbiota or distinguishing pathogens using specific receptors, or by triggering signals that support plant-microbiome homeostasis. Second, we analyzed the main environmental or biotic factors that modulate the structure and successional dynamics of microbial communities. Finally, we review how the associated microbiome is capable of engaging with other synergistic microbes, hence providing an additional element of selection. Collectively, this study reveals the importance of understanding the complex network of plant interactions, which will improve the understanding of bioinoculant application in agriculture, based on a microbiome that interacts efficiently with plant organs under different environmental conditions.
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Affiliation(s)
- Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico.
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Hernández-Pacheco CE, Orozco-Mosqueda MDC, Flores A, Valencia-Cantero E, Santoyo G. Tissue-specific diversity of bacterial endophytes in Mexican husk tomato plants ( Physalis ixocarpa Brot. ex Horm.), and screening for their multiple plant growth-promoting activities. Curr Res Microb Sci 2021; 2:100028. [PMID: 34841319 PMCID: PMC8610326 DOI: 10.1016/j.crmicr.2021.100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022] Open
Abstract
Endophytic bacterial diversity of root, stem, and leaf tissues of Physalis ixocarpa was deciphered. Unique and shared species were found for each plant compartment analyzed. Extensive screening of various isolates exhibited antagonism against fungal pathogens. Diverse endophytes stimulated the growth of Physalis ixocarpa seedlings. Neobacillus drentensis CH23 stood out as an excellent plant growth-promoting bacterium.
The endophytic bacterial diversity of root, stem, and leaf tissues of Mexican husk tomato plants (Physalis ixocarpa) was compared and deciphered, and screened for their plant growth-promoting activity and antagonism against fungal phytopathogens. Total 315 isolates (108 roots, 102 stems, and 105 leaves) were obtained and characterized by 16S ribosomal gene sequencing. The most abundant genera were Bacillus, Microbacterium, Pseudomonas, and Stenotrophomonas. Unique species were found for each tissue analyzed, along with B. thuringiensis, B. toyonensis, Neobacillus drentensis, Paenibacillus castaneae, P. fluorescens, P. poae, and S. maltophilia present throughout the plant. Biodiversity indices did not show significant differences, but root tissues showed the highest abundance of bacterial endophytes. Several isolates showed excellent promotion activities in Physalis ixocarpa seedlings, increasing the length and weight of the root, total biomass, and chlorophyll content. Various isolates also exhibited antagonism against fungal pathogens. Among screened isolates, Neobacillus drentensis CH23 was found in all plant compartments, exhibiting growth-promoting activity and fungal antagonism. Strain CH23 and other endophytes showed the production of indoleacetic acid, siderophores, proteases, and solubilization of phosphates. These results demonstrate that the husk tomato plant endobiome has a high potential as a bioinoculating agent for agriculturally important crops.
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Affiliation(s)
- Claudia E Hernández-Pacheco
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico
| | - Ma Del Carmen Orozco-Mosqueda
- Facultad de Agrobiología "Presidente Juárez", Universidad Michoacana de San Nicolás de Hidalgo, Uruapan, Michoacán, Mexico
| | - Aurora Flores
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico
| | - Eduardo Valencia-Cantero
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico
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Morales-Cedeño LR, de Los Santos-Villalobos S, Santoyo G. Functional and Genomic Analysis of Rouxiella badensis SER3 as a Novel Biocontrol Agent of Fungal Pathogens. Front Microbiol 2021; 12:709855. [PMID: 34421868 PMCID: PMC8375033 DOI: 10.3389/fmicb.2021.709855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
In recent decades, various bacterial species have been characterized as biocontrol agents for plant crop diseases; however, only a few genera have been predominantly reported in the literature. Therefore, the identification of new antagonists against phytopathogens is essential for boosting sustainable food production systems. In this study, we evaluated the role of strain SER3 from the recently discovered Rouxiella badensis as a biocontrol agent. SER3 was isolated from the phyllosphere of decaying strawberry fruit (Fragaria × ananassa) and showed different grades of antagonism against 20 fungal pathogens of berries, based on confrontation assays, due to the action of its diffusible and volatile compounds. These fungal pathogens were isolated from decayed strawberry, blackberry, and blueberry fruit and were characterized through internal transcribed spacer (ITS) sequencing and homology searches, exhibiting similarity with well-known postharvest pathogens such as Botrytis, Fusarium, Geotrichum, Mucor, Penicillium, Alternaria, and Botryosphaeria. Koch’s postulates were confirmed for most pathogens by reinfecting berry fruit. SER3 showed good capacity to inhibit the growth of Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development. To gain better understanding of the genetic and metabolic capacities of the SER3 strain, its draft genome was determined and was found to comprise a single chromosome of 5.08 Mb, 52.8% G + C content, and 4,545 protein-coding genes. Phylogenetic analysis indicated that the SER3 strain is affiliated with the R. badensis species, with an average nucleotide identity >96% and a genome-to-genome distance >70%. A comparison of the genomic properties of R. badensis SER3 and other close bacterial relatives showed several genes with potential functions in biocontrol activities, such as those encoding siderophores, non-ribosomal peptide synthetases, and polyketide synthases. This is the first study to demonstrate a novel role of the recently discovered R. badensis species (and any other species of the genus Rouxiella) as a biocontrol agent against postharvest fungal pathogens.
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Affiliation(s)
- Luzmaria R Morales-Cedeño
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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Hurtado-Bautista E, Pérez Sánchez LF, Islas-Robles A, Santoyo G, Olmedo-Alvarez G. Phenotypic plasticity and evolution of thermal tolerance in bacteria from temperate and hot spring environments. PeerJ 2021; 9:e11734. [PMID: 34386300 PMCID: PMC8312496 DOI: 10.7717/peerj.11734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 06/16/2021] [Indexed: 01/02/2023] Open
Abstract
Phenotypic plasticity allows individuals to respond to the selective forces of a new environment, followed by adaptive evolution. We do not know to what extent phenotypic plasticity allows thermal tolerance evolution in bacteria at the border of their physiological limits. We analyzed growth and reaction norms to temperature of strains of two bacterial lineages, Bacillus cereus sensu lato and Bacillus subtilis sensu lato, that evolved in two contrasting environments, a temperate lagoon (T) and a hot spring (H). Our results showed that despite the co-occurrence of members of both lineages in the two contrasting environments, norms of reactions to temperature exhibited a similar pattern only in strains within the lineages, suggesting fixed phenotypic plasticity. Additionally, strains from the H environment showed only two to three degrees centigrade more heat tolerance than strains from the T environment. Their viability decreased at temperatures above their optimal for growth, particularly for the B. cereus lineage. However, sporulation occurred at all temperatures, consistent with the known cell population heterogeneity that allows the Bacillus to anticipate adversity. We suggest that these mesophilic strains survive in the hot-spring as spores and complete their life cycle of germination and growth during intermittent opportunities of moderate temperatures. The limited evolutionary changes towards an increase in heat tolerance in bacteria should alert us of the negative impact of climate change on all biological cycles in the planet, which at its most basic level depends on microorganisms.
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Affiliation(s)
- Enrique Hurtado-Bautista
- Departamento de Ingeniería Genética, Unidad Irapuato, de (Centro de Investigación y de Estudios Avanzados) del IPN, Irapuato, Guanajuato, México
| | - Laura F Pérez Sánchez
- Departamento de Ingeniería Genética, Unidad Irapuato, de (Centro de Investigación y de Estudios Avanzados) del IPN, Irapuato, Guanajuato, México
| | - Africa Islas-Robles
- Departamento de Ingeniería Genética, Unidad Irapuato, de (Centro de Investigación y de Estudios Avanzados) del IPN, Irapuato, Guanajuato, México
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Gabriela Olmedo-Alvarez
- Departamento de Ingeniería Genética, Unidad Irapuato, de (Centro de Investigación y de Estudios Avanzados) del IPN, Irapuato, Guanajuato, México
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Srivastava AK, Kashyap PL, Santoyo G, Newcombe G. Editorial: Plant Microbiome: Interactions, Mechanisms of Action, and Applications. Front Microbiol 2021; 12:706049. [PMID: 34290690 PMCID: PMC8287647 DOI: 10.3389/fmicb.2021.706049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Prem Lal Kashyap
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - George Newcombe
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, ID, United States
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Santoyo G, Urtis-Flores CA, Loeza-Lara PD, Orozco-Mosqueda MDC, Glick BR. Rhizosphere Colonization Determinants by Plant Growth-Promoting Rhizobacteria (PGPR). Biology (Basel) 2021; 10:biology10060475. [PMID: 34072072 PMCID: PMC8229920 DOI: 10.3390/biology10060475] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Plant growth-promoting rhizobacteria (PGPR) are an eco-friendly alternative to the use of chemicals in agricultural production and crop protection. However, the efficacy of PGPR as bioinoculants can be diminished by a low capacity to colonize spaces in the rhizosphere. In this work, we review pioneering and recent developments on several important functions that rhizobacteria exhibit in order to compete, colonize, and establish themselves in the plant rhizosphere. Therefore, the use of highly competitive strains in open field trials should be a priority, in order to have consistent and better results in agricultural production activities. Abstract The application of plant growth-promoting rhizobacteria (PGPR) in the field has been hampered by a number of gaps in the knowledge of the mechanisms that improve plant growth, health, and production. These gaps include (i) the ability of PGPR to colonize the rhizosphere of plants and (ii) the ability of bacterial strains to thrive under different environmental conditions. In this review, different strategies of PGPR to colonize the rhizosphere of host plants are summarized and the advantages of having highly competitive strains are discussed. Some mechanisms exhibited by PGPR to colonize the rhizosphere include recognition of chemical signals and nutrients from root exudates, antioxidant activities, biofilm production, bacterial motility, as well as efficient evasion and suppression of the plant immune system. Moreover, many PGPR contain secretion systems and produce antimicrobial compounds, such as antibiotics, volatile organic compounds, and lytic enzymes that enable them to restrict the growth of potentially phytopathogenic microorganisms. Finally, the ability of PGPR to compete and successfully colonize the rhizosphere should be considered in the development and application of bioinoculants.
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Affiliation(s)
- Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico;
- Correspondence:
| | - Carlos Alberto Urtis-Flores
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico;
| | - Pedro Damián Loeza-Lara
- Licenciatura en Genómica Alimentaria, Universidad de La Ciénega del Estado de Michoacán de Ocampo, Sahuayo 59103, Mexico;
| | - Ma. del Carmen Orozco-Mosqueda
- Facultad de Agrobiología “Presidente Juárez”, Universidad Michoacana de San Nicolás de Hidalgo, Melchor Ocampo, Uruapan 60170, Mexico;
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
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Abstract
Soil microbiota plays an important role in the sustainable production of the different types of agrosystems. Among the members of the plant microbiota, mycorrhizal fungi (MF) and plant growth-promoting bacteria (PGPB) interact in rhizospheric environments leading to additive and/or synergistic effects on plant growth and heath. In this manuscript, the main mechanisms used by MF and PGPB to facilitate plant growth are reviewed, including the improvement of nutrient uptake, and the reduction of ethylene levels or biocontrol of potential pathogens, under both normal and stressful conditions due to abiotic or biotic factors. Finally, it is necessary to expand both research and field use of bioinoculants based on these components and take advantage of their beneficial interactions with plants to alleviate plant stress and improve plant growth and production to satisfy the demand for food for an ever-increasing human population.
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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. Front Sustain Food Syst 2021. [DOI: 10.3389/fsufs.2020.614739] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
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Khatoon Z, Huang S, Rafique M, Fakhar A, Kamran MA, Santoyo G. Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems. J Environ Manage 2020; 273:111118. [PMID: 32741760 DOI: 10.1016/j.jenvman.2020.111118] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/13/2020] [Accepted: 07/19/2020] [Indexed: 05/06/2023]
Abstract
The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.
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Affiliation(s)
- Zobia Khatoon
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Key Laboratory of Urban Ecological Environment Rehabilitation and Pollution Control of Tianjin, Numerical Stimulation Group for Water Environment, College of Environmental Science and Engineering Nankai University, Tianjin, 300350, China
| | - Suiliang Huang
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Key Laboratory of Urban Ecological Environment Rehabilitation and Pollution Control of Tianjin, Numerical Stimulation Group for Water Environment, College of Environmental Science and Engineering Nankai University, Tianjin, 300350, China
| | - Mazhar Rafique
- Department of Soil Science, The University of Haripur, 22630, KPK, Pakistan
| | - Ali Fakhar
- Department of Soil Science, Sindh Agricultural University, Tandojam, Pakistan
| | | | - Gustavo Santoyo
- Genomic Diversity Laboratory, Institute of Biological and Chemical Research, Universidad Michoacana de San Nicolas de Hidalgo, 58030, Morelia, Mexico.
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Morales-Cedeño LR, Orozco-Mosqueda MDC, Loeza-Lara PD, Parra-Cota FI, de Los Santos-Villalobos S, Santoyo G. Plant growth-promoting bacterial endophytes as biocontrol agents of pre- and post-harvest diseases: Fundamentals, methods of application and future perspectives. Microbiol Res 2020; 242:126612. [PMID: 33059112 DOI: 10.1016/j.micres.2020.126612] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/23/2020] [Accepted: 09/24/2020] [Indexed: 02/08/2023]
Abstract
Sustainable agriculture requires the recruitment of bacterial agents to control diverse plant diseases such as bacterial endophytes. Bacterial endophytes colonize and inhabit internal plant tissues without causing any apparent damage. Within the plant, these bacteria exert multiple beneficiary effects, including direct stimulation of plant growth by the action of phytohormones or the production of metabolites. However, bacterial endophytes also protect their plant host through biocontrol pathogens or by inducing plant innate immune system. The present work makes a systematic and in-depth review on the current state of endophytic bacterial diversity, their plant colonization strategies, and their potential roles as protective agents against plant diseases during pre- and post-harvest stages of crop productivity. In addition, an exploration of their beneficial effects on sustainable agriculture by reducing/eliminating the use of toxic agrochemicals was conducted. Finally, we propose diverse effective strategies for the application of endophytic bacteria as biological agents during both pre- and post-harvest stages, with the aim of protecting crop plants and their agricultural products.
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Affiliation(s)
- Luzmaria R Morales-Cedeño
- Instituto De Investigaciones Químico-Biológicas, Universidad Michoacana De San Nicolás De Hidalgo, Morelia, Michoacán, Mexico
| | - Ma Del Carmen Orozco-Mosqueda
- Facultad De Agrobiología (··)Presidente Juárez(··), Universidad Michoacana De San Nicolás De Hidalgo, Uruapan, Michoacán, Mexico
| | - Pedro D Loeza-Lara
- Licenciatura en Genómica Alimentaria, Universidad de La Ciénega del Estado de Michoacán de Ocampo, Mexico
| | - Fannie I Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Ciudad Obregón, Sonora, Mexico
| | | | - Gustavo Santoyo
- Instituto De Investigaciones Químico-Biológicas, Universidad Michoacana De San Nicolás De Hidalgo, Morelia, Michoacán, Mexico.
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Rojas-Solis D, Vences-Guzmán MA, Sohlenkamp C, Santoyo G. Bacillus toyonensis COPE52 Modifies Lipid and Fatty Acid Composition, Exhibits Antifungal Activity, and Stimulates Growth of Tomato Plants Under Saline Conditions. Curr Microbiol 2020; 77:2735-2744. [PMID: 32504325 DOI: 10.1007/s00284-020-02069-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/30/2020] [Indexed: 02/07/2023]
Abstract
Salinity is one of the most important factors that limit the productivity of agricultural soils. Certain plant growth-promoting bacteria (PGPB) have the ability to stimulate the growth of crop plants even under salt stress. In the present study, we analysed the potential of PGPB Bacillus toyonensis COPE52 to improve the growth of tomato plants and its capacity to modify its membrane lipid and fatty acid composition under salt stress. Thus, strain COPE52 increased the relative amount of branched chain fatty acids (15:0i and 16:1∆9) and accumulation of an unknown membrane lipid, while phosphatidylethanolamine (PE) levels decreased during growth with 100 and 200 mM NaCl. Importantly, direct and indirect plant growth-promoting (PGP) mechanisms of B. toyonensis COPE52, such as indole-3-acetic acid (IAA), protease activity, biofilm formation, and antifungal activity against Botrytis cinerea, remained unchanged in the presence of NaCl in vitro, compared to controls without salt. In a greenhouse experiment, tomato plants (Lycopersicon esculentum 'Saladette') showed increased shoot and root length, higher dry biomass, and chlorophyll content when inoculated with B. toyonensis COPE52 at 0 and 100 mM NaCl. In summary, these results indicate that Bacillus toyonensis COPE52 can modify cell membrane lipid components as a potential protecting mechanism to maintain PGP traits under saline-soil conditions.
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Affiliation(s)
- Daniel Rojas-Solis
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Miguel A Vences-Guzmán
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México. .,Laboratorio de Diversidad Genómica, Instituto de Investigaciones Químico-Biológicas de la Universidad Michoacana de San Nicolás de Hidalgo, Edificio A1´, Ciudad Universitaria, C.P. 58063, Morelia, Michoacán, México.
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Santoyo G, Hernández-Flores B, Hernández Salmerón J, Rojas Solís D, Contreras-Pérez M, Loaeza-Lara PD, Orozco-Mosqueda MDC. Detección de los genes phlD y hcnC en bacterias antagonistas productoras de sideróforos asociadas a Rubus fruticosus L. NS 2020. [DOI: 10.21640/ns.v12i24.2160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introducción: Las plantas albergan un microbioma que incluye bacterias promotoras del crecimiento vegetal, las cuales pueden fungir como agentes biológicos que antagonizan el crecimiento de fitopatógenos, disminuyendo o eliminando su efectos nocivos en plantas. En este trabajo se evaluó la presencia de los genes antifúngicos phlD y hcnC con la producción de sideróforos (agentes quelantes de Fe) en bacterias aisladas de la endósfera y rizósfera de plantas de zarzamora (Rubus fruticosus L.).Método: Se analizaron 410 aislados bacterianos asociados a plantas de zarzamora (Rubus fruticosus L.), provenientes de la rizósfera (205) y endosfera (205) para la detección de los genes antimicrobianos phlD y hcnC por reacción en cadena de la polimerasa y posterior secuenciación. La búsqueda de los genes se realizó únicamente en cepas productoras de sideróforos, utilizando el medio CAS (Cromo Azurol) para su producción. De las cepas seleccionadas, se realizaron los bioensayos de antagonismo contra los patógenos de plantas Botrytis cinerea, Fusarium oxysporum, F. solani y Rhizoctonia solani.Resultados: Los resultados de este trabajo muestran que, de los 410 aislados bacterianos analizados (50% rizosféricos y 50% endófitos), 70 aislados fueron productores de sideróforos (24 rizosféricas y 46 endófitas). Se observó que el 70% (49/70) de las cepas productoras de sideróforos, presentaron uno o dos de los genes phlD y/o hcnC. Las secuencias nucleotídicas de los genes phlD y/o hcnC mostraron una alta identidad con genes homólogos a las especies Pseudomonas sp., P. fluorescens, P. chlororaphis, P. protegens, P. putida y P. brassicacearum. La abundancia del gen hcnC fue mayor en los aislados endófitos y rizosféricos (36/70), con respecto al gen phlD (13/70). Se detectaron mayoritariamente los genes phlD y/o hcnC en cepas aisladas de la endósfera (43/70), comparado con aquellas cepas rizosféricas (6/70). Finalmente, se observó una alta relación entre la producción de sideróforos, la presencia de genes phlD y/o hcnC y la actividad antagónica hacia los fitopatógenos Botrytis cinerea, Fusarium oxysporum, Fusarium solani y Rhizoctonia solani.Conclusión: Estos resultados muestran el potencial de identificar de forma rápida, eficiente y a bajo costo, mecanismos de antagonismo hacia fitópatógenos en bacterias asociadas a plantas de zarzamora (Rubus fruticosus L.), tales como la producción de sideróforos.
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Flores A, Diaz-Zamora JT, Orozco-Mosqueda MDC, Chávez A, de Los Santos-Villalobos S, Valencia-Cantero E, Santoyo G. Bridging genomics and field research: draft genome sequence of Bacillus thuringiensis CR71, an endophytic bacterium that promotes plant growth and fruit yield in Cucumis sativus L. 3 Biotech 2020; 10:220. [PMID: 32355594 DOI: 10.1007/s13205-020-02209-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/15/2020] [Indexed: 12/16/2022] Open
Abstract
Here we report the draft genome sequence of bacterial strain CR71, consisting of a single chromosome with 5,914,775 base pairs (bp), 34.7% G + C content, and 5733 protein-coding genes. Phylogenetic analysis indicates that the CR71 strain is affiliated with Bacillus thuringiensis species, with an average nucleotide identity > 96% and genome to genome distance > 70%. The genome of B. thuringiensis strain CR71 contains genes potentially involved in a wide variety of both plant pathogen-antagonistic and plant-growth-promoting activities, such as biofilm production; acetoin, butanediol, and indoleacetic acid (IAA) synthesis; production of quorum-sensing molecules; synthesis of toxins and lytic enzymes; and promotion of tolerance to oxidative, metal, and salt stress. Additionally, antiSMASH analysis revealed a potential synthesis of siderophores and peptide antibiotics. To confirm the in silico data, strain CR71 was inoculated into cucumber plants (Cucumis sativus L.) in a field trial, in which we observed an increase in stem thickness, as well as shoot fresh weight and length. Importantly, compared to un-inoculated control plants, plants inoculated with strain CR71 increased the size/weight ratio of cucumber fruits (34.99%), biovolume index (16.8%), and total fruit yield (34.97%). In conclusion, genome analysis of strain CR71 confirmed multifactorial plant-beneficial mechanisms and the potential of CR71 as an agricultural bio-inoculant.
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Affiliation(s)
- Aurora Flores
- 1Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, 58030 Morelia, Michoacán México
| | - J Trinidad Diaz-Zamora
- 2Facultad de Agrobiología "Presidente Juárez", Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Paseo Lázaro Cárdenas S/N Esq. Berlín, Col. Viveros, 60190 Uruapan, Michoacán México
| | - Ma Del Carmen Orozco-Mosqueda
- 2Facultad de Agrobiología "Presidente Juárez", Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Paseo Lázaro Cárdenas S/N Esq. Berlín, Col. Viveros, 60190 Uruapan, Michoacán México
| | - Ana Chávez
- 2Facultad de Agrobiología "Presidente Juárez", Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Paseo Lázaro Cárdenas S/N Esq. Berlín, Col. Viveros, 60190 Uruapan, Michoacán México
| | | | - Eduardo Valencia-Cantero
- 1Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, 58030 Morelia, Michoacán México
| | - Gustavo Santoyo
- 1Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, 58030 Morelia, Michoacán México
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Orozco-Mosqueda MDC, Glick BR, Santoyo G. ACC deaminase in plant growth-promoting bacteria (PGPB): An efficient mechanism to counter salt stress in crops. Microbiol Res 2020; 235:126439. [PMID: 32097862 DOI: 10.1016/j.micres.2020.126439] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/12/2020] [Accepted: 02/15/2020] [Indexed: 11/27/2022]
Abstract
Salinity in agricultural soil is a major problem around the world, with negative consequences for the growth and production of a wide range of crops. To counteract these harmful effects, plants sometimes have bacterial partners that contain the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, which acts by degrading ACC (the precursor of ethylene in all higher plants). The enzymatic activity of ACC deaminase results in the production of α-ketobutyrate and ammonia, which, by lowering ACC levels, prevents excessive increases in the synthesis of ethylene under various stress conditions and is one of the most efficient mechanisms to induce plant tolerance to salt stress. In the present review, recent works on the role of ACC deaminase are discussed alongside its importance in promoting plant growth under conditions of salt stress in endophytic and rhizospheric bacteria, with some emphasis on Bacillus species. In addition, the toxic effects of soil salinity on plants and microbial biodiversity are analysed. Recent findings on the synergetic functioning of ACC deaminase and other bacterial mechanisms of salt stress tolerance, such as trehalose accumulation, are also summarized. Finally, we discuss the various advantages of ACC deaminase-producing bacilli as bioinoculants to address the problem of salinity in agricultural soils.
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Affiliation(s)
- Ma Del Carmen Orozco-Mosqueda
- Facultad de Agrobiología "Presidente Juárez", Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Paseo Lázaro Cárdenas s/n Esq, Berlín, Col. Viveros, 60190, Uruapan, Michoacán, Mexico
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico.
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Díaz Rodríguez AM, Parra Cota FI, Santoyo G, de Los Santos Villalobos S. Chlorothalonil tolerance of indole producing bacteria associated to wheat (Triticum turgidum L.) rhizosphere in the Yaqui Valley, Mexico. Ecotoxicology 2019; 28:569-577. [PMID: 31129746 DOI: 10.1007/s10646-019-02053-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/07/2019] [Indexed: 05/27/2023]
Abstract
Chlorothalonil is a commonly used fungicide to control the karnal bunt caused by Tilletia indica Mitra in wheat production from the Yaqui Valley, Mexico. Here, the effect of Chlorothalonil on the growth of 132 bacterial strains associated with wheat rhizosphere from the Yaqui Valley was evaluated, as well as their ability to produce indoles. Thirty-three percent of the evaluated strains were inhibited by Chlorothalonil, being Bacillus and Paenibacillus the most inhibited genera, observing an inhibition >50% of their strains. In addition, 49% of the inhibited strains showed the ability to produce indoles (>5 μg/mL), where the genus Bacillus was the most abundant (80%). The remaining strains (67%) were tolerant to the evaluated fungicide, but only 37% of those showed the ability to produce indoles, which could be considered as Plant Growth Promoting Rhizobacteria (PGPR). These results showed that Chlorothalonil is not only an antifungal compound but also inhibits the growth of bacterial strains with the ability to produce indoles. Thus, the intensive application of fungicides to agro-systems needs more validation in order to develop sustainable agricultural practices for food production.
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Affiliation(s)
- Alondra M Díaz Rodríguez
- Instituto Tecnológico de Sonora, 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora, Mexico
| | - Fannie I Parra Cota
- Campo Experimental Norman E. Borlaug-INIFAP, 85000 Norman E. Borlaug Km. 12, Ciudad Obregón, Sonora, Mexico
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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Orozco-Mosqueda MDC, Duan J, DiBernardo M, Zetter E, Campos-García J, Glick BR, Santoyo G. The Production of ACC Deaminase and Trehalose by the Plant Growth Promoting Bacterium Pseudomonas sp. UW4 Synergistically Protect Tomato Plants Against Salt Stress. Front Microbiol 2019; 10:1392. [PMID: 31275294 PMCID: PMC6594411 DOI: 10.3389/fmicb.2019.01392] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/03/2019] [Indexed: 11/21/2022] Open
Abstract
Soil salinity is a major problem in agriculture. However, crop growth and productivity can be improved by the inoculation of plants with beneficial bacteria that promote plant growth under stress conditions such as high salinity. Here, we evaluated 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity and trehalose accumulation of the plant growth promoting bacterium Pseudomonas sp. UW4. Mutant strains (mutated at acdS, treS, or both) and a trehalose over-expressing strain (OxtreS) were constructed. The acdS mutant was ACC deaminase minus; the treS- strain significantly decreased its accumulation of trehalose, and the double mutant was affected in both characteristics. The OxtreS strain accumulated more trehalose than the wild-type strain UW4. Inoculating tomato plants subjected to salt stress with these strains significantly impacted root and shoot length, total dry weight, and chlorophyll content. The evaluated parameters in the single acdS and treS mutants were impaired. The double acdS/treS mutant was negatively affected to a greater extent than the single-gene mutants, suggesting a synergistic action of these activities in the protection of plants against salt stress. Finally, the OxtreS overproducing strain protected tomato plants to a greater extent under stress conditions than the wild-type strain. Taken together, these results are consistent with the synergistic action of ACC deaminase and trehalose in Pseudomonas sp. UW4 in the protection of tomato plants against salt stress.
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Affiliation(s)
- Ma Del Carmen Orozco-Mosqueda
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.,Facultad de Agrobiología "Presidente Juárez," Universidad Michoacana de San Nicolás de Hidalgo, Uruapan, Mexico
| | - Jin Duan
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | - Elizabeth Zetter
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Jesús Campos-García
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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