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Rojas-Rojas FU, Gómez-Vázquez IM, Estrada-de Los Santos P, Shimada-Beltrán H, Vega-Arreguín JC. The potential of Paraburkholderia species to enhance crop growth. World J Microbiol Biotechnol 2025; 41:62. [PMID: 39904926 PMCID: PMC11794353 DOI: 10.1007/s11274-025-04256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 01/07/2025] [Indexed: 02/06/2025]
Abstract
Agrochemicals are the primary alternative for maintaining the high yields necessary to produce sufficient plant-based foods to supply the world population. In recent decades, one of the most extensively explored alternatives to replace agrochemicals and reduce their environmental impact has been the use of microorganism-based products to boost crop yields with less environmental impact. This review focuses on the results of studies that have demonstrated the potential of the genus Paraburkholderia to increase crop yields and be utilized in biofertilizers and biocontrol products. A literature search was performed electronically considering articles and books published until August 19, 2024. We identified 24 species of Paraburkholderia with the ability to improve crop yields after their inoculation by different methods on seeds, seedlings, plantlets, adult crops, or fruits. The effects of these bacteria have been tested under laboratory, greenhouse, or field conditions. These Paraburkholderia species mediate their positive impact on crop growth by direct and indirect plant growth-promoting mechanisms, which include improving nutrient uptake, stimulating growth by phytohormone production, regulation and stimulation of metabolic pathways, induction of abiotic stress tolerance, and disease control by direct pathogen inhibition or induction of systemic resistance in plants. The literature reviewed here supports the use of Paraburkholderia in bio-inputs under the actual panorama of climate change and the necessity to increase sustainable agriculture worldwide.
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Affiliation(s)
- Fernando Uriel Rojas-Rojas
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México
- Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México
| | - Ingrid Melissa Gómez-Vázquez
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México
- Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México
| | - Paulina Estrada-de Los Santos
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N Col. Santo Tomás Alc., 11340, Miguel Hidalgo, Ciudad de México, México
| | - Harumi Shimada-Beltrán
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México
- Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México
| | - Julio C Vega-Arreguín
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México.
- Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México.
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González-Cardona C, López WR, Jovel J, Soto-Suárez M, Ceballos-Aguirre N. Paraburkholderia tropica Primes a Multilayered Transcriptional Defense Response to the Nematode Meloidogyne spp. in Tomato. Int J Mol Sci 2024; 25:12584. [PMID: 39684296 DOI: 10.3390/ijms252312584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 11/18/2024] [Accepted: 11/20/2024] [Indexed: 12/18/2024] Open
Abstract
Meloidogyne causes a devastating disease known as root-knot that affects tomatoes and other cash crops worldwide. Conversely, Paraburkholderia tropica has proven beneficial in mitigating the effects of various pathogens in plants. We aimed to unravel the molecular events that underlie the beneficial effects of the bacterium and the detrimental impacts of the nematode when inoculated separately or together in tomato plants. The transcriptional responses induced by P. tropica (TB group (tomato-bacteria group)), Meloidogyne spp. (TN group (tomato-nematode group)) or by the two agents (TBN group (tomato-bacteria-nematode group)) in tomato were assessed by RNA-seq. We implemented a transcript discovery pipeline which allowed the identification of 2283 putative novel transcripts. Differential expression analysis revealed that upregulated transcripts were much more numerous than downregulated ones. At the gene ontology level, the most activated term was 'hydrolase activity acting on ester bonds' in all groups. In addition, when both microbes were inoculated together, 'hydrolase activity acting on O-glycosyl compounds' was activated. This finding suggests defense responses related to lipid and carbohydrate metabolism, membrane remodeling and signal transduction. Notably, defense genes, transcription factors and protein kinases stood out. Differentially expressed transcripts suggest the activation of a multifaceted plant defense response against the nematode occurred, which was exacerbated by pre-inoculation of P. tropica.
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Affiliation(s)
- Carolina González-Cardona
- Facultad de Ciencias Agropecuarias, Universidad de Caldas, Calle 65 No. 26-10, Manizales 170003, Caldas, Colombia
| | - Walter Ricardo López
- Departamento de Física y Química, Facultad de Ciencias Naturales, Universidad Nacional de Colombia Sede Manizales, km 9 vía Aeropuerto la Nubia, Manizales 170003, Caldas, Colombia
| | - Juan Jovel
- Facultad de Ciencias Agropecuarias, Universidad de Caldas, Calle 65 No. 26-10, Manizales 170003, Caldas, Colombia
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
| | - Mauricio Soto-Suárez
- Facultad de Ciencias Agropecuarias, Universidad de Caldas, Calle 65 No. 26-10, Manizales 170003, Caldas, Colombia
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, km 14 vía Mosquera-Bogotá, Mosquera 250047, Cundinamarca, Colombia
| | - Nelson Ceballos-Aguirre
- Facultad de Ciencias Agropecuarias, Universidad de Caldas, Calle 65 No. 26-10, Manizales 170003, Caldas, Colombia
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Clagnan E, Costanzo M, Visca A, Di Gregorio L, Tabacchioni S, Colantoni E, Sevi F, Sbarra F, Bindo A, Nolfi L, Magarelli RA, Trupo M, Ambrico A, Bevivino A. Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture. Front Microbiol 2024; 15:1473666. [PMID: 39526137 PMCID: PMC11544545 DOI: 10.3389/fmicb.2024.1473666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 10/11/2024] [Indexed: 11/16/2024] Open
Abstract
Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients' cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land management practices and conservation efforts. Recent advancements in molecular technologies, such as high-throughput sequencing, revealed the incredible diversity of soil microbiomes. On one hand, metagenomic sequencing allows the characterization of the entire genetic composition of soil microbiomes, and the examination of their functional potential and ecological roles; on the other hand, culturomics-based approaches and metabolic fingerprinting offer complementary information by providing snapshots of microbial diversity and metabolic activities both in and ex-situ. Long-term storage and cryopreservation of mixed culture and whole microbiome are crucial to maintain the originality of the sample in microbiome biobanking and for the development and application of microbiome-based innovation. This review aims to elucidate the available approaches to characterize diversity, function, and resilience of soil microbial communities and to develop microbiome-based solutions that can pave the way for harnessing nature's untapped resources to cultivate crops in healthy soils, to enhance plant resilience to abiotic and biotic stresses, and to shape thriving ecosystems unlocking the potential of soil microbiomes is key to sustainable agriculture. Improving management practices by incorporating beneficial microbial consortia, and promoting resilience to climate change by facilitating adaptive strategies with respect to environmental conditions are the global challenges of the future to address the issues of climate change, land degradation and food security.
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Affiliation(s)
- Elisa Clagnan
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
- Gruppo Ricicla Labs, Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy (DiSAA), University of Milan, Milan, Italy
| | - Manuela Costanzo
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Andrea Visca
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Luciana Di Gregorio
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Silvia Tabacchioni
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Eleonora Colantoni
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Filippo Sevi
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Federico Sbarra
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
- Department of Life Sciences and System Biology (DBIOS), University of Turin, Turin, Italy
| | - Arianna Bindo
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Turin, Italy
| | - Lorenzo Nolfi
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Rosaria Alessandra Magarelli
- Sustainable AgriFood Systems Division, Department for Sustainability, Trisaia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Mario Trupo
- Sustainable AgriFood Systems Division, Department for Sustainability, Trisaia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Alfredo Ambrico
- Sustainable AgriFood Systems Division, Department for Sustainability, Trisaia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Annamaria Bevivino
- Sustainable AgriFood Systems Division, Department for Sustainability, Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
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Duan Y, Wang T, Zhang P, Zhao X, Jiang J, Ma Y, Zhu X, Fang W. The effect of intercropping leguminous green manure on theanine accumulation in the tea plant: A metagenomic analysis. PLANT, CELL & ENVIRONMENT 2024; 47:1141-1159. [PMID: 38098148 DOI: 10.1111/pce.14784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/15/2023] [Accepted: 12/06/2023] [Indexed: 03/05/2024]
Abstract
Intercropping is a widely recognised technique that contributes to agricultural sustainability. While intercropping leguminous green manure offers advantages for soil health and tea plants growth, the impact on the accumulation of theanine and soil nitrogen cycle are largely unknown. The levels of theanine, epigallocatechin gallate and soluble sugar in tea leaves increased by 52.87% and 40.98%, 22.80% and 6.17%, 22.22% and 29.04% in intercropping with soybean-Chinese milk vetch rotation and soybean alone, respectively. Additionally, intercropping significantly increased soil amino acidnitrogen content, enhanced extracellular enzyme activities, particularly β-glucosidase and N-acetyl-glucosaminidase, as well as soil multifunctionality. Metagenomics analysis revealed that intercropping positively influenced the relative abundances of several potentially beneficial microorganisms, including Burkholderia, Mycolicibacterium and Paraburkholderia. Intercropping resulted in lower expression levels of nitrification genes, reducing soil mineral nitrogen loss and N2 O emissions. The expression of nrfA/H significantly increased in intercropping with soybean-Chinese milk vetch rotation. Structural equation model analysis demonstrated that the accumulation of theanine in tea leaves was directly influenced by the number of intercropping leguminous green manure species, soil ammonium nitrogen and amino acid nitrogen. In summary, the intercropping strategy, particularly intercropping with soybean-Chinese milk vetch rotation, could be a novel way for theanine accumulation.
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Affiliation(s)
- Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ting Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Peixi Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinjie Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jie Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Liu R, Li R, Li Y, Li M, Ma W, Zheng L, Wang C, Zhang K, Tong Y, Huang G, Li X, Zhu XG, You C, Zhong Y, Liao H. Benzoic acid facilitates ANF in monocot crops by recruiting nitrogen-fixing Paraburkholderia. THE ISME JOURNAL 2024; 18:wrae210. [PMID: 39437168 PMCID: PMC11632831 DOI: 10.1093/ismejo/wrae210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 09/25/2024] [Accepted: 10/19/2024] [Indexed: 10/25/2024]
Abstract
Associative nitrogen fixation contributes large portion of N input to agro-ecosystems through monocot-diazotrophic associations. However, the contribution of associative nitrogen fixation is usually neglected in modern agriculture, and the underlying mechanisms of association between monocot and diazotrophs remain elusive. Here, we demonstrated that monocot crops employ mucilage and associated benzoic acid to specially enrich diazotrophic partners in response to nitrogen deficiency, which could be used for enhancing associative nitrogen fixation in monocot crops. To be specific, mucilage and benzoic acid induced in sugarcane roots by nitrogen deficiency mediated enrichment of nitrogen-fixing Paraburkholderia through specific recruitment whereas other bacteria were simultaneously repelled. Further studies suggest maize employs a similar strategy in promoting associations with diazotrophs. In addition, our results also suggest that benzoic acid application significantly increases copy numbers of the nifH gene in soils and enhances associative nitrogen fixation in maize using 15N enrichment assay. Taken together, these results reveal a mechanism regulating the association between monocot crops and nitrogen-fixing bacteria, and, thereby point towards ways to harness these beneficial microbes in efforts to increase nitrogen efficiency in monocot crops through pathways regulated by a specific signaling molecule.
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Affiliation(s)
- Ran Liu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruirui Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanjun Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingjia Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenjing Ma
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Zheng
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cunhu Wang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kefei Zhang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ya Tong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guoqiang Huang
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xinxin Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin-Guang Zhu
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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De-la-Vega-Camarillo E, Hernández-García JA, Villa-Tanaca L, Hernández-Rodríguez C. Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents. FRONTIERS IN PLANT SCIENCE 2023; 14:1247814. [PMID: 37860235 PMCID: PMC10582567 DOI: 10.3389/fpls.2023.1247814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.
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Affiliation(s)
| | | | | | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
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Bahulikar RA. Prevalence of Deltaproteobacterial sequences in nifH gene pools associated with the rhizosphere of native switchgrass from Tall Grass Prairie (Oklahoma, USA). 3 Biotech 2023; 13:210. [PMID: 37251732 PMCID: PMC10209375 DOI: 10.1007/s13205-023-03640-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
The potential nitrogen-fixing bacterial diversity in the rhizospheric soil of the native switchgrass (Panicum virgatum L.) from Tall Grass Prairies of Northern Oklahoma was studied using a partial region of nitrogenase structural gene-nifH. Eleven clone libraries constructed from nifH amplicons gave 407 good-quality sequences. More than 70% of sequences showed similarity of nifH with uncultured bacteria (< 98%). The dominance of sequences affiliated with Deltaproteobacterial nifH was observed, followed by Betaproteobacterial nifH sequences. The nifH gene library was dominated by the genera Geobacter, Rhizobacter, Paenibacillus, and Azoarcus. Sequences affiliated with rhizobia, such as Bradyrhizobium, Methylocystis, Ensifer, etc., were also in the rhizosphere in small numbers. From Deltaproteobacteria, five genera, namely Geobacter, Pelobacter, Geomonas, Desulfovibrio, and Anaeromyxobacter, contributed to 48% of the total sequences suggesting the dominance of group Deltaproteobacteria in the rhizosphere of native switchgrass. Considering the percent similarity of the nifH sequences with cultivated bacteria, this study demonstrated the presence of novel bacterial species in switchgrass rhizospheric soil from Tall Grass Prairie.
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Affiliation(s)
- Rahul A. Bahulikar
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- Present Address: BAIF Development Research Foundation, Central Research Station, Urali Kanchan, Pune, 412 202 India
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8
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Gou Z, Liu G, Wang Y, Li X, Wang H, Chen S, Su Y, Sun Y, Ma NL, Chen G. Enhancing N uptake and reducing N pollution via green, sustainable N fixation-release model. ENVIRONMENTAL RESEARCH 2022; 214:113934. [PMID: 36027962 DOI: 10.1016/j.envres.2022.113934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
The overuse of N fertilizers has caused serious environmental problems (e.g., soil acidification, excessive N2O in the air, and groundwater contamination) and poses a serious threat to human health. Improving N fertilizer utilization efficiency and plant uptake is an alternative for N fertilizers overuses. Enterobacter cloacae is an opportunistic pathogen, also used as plant growth-promoting rhizobacteria (PGPR), has been widely presented in the fields of bioremediation and bioprotection. Here we developed a new N fixation-release model by combining biochar with E. cloacae. The efficiency of the model was evaluated using a greenhouse pot experiment with maize (Zea mays L.) as the test crop. The results showed that biochar combined with E. cloacae significantly increased the N content. The application of biochar combined with E. cloacae increased total N in soil by 33% compared with that of N fertilizers application. The N-uptake and utilization efficiency (NUE) in plant was increased 17.03% and 14.18%, respectively. The activities of urease, dehydrogenase and fluorescein diacetate hydrolase (FDA) was improved, the catalase (CAT) activity decreased. Analysis of the microbial community diversity revealed the abundance of Proteobacteria, Actinobacteria, Firmicutes, and Gemmatimonadetes were significantly improved. The mechanism under the model is that E. cloacae acted as N-fixation by capturing N2 from air. Biochar served as carrier, supporting better living environment for E. cloacae, also as adsorbent adsorbing N from fertilizer and from fixed N by E. cloacae, the adsorption in turn slower the N release. Altogether, the model promotes N utilization by plants, improves the soil environment, and reduces N pollution.
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Affiliation(s)
- Zechang Gou
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Guoqing Liu
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yisheng Wang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Xiufeng Li
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Huiqiong Wang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Siji Chen
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yingjie Su
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yang Sun
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
| | - Nyuk Ling Ma
- Faculty of Science and Marine Environment, University Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Guang Chen
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
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9
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Bartoli C, Boivin S, Marta M, Gris C, Gasciolli V, Gaston M, Auriac MC, Debellé F, Cottret L, Carlier A, Masson-Boivin C, Lepetit M, Lefebvre B. Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root development. Environ Microbiol 2022; 24:5509-5523. [PMID: 35920038 DOI: 10.1111/1462-2920.16148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Although rhizobia that establish a nitrogen-fixing symbiosis with legumes are also known to promote growth in non-legumes, studies on rhizobial associations with wheat roots are scarce. We searched for Rhizobium leguminosarum symbiovar viciae (Rlv) strains naturally competent to endophytically colonize wheat roots. We isolated 20 strains from surface-sterilized wheat roots, and found a low diversity of Rlv compared to that observed in the Rlv species complex. We tested the ability of a subset of these Rlv for wheat root colonization when co-inoculated with other Rlv. Only a few strains, including those isolated from wheat roots, and one strain isolated from pea nodules, were efficient in colonizing roots in co-inoculation conditions, while all the strains tested in single strain inoculation conditions were found to colonize the surface and interior of roots. Furthermore, Rlv strains isolated from wheat roots were able to stimulate root development and early arbuscular mycorrhizal fungi colonization. These responses were strain and host genotype dependent. Our results suggest that wheat can be an alternative host for Rlv; nevertheless, there is a strong competition between Rlv strains for wheat root colonization. In addition, we showed that Rlv are endophytic wheat root bacteria with potential ability to modify wheat development.
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Affiliation(s)
- Claudia Bartoli
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.,LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes INRAE, IRD, CIRAD, University of Montpellier, Montpellier SupAgro Montpellier, France
| | - Marchetti Marta
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Carine Gris
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Mégane Gaston
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Marie-Christine Auriac
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.,FRAIB-TRI Imaging Platform Facilities, Université de Toulouse, CNRS, 24 chemin de Borderouge, Castanet-Tolosan, France
| | - Frédéric Debellé
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Aurélien Carlier
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes INRAE, IRD, CIRAD, University of Montpellier, Montpellier SupAgro Montpellier, France.,Institut Sophia Agrobiotech INRAE, CNRS, University Côte d'azur, Sophia Antipolis, France
| | - Benoit Lefebvre
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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10
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Vio SA, Bernabeu PR, García SS, Galar ML, Luna MF. Tracking and plant growth-promoting effect of Paraburkholderia tropica MTo-293 applied to Solanum lycopersicum. J Basic Microbiol 2022; 62:875-886. [PMID: 35575471 DOI: 10.1002/jobm.202100628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/31/2022] [Accepted: 04/23/2022] [Indexed: 11/08/2022]
Abstract
Paraburkholderia tropica MTo-293 was applied as an experimental bio-input to Solanum lycopersicum (tomato) cv. Platense. Different plant growth systems and inoculation strategies were tested to evaluate P. tropica plant colonization at the seedling stage (growth chamber) using culture-dependent and -independent techniques. The effect of P. tropica on plant growth was evaluated in the growth chamber and greenhouse (productive stage) by biomass accumulation and fruit production, respectively. P. tropica was able to colonize the surface and inner root and stem of tomato seedlings regardless of the inoculation strategy-at sowing and/or before transplanting-showing the competitive nature of P. tropica in nonsterile substrate systems. A nested polymerase chain reaction was validated to track P. tropica in tomato plants even in the inner stem with endophytic P. tropica populations of less than 102 CFU g-1 of fresh weight. Efficient colonization of P. tropica correlated with a positive effect on tomato growth when applied at sowing and/or before transplanting: plant growth promotion was observed not only at the seedling stage but also at productive stages improving crop yield in two different seasons. To our knowledge, this report is the first to track and evaluate the plant growth-promoting effect of P. tropica MTo-293 in tomato plants grown in nonsterile substrate systems.
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Affiliation(s)
- Santiago A Vio
- Departamento de Química, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, UNLP, CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Pamela R Bernabeu
- Departamento de Química, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, UNLP, CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Sabrina S García
- Departamento de Química, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, UNLP, CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María L Galar
- Departamento de Química, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, UNLP, CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María F Luna
- Departamento de Química, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, UNLP, CONICET La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.,Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata, Argentina
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11
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Immobilization-Based Bio-formulation of Aspergillus awamori S29 and Evaluation of Its Shelf Life and Re-usability in the Soil-Plant Experiment. Curr Microbiol 2022; 79:163. [PMID: 35435528 DOI: 10.1007/s00284-022-02854-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/24/2022] [Indexed: 11/03/2022]
Abstract
The present study was an attempt to evaluate the bio-formulations of phosphate-solubilizing fungus Aspergillus awamori S29 using two economically viable carriers (calcium alginate and agar) in repeated batch fermentation. Further, the viable cell count under storage and response of these stored bio-formulations on the growth of wheat plants were studied at the end of 2, 4, and 6 months of incubation. Also, the response of these formulations in next season on pearl millet (bajra) was studied without further inoculation. In repeated batch fermentation assay, immobilized form performed significantly better than free form. The viability of fungal inoculant was 88.2% in calcium alginate-based bio-formulation after six months of storage. These bio-formulations showed not only a statistically significant increase in the growth of wheat crop in first season but also of pearl millet in next season. This work strengthens the re-usability potential of immobilized bio-formulations for next season crop.
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12
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Kumar S, Diksha, Sindhu SS, Kumar R. Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 3:100094. [PMID: 35024641 PMCID: PMC8724949 DOI: 10.1016/j.crmicr.2021.100094] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023] Open
Abstract
Modern intensive agricultural practices face numerous challenges that pose major threats to global food security. In order to address the nutritional requirements of the ever-increasing world population, chemical fertilizers and pesticides are applied on large scale to increase crop production. However, the injudicious use of agrochemicals has resulted in environmental pollution leading to public health hazards. Moreover, agriculture soils are continuously losing their quality and physical properties as well as their chemical (imbalance of nutrients) and biological health. Plant-associated microbes with their plant growth- promoting traits have enormous potential to solve these challenges and play a crucial role in enhancing plant biomass and crop yield. The beneficial mechanisms of plant growth improvement include enhanced nutrient availability, phytohormone modulation, biocontrol of phytopathogens and amelioration of biotic and abiotic stresses. Solid-based or liquid bioinoculant formulation comprises inoculum preparation, addition of cell protectants such as glycerol, lactose, starch, a good carrier material, proper packaging and best delivery methods. Recent developments of formulation include entrapment/microencapsulation, nano-immobilization of microbial bioinoculants and biofilm-based biofertilizers. This review critically examines the current state-of-art on use of microbial strains as biofertilizers and the important roles performed by these beneficial microbes in maintaining soil fertility and enhancing crop productivity.
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Key Words
- ABA, Abscisic acid
- ACC, 1-aminocyclopropane-1-carboxylic acid
- AM, Arbuscular mycorrhiza
- APX, Ascorbate peroxidase
- BGA, Blue green algae
- BNF, Biological nitrogen fixation
- Beneficial microorganisms
- Biofertilizers
- CAT, Catalase
- Crop production
- DAPG, 2, 4-diacetyl phloroglucinol
- DRB, Deleterious rhizospheric bacteria
- GA, Gibberellic acid
- GPX, Glutathione/thioredoxin peroxidase
- HCN, Hydrogen cyanide
- IAA, Indole acetic acid
- IAR, Intrinsic antibiotic resistance
- ISR, Induced systemic resistance
- KMB, Potassium mobilizing bacteria
- KSMs, Potassium-solubilizing microbes
- MAMPs, Microbes associated molecular patterns
- PAMPs, Pathogen associated molecular patterns
- PCA, Phenazine-1-carboxylic acid
- PGP, Plant growth-promoting
- PGPR, Plant growth-promoting rhizobacteria
- POD, Peroxidase
- PSB, Phosphate-solubilizing bacteria
- Rhizosphere
- SAR, Systemic acquired resistance
- SOB, Sulphur oxidizing bacteria
- Soil fertility
- Sustainable agriculture
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Affiliation(s)
- Satish Kumar
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Diksha
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Satyavir S. Sindhu
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Rakesh Kumar
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
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13
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From Lab to Farm: Elucidating the Beneficial Roles of Photosynthetic Bacteria in Sustainable Agriculture. Microorganisms 2021; 9:microorganisms9122453. [PMID: 34946055 PMCID: PMC8707939 DOI: 10.3390/microorganisms9122453] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Photosynthetic bacteria (PSB) possess versatile metabolic abilities and are widely applied in environmental bioremediation, bioenergy production and agriculture. In this review, we summarize examples of purple non-sulfur bacteria (PNSB) through biofertilization, biostimulation and biocontrol mechanisms to promote plant growth. They include improvement of nutrient acquisition, production of phytohormones, induction of immune system responses, interaction with resident microbial community. It has also been reported that PNSB can produce an endogenous 5-aminolevulinic acid (5-ALA) to alleviate abiotic stress in plants. Under biotic stress, these bacteria can trigger induced systemic resistance (ISR) of plants against pathogens. The nutrient elements in soil are significantly increased by PNSB inoculation, thus improving fertility. We share experiences of researching and developing an elite PNSB inoculant (Rhodopseudomonas palustris PS3), including strategies for screening and verifying beneficial bacteria as well as the establishment of optimal fermentation and formulation processes for commercialization. The effectiveness of PS3 inoculants for various crops under field conditions, including conventional and organic farming, is presented. We also discuss the underlying plant growth-promoting mechanisms of this bacterium from both microbial and plant viewpoints. This review improves our understanding of the application of PNSB in sustainable crop production and could inspire the development of diverse inoculants to overcome the changes in agricultural environments created by climate change.
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14
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Sun Z, Yue Z, Liu H, Ma K, Li C. Microbial-Assisted Wheat Iron Biofortification Using Endophytic Bacillus altitudinis WR10. Front Nutr 2021; 8:704030. [PMID: 34414208 PMCID: PMC8368724 DOI: 10.3389/fnut.2021.704030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/02/2021] [Indexed: 12/20/2022] Open
Abstract
Microbial-assisted biofortification attracted much attention recently due to its sustainable and eco-friendly nature for improving nutrient content in wheat. An endophytic strain Bacillus altitudinis WR10, which showed sophistical regulation of iron (Fe) homeostasis in wheat seedlings, inspired us to test its potential for enhancing Fe biofortification in wheat grain. In this study, assays in vitro indicated that WR10 has versatile plant growth-promoting (PGP) traits and bioinformatic analysis predicted its non-pathogenicity. Two inoculation methods, namely, seed soaking and soil spraying, with 107 cfu/ml WR10 cells were applied once before sowing of wheat (Triticum aestivum L. cv. Zhoumai 36) in the field. After wheat maturation, evaluation of yield and nutrients showed a significant increase in the mean number of kernels per spike (KPS) and the content of total nitrogen (N), potassium (K), and Fe in grains. At the grain filling stage, the abundance of Bacillus spp. and the content of N, K, and Fe in the root, the stem, and the leaf were also increased in nearly all tissues, except Fe in the stem and the leaf. Further correlation analysis revealed a positive relationship between the total abundance of Bacillus spp. and the content of N, K, and Fe in grains. Seed staining confirmed the enhanced accumulation of Fe, especially in the embryo and the endosperm. Finally, using a hydroponic coculture model, qPCR quantification indicated effective colonization, internalization, translocation, and replication of strain WR10 in wheat within 48 h. Collectively, strain WR10 assisted successful Fe biofortification in wheat in the field, laying a foundation for further large-scale investigation of its applicability and effectiveness.
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Affiliation(s)
- Zhongke Sun
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.,College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Zonghao Yue
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Hongzhan Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Keshi Ma
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Chengwei Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
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15
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Paulitsch F, Dos Reis FB, Hungria M. Twenty years of paradigm-breaking studies of taxonomy and symbiotic nitrogen fixation by beta-rhizobia, and indication of Brazil as a hotspot of Paraburkholderia diversity. Arch Microbiol 2021; 203:4785-4803. [PMID: 34245357 DOI: 10.1007/s00203-021-02466-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 10/20/2022]
Abstract
Twenty years ago, the first members of the genus Burkholderia capable of nodulating and fixing N2 during symbiosis with leguminous plants were reported. The discovery that β-proteobacteria could nodulate legumes represented a breakthrough event because, for over 100 years, it was thought that all rhizobia belonged exclusively to the α-Proteobacteria class. Over the past 20 years, efforts toward robust characterization of these bacteria with large-scale phylogenomic and taxonomic studies have led to the separation of clinically important and phytopathogenic members of Burkholderia from environmental ones, and the symbiotic nodulating species are now included in the genera Paraburkholderia and Trinickia. Paraburkholderia encompasses the vast majority of β-rhizobia and has been mostly found in South America and South Africa, presenting greater symbiotic affinity with native members of the families Mimosoideae and Papilionoideae, respectively. Being the main center of Mimosa spp. diversity, Brazil is also known as the center of symbiotic Paraburkholderia diversity. Of the 21 symbiotic Paraburkholderia species described to date, 11 have been isolated in Brazil, and others first isolated in different countries have also been found in this country. Additionally, besides the symbiotic N2-fixation capacity of some of its members, Paraburkholderia is considered rich in other beneficial interactions with plants and can promote growth through several direct and indirect mechanisms. Therefore, these bacteria can be considered biological resources employed as environmentally friendly alternatives that could reduce the agricultural dependence on agrochemical inputs.
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Affiliation(s)
- Fabiane Paulitsch
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil.,Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, Londrina, Paraná, 86057-970, Brazil.,Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, Brasília, Distrito Federal, 70040-020, Brazil
| | | | - Mariangela Hungria
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil. .,Departamento de Microbiologia, Universidade Estadual de Londrina, C.P. 10011, Londrina, Paraná, 86057-970, Brazil.
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16
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Wang K, Wu Y, Ye M, Yang Y, Asiegbu FO, Overmyer K, Liu S, Cui F. Comparative Genomics Reveals Potential Mechanisms of Plant Beneficial Effects of a Novel Bamboo-Endophytic Bacterial Isolate Paraburkholderia sacchari Suichang626. Front Microbiol 2021; 12:686998. [PMID: 34220778 PMCID: PMC8250432 DOI: 10.3389/fmicb.2021.686998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Plant-beneficial microbes have drawn wide attention due to their potential application as bio-control agents and bio-fertilizers. Moso bamboo, which is among the monocots with the highest growth rate, lives perennially with abundant microbes that may benefit annually growing crops. Genome information of moso bamboo associated bacteria remains underexplored. We isolated and identified a novel Paraburkholderia strain Suichang626 from moso bamboo roots. Growth promoting effects of Suichang626 on both moso bamboo and seedlings of the model dicot Arabidopsis thaliana were documented in laboratory conditions. To gain insight into the genetic basis of this growth promotion effect, we sequenced the genome of Suichang626. Evidenced by genome-wide phylogeny data, we propose that Suichang626 is a novel strain of Paraburkholderia sacchari. Gene homologs encoding biosynthesis of the plant growth-promoting chemicals, acetoin and 2,3-butanediol, were identified in the genome of Suichang626. Comparative genomics was further performed with plant-beneficial and plant/animal pathogenic species of Paraburkholderia and Burkholderia. Genes related to volatile organic compounds, nitrogen fixation, and auxin biosynthesis were discovered specifically in the plant growth-promoting species of both genera.
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Affiliation(s)
- Kai Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.,Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Ying Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Mengyuan Ye
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Yifan Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Fred O Asiegbu
- Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Kirk Overmyer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Fuqiang Cui
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
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17
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Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture. Microorganisms 2021; 9:microorganisms9020426. [PMID: 33669534 PMCID: PMC7922931 DOI: 10.3390/microorganisms9020426] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 01/28/2023] Open
Abstract
A growing body of evidence demonstrates the potential of various microbes to enhance plant productivity in cropping systems although their successful field application may be impaired by several biotic and abiotic constraints. In the present work, we aimed at developing multifunctional synthetic microbial consortia to be used in combination with suitable bioactive compounds for improving crop yield and quality. Plant growth-promoting microorganisms (PGPMs) with different functional attributes were identified by a bottom-up approach. A comprehensive literature survey on PGPMs associated with maize, wheat, potato and tomato, and on commercial formulations, was conducted by examining peer-reviewed scientific publications and results from relevant European projects. Metagenome fragment recruitments on genomes of potential PGPMs represented in databases were also performed to help identify plant growth-promoting (PGP) strains. Following evidence of their ability to coexist, isolated PGPMs were synthetically assembled into three different microbial consortia. Additionally, the effects of bioactive compounds on the growth of individually PGPMs were tested in starvation conditions. The different combination products based on microbial and non-microbial biostimulants (BS) appear worth considering for greenhouse and open field trials to select those potentially adoptable in sustainable agriculture.
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18
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Cesa-Luna C, Baez A, Aguayo-Acosta A, Llano-Villarreal RC, Juárez-González VR, Gaytán P, Bustillos-Cristales MDR, Rivera-Urbalejo A, Muñoz-Rojas J, Quintero-Hernández V. Growth inhibition of pathogenic microorganisms by Pseudomonas protegens EMM-1 and partial characterization of inhibitory substances. PLoS One 2020; 15:e0240545. [PMID: 33057351 PMCID: PMC7561207 DOI: 10.1371/journal.pone.0240545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/28/2020] [Indexed: 11/18/2022] Open
Abstract
The bacterial strain, EMM-1, was isolated from the rhizosphere of red maize ("Rojo Criollo") and identified as Pseudomonas protegens EMM-1 based on phylogenetic analysis of 16S rDNA, rpoB, rpoD, and gyrB gene sequences. We uncovered genes involved in the production of antimicrobial compounds like 2,4-diacetylphloroglucinol (2,4-DAPG), pyoluteorin, and lectin-like bacteriocins. These antimicrobial compounds are also produced by other fluorescent pseudomonads alike P. protegens. Double-layer agar assay showed that P. protegens EMM-1 inhibited the growth of several multidrug-resistant (MDR) bacteria, especially clinical isolates of the genera Klebsiella and β-hemolytic Streptococcus. This strain also displayed inhibitory effects against diverse fungi, such as Aspergillus, Botrytis, and Fusarium. Besides, a crude extract of inhibitory substances secreted into agar was obtained after the cold-leaching process, and physicochemical characterization was performed. The partially purified inhibitory substances produced by P. protegens EMM-1 inhibited the growth of Streptococcus sp. and Microbacterium sp., but no inhibitory effect was noted for other bacterial or fungal strains. The molecular weight determined after ultrafiltration was between 3 and 10 kDa. The inhibitory activity was thermally stable up to 60°C (but completely lost at 100°C), and the inhibitory activity remained active in a wide pH range (from 3 to 9). After treatment with a protease from Bacillus licheniformis, the inhibitory activity was decreased by 90%, suggesting the presence of proteic natural compounds. All these findings suggested that P. protegens EMM-1 is a potential source of antimicrobials to be used against pathogens for humans and plants.
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Affiliation(s)
- Catherine Cesa-Luna
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - Antonino Baez
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - Alberto Aguayo-Acosta
- Department of Microbiology and Immunology, Biological Sciences Faculty, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de la Garza, Nuevo León, México
| | - Roberto Carlos Llano-Villarreal
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - Víctor Rivelino Juárez-González
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Paul Gaytán
- Unidad de Síntesis y Secuenciación de ADN, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - María del Rocío Bustillos-Cristales
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - América Rivera-Urbalejo
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
- Facultad de Estomatología, BUAP, Puebla, Pue., México
| | - Jesús Muñoz-Rojas
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
| | - Verónica Quintero-Hernández
- Ecology and Survival of Microorganisms Group (ESMG), Laboratorio de Ecología Molecular Microbiana (LEMM), Centro de Investigaciones en Ciencias Microbiológicas (CICM), Instituto de Ciencias (IC), Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Pue., México
- CONACYT–ESMG, LEMM, CICM, IC-BUAP, Puebla, Pue., México
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19
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Lobo CB, Juárez Tomás MS, Viruel E, Ferrero MA, Lucca ME. Development of low-cost formulations of plant growth-promoting bacteria to be used as inoculants in beneficial agricultural technologies. Microbiol Res 2018; 219:12-25. [PMID: 30642462 DOI: 10.1016/j.micres.2018.10.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/23/2018] [Accepted: 10/31/2018] [Indexed: 01/10/2023]
Abstract
Phosphorus is one of the main macronutrients for plant development. Despite its large deposits in soils, it is scarcely available for plants. Phosphate-solubilizing bacteria, belonging to the group of plant growth-promoting rhizobacteria (PGPR), are capable of mobilizing deposits of insoluble phosphates in the soil. The use of PGPR as inoculants provides an environmentally sustainable approach to increase crop production. The effectiveness of inoculants depends on their proper production, formulation and storage in order to ensure the application of the required number of viable microbial cells. In order to develop inexpensive technology, low-cost compounds for biomass production and protection should be used. After the biomass production process, the product should be formulated in a liquid or a solid form, taking into account required storage time, use of protectors/carriers, storage conditions (temperature, humidity, etc.), ease of application and maintenance of beneficial effects on crops. Careful determination of these optimal conditions would ensure a low-cost efficient inoculant that would promote the growth and yield of various crops.
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Affiliation(s)
- Constanza Belén Lobo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET, Avenida Belgrano y Pasaje Caseros, San Miguel de Tucumán T4001MVB, Tucumán, Argentina.
| | - María Silvina Juárez Tomás
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET, Avenida Belgrano y Pasaje Caseros, San Miguel de Tucumán T4001MVB, Tucumán, Argentina.
| | - Emilce Viruel
- Instituto de Investigación Animal del Chaco Semiárido (IIACS), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Leales, Tucumán, Argentina.
| | - Marcela Alejandra Ferrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET, Avenida Belgrano y Pasaje Caseros, San Miguel de Tucumán T4001MVB, Tucumán, Argentina; Microbiología Superior, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), Ayacucho 471, San Miguel de Tucumán T4000INI, Tucumán, Argentina.
| | - María Ester Lucca
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CONICET, Avenida Belgrano y Pasaje Caseros, San Miguel de Tucumán T4001MVB, Tucumán, Argentina; Microbiología Superior, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), Ayacucho 471, San Miguel de Tucumán T4000INI, Tucumán, Argentina.
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