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Ercole TG, Kava VM, Petters-Vandresen DAL, Ribeiro RA, Hungria M, Galli LV. Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417. Curr Microbiol 2024; 81:247. [PMID: 38951210 DOI: 10.1007/s00284-024-03784-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024]
Abstract
Stenotrophomonas species are recognized as rhizobacteria that play a pivotal role in promoting plant growth by making substantial contributions to enhanced soil fertility, nutrient recycling, and phytopathogen control. Employing them as bioinputs constitutes an environmentally sound strategy, particularly within the rhizospheric community. This study revealed the draft genome sequence of Stenotrophomonas geniculata LGMB417, which was originally isolated from root samples of maize (Zea mays L.). This research assessed the potential of a bacterial strain at the molecular level through genome mining, aiming to identify genes with biotechnological significance for promoting plant growth and protection. The assembly findings indicate that strain LGMB417 possesses a genome size of 4,654,011 bp, with a G + C content of 66.50%. The draft genome sequence revealed the presence of gene clusters responsible for the synthesis of secondary metabolites and carbohydrate active enzymes (CAZymes), glycoside hydrolases (23), glycosyltransferases (18), carbohydrate esterases (5), polysaccharide lyases (2), carbohydrate-binding modules (2), and auxiliary activities (1). Several genes related to growth promotion were found in the genome, including those associated with phosphate transport and solubilization, nitrogen metabolism, siderophore production and iron transport, hormonal modulation, stress responses (such as to drought, temperature fluctuations, osmotic challenges, and oxidative conditions), and volatile organic compounds (VOCs). Subsequent phases will encompass investigations utilizing gene expression methodologies, with future explorations concentrating on facets pertinent to agricultural production, including comprehensive field studies.
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Affiliation(s)
- Tairine Graziella Ercole
- Postgraduate Program in Genetics, Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil.
| | - Vanessa Merlo Kava
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil
| | - Desirrê Alexia Lourenço Petters-Vandresen
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | | | - Lygia Vitoria Galli
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, Curitiba, PR, 81531-980, Brazil.
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Ercole TG, Kava VM, Petters-Vandresen DAL, Nassif Gomes ME, Aluizio R, Ribeiro RA, Hungria M, Galli LV. Unlocking the growth-promoting and antagonistic power: A comprehensive whole genome study on Bacillus velezensis strains. Gene 2024; 927:148669. [PMID: 38866259 DOI: 10.1016/j.gene.2024.148669] [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: 02/29/2024] [Revised: 05/14/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Bacillus species are extensively documented as plant growth-promoting rhizobacteria, contributing significantly to the enhancement of soil fertility, nutrient recycling, and the control of phytopathogens. Utilizing them as biocontrol agents represents an environmentally friendly strategy, particularly within the rhizospheric community. This study presents the comprehensive genome sequences of three B. velezensis strains (LGMB12, LGMB319, and LGMB426) which were previously isolated from root samples of maize (Zea mays L.), along with a type strain FZB42. The research assesses the capability of the three strains for antagonizing fungi, specifically Fusarium graminearum, Fusarium verticillioides, Colletotrichum graminicola, and Stenocarpella sp. In paired cultures involving maize fungi, treatments containing bacteria B. velezensis exhibited statistically significant differences compared to both negative and positive treatments in terms of antagonism. Furthermore, genome mining techniques were employed to explore their inherent antagonistic potential. The assembly revealed that strains LGMB12, LGMB319, LGMB426, and FZB42 exhibit genome sizes of 4,187,541 bp, 4,244,954 bp, 3,976,537 bp, and 3,990,518 respectively. Their respective G + C content stands at 46.42 %, 46.50 %, 46.51 %, and 46.38 %. Moreover, the genomes present multiple gene clusters responsible for the synthesis of secondary metabolites and carbohydrate-active enzymes (CAZymes). These clusters highlight a diverse array of antibacterial and antifungal properties, complemented by numerous plant growth-promoting genes. These results highlight the potential of B. velezensis LGMB12, LGMB319, and LGMB426 strains as biocontrol and plant growth promotion agents, being promising candidates for further studies in agricultural production, including field trials.
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Affiliation(s)
- Tairine Graziella Ercole
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Vanessa Merlo Kava
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Desirrê Alexia Lourenço Petters-Vandresen
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Maria Eduarda Nassif Gomes
- Pontifical Catholic University of Paraná, Imaculada Conceição St., 1155, 80215-901 Curitiba, PR, Brazil.
| | - Rodrigo Aluizio
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil.
| | | | - Lygia Vitoria Galli
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
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Ujvári G, Capo L, Grassi A, Cristani C, Pagliarani I, Turrini A, Blandino M, Giovannetti M, Agnolucci M. Agronomic strategies to enhance the early vigor and yield of maize. Part I: the role of seed applied biostimulant, hybrid and starter fertilization on rhizosphere bacteria profile and diversity. FRONTIERS IN PLANT SCIENCE 2023; 14:1240310. [PMID: 38023909 PMCID: PMC10651756 DOI: 10.3389/fpls.2023.1240310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
The sustainable intensification of maize-based systems may reduce greenhouse-gas emissions and the excessive use of non-renewable inputs. Considering the key role that the microbiological fertility has on crop growth and resilience, it is worth of interest studying the role of cropping system on the rhizosphere bacterial communities, that affect soil health and biological soil fertility. In this work we monitored and characterized the diversity and composition of native rhizosphere bacterial communities during the early growth phases of two maize genotypes of different early vigor, using a nitrogen (N)-phosphorus (P) starter fertilization and a biostimulant seed treatment, in a growth chamber experiment, by polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA gene and amplicon sequencing. Cluster analyses showed that the biostimulant treatment affected the rhizosphere bacterial microbiota of the ordinary hybrid more than that of the early vigor, both at plant emergence and at the 5-leaf stage. Moreover, the diversity indices calculated from the community profiles, revealed significant effects of NP fertilization on richness and the estimated effective number of species (H2) in both maize genotypes, while the biostimulant had a positive effect on plant growth promoting community of the ordinary hybrid, both at the plant emergence and at the fifth leaf stage. Our data showed that maize genotype was the major factor shaping rhizosphere bacterial community composition suggesting that the root system of the two maize hybrids recruited a different microbiota. Moreover, for the first time, we identified at the species and genus level the predominant native bacteria associated with two maize hybrids differing for vigor. These results pave the way for further studies to be performed on the effects of cropping system and specific crop practices, considering also the application of biostimulants, on beneficial rhizosphere microorganisms.
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Affiliation(s)
- Gergely Ujvári
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Luca Capo
- Department of Agriculture, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Arianna Grassi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Caterina Cristani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Irene Pagliarani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Massimo Blandino
- Department of Agriculture, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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Yuan T, Qazi IH, Yang P, Zhang X, Li J, Liu J. Analysis of endophytic bacterial flora of mulberry cultivars susceptible and resistant to bacterial wilt using metagenomic sequencing and culture-dependent approach. World J Microbiol Biotechnol 2023; 39:163. [PMID: 37067654 DOI: 10.1007/s11274-023-03599-z] [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: 11/16/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023]
Abstract
Endophytes have a wide range of potential in maintaining plant health and sustainable agricultural environmental conditions. In this study, we analysed the diversity of endophytic bacteria in four mulberry cultivars with different resistance capacity against bacterial wilt using metagenomic sequencing and culture-dependent approaches. We further assessed the role of 11 shared genera in the control of bacterial wilt of mulberry. The results of the present study showed that Actinobacteria, Firmicutes, and Proteobacteria were the three dominant phyla in all communities, with the representative genera Acinetobacter and Pseudomonas. The diversity analysis showed that the communities of the highly and moderately resistant varieties were more diverse compared to those of the weakly resistant and susceptible varieties. The control tests of mulberry bacterial wilt showed that Pantoea, Atlantibacter, Stenotrophomonas, and Acinetobacter were effective, with a control rate of over 80%. Microbacterium and Kosakonia were moderately effective, with a control rate between 50 and 80%. At the same time, Escherichia, Lysinibacillus, Pseudomonas, and Rhizobium were found to be less effective, with a control rate of less than 40%. In conclusion, this study provides a reasonable experimental reference data for the control of bacterial wilt of mulberry.
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Affiliation(s)
- Ting Yuan
- College of Animal Science, Regional Sericulture Training Center For Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Izhar Hyder Qazi
- College of Animal Science, Regional Sericulture Training Center For Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, 510642, Guangdong, China
- Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, 67210, Pakistan
| | - Peijia Yang
- College of Animal Science, Regional Sericulture Training Center For Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Xueyin Zhang
- College of Animal Science, Regional Sericulture Training Center For Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Jinhao Li
- College of Animal Science, Regional Sericulture Training Center For Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, 510642, Guangdong, China
| | - Jiping Liu
- College of Animal Science, Regional Sericulture Training Center For Asia-Pacific, South China Agriculture University, Wushan Road, Guangzhou, 510642, Guangdong, China.
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Pastuszczak M, Stanek-Tarkowska J, Kačániová M. Impact of Soil Fertilized with Biomass Ash on Depth-Related Variability of Culturable Bacterial Diversity and Selected Physicochemical Parameters in Spring Barley Cultivation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192113721. [PMID: 36360601 PMCID: PMC9658306 DOI: 10.3390/ijerph192113721] [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: 08/27/2022] [Revised: 10/08/2022] [Accepted: 10/17/2022] [Indexed: 05/10/2023]
Abstract
This study investigated the effect of different doses of fertilization with biomass combustion ash (Salix viminalis L. willow) on changes in the biological, chemical, and physical properties of soil. The experiment was carried out on podzolic and chernozem soils in a one-way field experiment (fertilization dose: control (without fertilization), NPK (nitrogen (N), phosphorus (P) and potassium (K)), 100, 200, 300, 400, 500 kg K2O ha-1). The biomass ash was characterized by a pH value of 12.83 ± 0.68 and a high content of macronutrients. The samples were collected from 0-5, 10-15, and 20-25 cm soil layers under the cultivation of spring barley (Hordeum vulgare L) cv. Planet in April and August 2021. Mass spectrometry (MALDI-TOF MS) was used for microbiological analyses, which revealed the presence of 53 culturable species from 11 genera: Bacillus, Pseudomonas, Paenibacillus, Lysinibacillus, Pseudarthrobacter, Arthrobacter, Staphylococcus, Paenarthrobacter, Micrococcus, Rhodococcus, and Flavobacterium. The podzolic and chernozem soils exhibited the presence of 28 and 44 culturable species, respectively. The study showed an increase in the number of microorganisms in the top layer of the soil profile. However, the number of bacteria decreased at the depths of 10-15 cm and 20-25 cm. With depth, the bulk density (BD) and moisture increased.
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Affiliation(s)
- Miłosz Pastuszczak
- Department of Soil Science, Environmental Chemistry and Hydrology, University of Rzeszow, 35-601 Rzeszów, Poland
- Correspondence:
| | - Jadwiga Stanek-Tarkowska
- Department of Soil Science, Environmental Chemistry and Hydrology, University of Rzeszow, 35-601 Rzeszów, Poland
| | - Miroslava Kačániová
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food and Nutrition Technology, University of Rzeszow, 35-959 Rzeszow, Poland
- Faculty of Horticulture and Landscape Engineering, Institute of Horticulture, Slovak University of Agriculture, 94976 Nitra, Slovakia
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