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Daranas N, Badosa E, Montesinos E, Bonaterra A. Colonization and population dynamics of total, viable, and culturable cells of two biological control strains applied to apricot, peach, and grapevine crops. Front Microbiol 2024; 14:1324965. [PMID: 38249452 PMCID: PMC10797078 DOI: 10.3389/fmicb.2023.1324965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024] Open
Abstract
The ecological fitness of the biological control strains Bacillus velezensis A17 and Lactiplantibacillus plantarum PM411 was evaluated in different crops, geographical zones, and growing seasons. Both strains (2 g L-1 of dried formulation) were spray-inoculated on apricot trees, peach trees, and grapevines. Depending on the crop, flowers, fruits, and leaves were picked at several sampling time points. The population dynamics of viable, viable but non-culturable, and dead cells were studied by comparing viability qPCR (v-qPCR), qPCR, and plate counting estimations. A17 showed high survival rates in apricot, peach, and grapevine organs. The A17 viability was confirmed since qPCR and v-qPCR estimations did not significantly differ and were rather constant after field applications. However, higher population levels were estimated by plate counting due to the non-selective characteristics of the medium used. The viability of PM411 was constrained by plant organ, crop, and climate conditions, being higher in apricot than in grapevine. PM411 survival declined after field application, indicating difficulties in its establishment. The PM411 population level was made up of dead, culturable, and viable but non-culturable cells since significant differences between the three methods were observed. In conclusion, A17 and PM411 differ strongly in their survival in grapevine, peach, and apricot.
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Affiliation(s)
| | | | | | - Anna Bonaterra
- Institute of Food and Agricultural Technology-CIDSAV, University of Girona, Girona, Spain
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2
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Rosić I, Nikolić I, Ranković T, Anteljević M, Medić O, Berić T, Stanković S. Genotyping-driven diversity assessment of biocontrol potent Bacillus spp. strain collection as a potential method for the development of strain-specific biomarkers. Arch Microbiol 2023; 205:114. [PMID: 36907935 DOI: 10.1007/s00203-023-03460-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 02/01/2023] [Accepted: 03/01/2023] [Indexed: 03/14/2023]
Abstract
Bacillus species are among the most researched and frequently applied biocontrol agents. To estimate their potential as environmentally friendly microbial-based products, reliable and rapid plant colonization monitoring methods are essential. We evaluated repetitive element-based (rep) and Random Amplified Polymorphic DNA (RAPD) PCR (Polymerase Chain Reaction) genotyping in a diversity assessment of 251 strains from bulk soil, straw, and manure samples across Serbia, highlighting their discriminative force and the presence of unique bands. RAPD 272, OPG 5, and (GTG)5 primers were most potent in revealing the high diversity of a sizable environmental Bacillus spp. collection. RAPD 272 also amplified a unique band for a proven biocontrol strain, opening the possibility of Sequence Characterized Amplified Region (SCAR) marker design. That will enable colonization studies using the SCAR marker for its specific detection. This study provides a guide for primer selection for diversity and monitoring studies of environmental Bacillus spp. isolates.
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Affiliation(s)
- Iva Rosić
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia.
| | - Ivan Nikolić
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Tamara Ranković
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Marina Anteljević
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Olja Medić
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Tanja Berić
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Slaviša Stanković
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
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Hernández I, Sant C, Martínez R, Almazán M, Caminal M, Quero V, El-Adak M, Casanova A, Garrido-Jurado I, Yousef-Yousef M, Quesada-Moraga E, Lara JM, Fernández C. Persistence of Metarhizium brunneum (Ascomycota: Hypocreales) in the Soil Is Affected by Formulation Type as Shown by Strain-Specific DNA Markers. J Fungi (Basel) 2023; 9:jof9020229. [PMID: 36836343 PMCID: PMC9966207 DOI: 10.3390/jof9020229] [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: 12/09/2022] [Revised: 01/20/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The genus Metarhizium has an increasingly important role in the development of Integrated Pest Control against Tephritid fruit flies in aerial sprays targeting adults and soil treatments targeting preimaginals. Indeed, the soil is considered the main habitat and reservoir of Metarhizium spp., which may be a plant-beneficial microorganism due to its lifestyle as an endophyte and/or rhizosphere-competent fungus. This key role of Metarhizium spp. for eco-sustainable agriculture highlights the priority of developing proper monitoring tools not only to follow the presence of the fungus in the soil and to correlate it with its performance against Tephritid preimaginals but also for risk assessment studies for patenting and registering biocontrol strains. The present study aimed at understanding the population dynamics of M. brunneum strain EAMb 09/01-Su, which is a candidate strain for olive fruit fly Bactrocera oleae (Rossi, 1790) preimaginal control in the soil, when applied to the soil at the field using different formulations and propagules. For this, strain-specific DNA markers were developed and used to track the levels of EAMb 09/01-Su in the soil of 4 field trials. The fungus persists over 250 days in the soil, and the levels of the fungus remained higher when applied as an oil-dispersion formulation than when applied as a wettable powder or encapsulated microsclerotia. Peak concentrations of EAMb 09/01-Su depend on the exogenous input and weakly on environmental conditions. These results will help us to optimize the application patterns and perform accurate risk assessments during further development of this and other entomopathogenic fungus-based bioinsecticides.
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Affiliation(s)
- Iker Hernández
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
- Correspondence: ; Tel.: +34-938182891
| | - Clara Sant
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
| | - Raquel Martínez
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
| | - Marta Almazán
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
| | - Marta Caminal
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
| | - Víctor Quero
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
| | - Mohammed El-Adak
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
| | - Albert Casanova
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
| | | | | | | | - José Manuel Lara
- Futureco Bioscience, Avda. Del Cadí 19-23, 08799 Olèrdola, Spain
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Ambreetha S, Balachandar D. SCAR marker: A potential tool for authentication of agriculturally important microorganisms. J Basic Microbiol 2023; 63:4-16. [PMID: 35916264 DOI: 10.1002/jobm.202200419] [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: 07/02/2022] [Accepted: 07/23/2022] [Indexed: 01/04/2023]
Abstract
Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.
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Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Helal DS, El-Khawas H, Elsayed TR. Molecular characterization of endophytic and ectophytic plant growth promoting bacteria isolated from tomato plants (Solanum lycopersicum L.) grown in different soil types. J Genet Eng Biotechnol 2022; 20:79. [PMID: 35608711 PMCID: PMC9130443 DOI: 10.1186/s43141-022-00361-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/02/2022] [Indexed: 11/24/2022]
Abstract
Background Successful rhizosphere colonization by plant growth promoting rhizobacteria (PGPR) is of crucial importance to perform the desired plant growth promoting activities. Since rhizocompetence is a dynamic process influenced by surrounding environmental conditions. In the present study, we hypothesized that bacterial isolates obtained from different tomato plant microhabitats (balk soil, rhizosphere, endorhiza, phyllosphere, and endoshoot) grown in different soils (sand, clay, and peat moss) will show different rhizocompetence abilities. Results To evaluate this hypothesis, bacterial isolates were obtained from different plant microhabitats and screened for their phosphate solubilizing and nitrogen fixing activates. BOX-PCR fingerprint profiles showed high genotypic diversity among the tested isolates and that same genotypes were shared between different soils and/or plant microhabitats. 16S rRNA gene sequences of 25 PGP isolates, representing different plant spheres and soil types, were affiliated to eight genera: Enterobacter, Paraburkholderia, Klebsiella, Bacillus, Paenibacillus, Stenotrophomonas, Pseudomonas, and Kosakonia. The rhizocompetence of each isolate was evaluated in the rhizosphere of tomato plants grown on a mixture of the three soils. Different genotypes of the same bacterial species displayed different rhizocompetence potentials. However, isolates obtained from the above-ground parts of the plant showed high rhizocompetence. In addition, biological control-related genes, ituD and srfC, were detected in the obtained spore forming bacterial isolates. Conclusion This study evaluates, for the first time, the relationship between plant microhabitat and the rhizocompetence ability in tomato rhizosphere. The results indicated that soil type and plant sphere can influence both the genotypic diversity and rhizocompetence ability of the same bacterial species. Bacterial isolates obtained in this study are promising to be used as an environmentally friendly substitution of chemical fertilizers. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00361-0.
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Affiliation(s)
- Donia S Helal
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Hussein El-Khawas
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Tarek R Elsayed
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Cairo, Egypt.
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Manfredini A, Malusà E, Costa C, Pallottino F, Mocali S, Pinzari F, Canfora L. Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil. Front Microbiol 2021; 12:698491. [PMID: 34531836 PMCID: PMC8438429 DOI: 10.3389/fmicb.2021.698491] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022] Open
Abstract
Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.
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Affiliation(s)
- Andrea Manfredini
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Eligio Malusà
- National Research Institute of Horticulture, Skierniewice, Poland
- Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Corrado Costa
- Council for Agricultural Research and Analysis of the Agricultural Economy, Research Centre for Engineering and Agro-Food Processing, Monterotondo, Italy
| | - Federico Pallottino
- Council for Agricultural Research and Analysis of the Agricultural Economy, Research Centre for Engineering and Agro-Food Processing, Monterotondo, Italy
| | - Stefano Mocali
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Flavia Pinzari
- Institute for Biological Systems, Council of National Research of Italy (CNR), Rome, Italy
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Loredana Canfora
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
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Zhang S, Ma Y, Jiang W, Meng L, Cao X, Hu J, Chen J, Li J. Development of a Strain-Specific Quantification Method for Monitoring Bacillus amyloliquefaciens TF28 in the Rhizospheric Soil of Soybean. Mol Biotechnol 2020; 62:521-533. [PMID: 32840729 DOI: 10.1007/s12033-020-00268-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 10/23/2022]
Abstract
Bacillus amyloliquefaciens TF28 can be used to control soybean root disease. To assess its commercial potential as a biocontrol agent, it is necessary to develop a strain-specific quantification method to monitor its colonization dynamics in the rhizospheric soil of soybean under field conditions. Based on genomic comparison with the same species in NCBI databases, a strain-unique gene ukfpg was used as molecular marker to develop strain-specific PCR assay. Among three primer pairs, only primer pairs (F2/R2) could specifically differentiate TF28 from other strains of B. amyloliquefaciens with the detection limit of 10 fg and 100 CFU/g for DNA extracted from pure culture and dry soil, respectively. Then, a colony count coupled with PCR assay was used to monitor the population of TF28 in the rhizospheric soil of soybean in the field. The results indicated that TF28 successfully colonized in the rhizospheric soil of soybean. The colonization population of TF28 changed dynamically within the 120-day growth period with high population at the branching (V6) and flowering stages (R2). This study provides an efficient method to quantitatively monitor the colonization dynamics of TF28 in the rhizospheric soil of soybean in the field and demonstrates the potential of TF28 as a biocontrol agent for commercial development.
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Affiliation(s)
- Shumei Zhang
- Institute of Microbiology, Heilongjiang Academy of Sciences, 68 Zhaolin Street, Daoli District, Harbin, 150010, Heilongjiang, China
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150020, China
| | - Yinpeng Ma
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150020, China
| | - Wei Jiang
- Institute of Microbiology, Heilongjiang Academy of Sciences, 68 Zhaolin Street, Daoli District, Harbin, 150010, Heilongjiang, China
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150020, China
| | - Liqiang Meng
- Institute of Microbiology, Heilongjiang Academy of Sciences, 68 Zhaolin Street, Daoli District, Harbin, 150010, Heilongjiang, China
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150020, China
| | - Xu Cao
- Institute of Microbiology, Heilongjiang Academy of Sciences, 68 Zhaolin Street, Daoli District, Harbin, 150010, Heilongjiang, China
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150020, China
| | - Jihua Hu
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150020, China
| | - Jingyu Chen
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150020, China
| | - Jing Li
- Institute of Microbiology, Heilongjiang Academy of Sciences, 68 Zhaolin Street, Daoli District, Harbin, 150010, Heilongjiang, China.
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, 150020, China.
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Hernández I, Sant C, Martínez R, Fernández C. Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains. Front Microbiol 2020; 11:208. [PMID: 32210925 PMCID: PMC7077341 DOI: 10.3389/fmicb.2020.00208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/29/2020] [Indexed: 11/29/2022] Open
Abstract
Biological control is emerging as a feasible alternative to chemical pesticides in agriculture. Measuring the microbial biocontrol agent (mBCA) populations in the environment is essential for an accurate environmental and health risk assessment and for optimizing the usage of an mBCA-based plant protection product. We hereby show a workflow to obtain a large number of qPCR markers suitable for robust strain-specific quantification. The workflow starts from whole genome sequencing data and consists of four stages: (i) identifying the strain-specific sequences, (ii) designing specific primer/probe sets for qPCR, and (iii) empirically verifying the performance of the assays. The first two stages involve exclusively computer work, but they are intended for researchers with little or no bioinformatic background: Only a knowledge of the BLAST suite tools and work with spreadsheets are required; a familiarity with the Galaxy environment and next-generation sequencing concepts are strongly advised. All bioinformatic work can be implemented using publicly available resources and a regular desktop computer (no matter the operating system) connected to the Internet. The workflow was tested with five bacterial strains from four different genera under development as mBCAs and yielded thousands of candidate markers and a triplex qPCR assay for each candidate mBCA. The qPCR assays were successfully tested in soils of different natures, water from different sources, and with samples from different plant tissues. The mBCA detection limits and population dynamics in the different matrices are similar to those in qPCR assays designed by other means. In summary, a new accessible, cost-effective, and robust workflow to obtain a large number of strain-specific qPCR markers is presented.
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Affiliation(s)
| | - Clara Sant
- Futureco Bioscience S.A., Barcelona, Spain
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Novinscak A, Filion M. Persistence ofPseudomonas fluorescensLBUM677 in the rhizosphere of corn gromwell (Buglossoides arvensis) under field conditions and its impact on seed oil and stearidonic acid bioaccumulation. J Appl Microbiol 2019; 127:208-218. [DOI: 10.1111/jam.14283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/02/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Affiliation(s)
- A. Novinscak
- Department of Biology Université de Moncton Moncton NB Canada
| | - M. Filion
- Department of Biology Université de Moncton Moncton NB Canada
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Reddypriya P, Soumare A, Balachandar D. Multiplex and quantitative PCR targeting SCAR markers for strain-level detection and quantification of biofertilizers. J Basic Microbiol 2018; 59:111-119. [PMID: 30318739 DOI: 10.1002/jobm.201800318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/23/2018] [Accepted: 09/22/2018] [Indexed: 11/12/2022]
Abstract
Biofertilizers are the eco-friendly bio-input being used to sustain the agriculture by reducing the chemical inputs and improving the soil health. Quality is the major concern of biofertilizer technology which often leads to poor performance in the field and thereby loses the farmers' faith. To authenticate the strain as well as its presumed cell load of a commercial product, sequence characterized amplified region (SCAR) markers were developed for three biofertilizer strains viz., Azospirillum brasilense (Sp7), Bacillus megaterium (Pb1) and Azotobacter chroococcum (Ac1). We evaluated the feasibility of multiplex-PCR and quantitative real-time PCR for SCAR marker-based quality assessment of the product as well as the persistence of the strains during crop growth. We showed that multiplex PCR can concurrently discriminate the strains based on the amplicons' size and detects up to 104 cells per g or per ml of carrier-based or liquid formulation of biofertilizer, respectively. The detection limit of quantitative PCR targeting SCAR markers is 103 cells per g or ml of biofertilizer. Both the PCR methods detected and quantified them in the maize rhizosphere. Hence SCAR marker-based quality assessment would be a sensitive tool to monitor the biofertilizer production as well as its persistence in the inoculated crop rhizosphere.
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Affiliation(s)
- Pasupuleti Reddypriya
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Abdoulaye Soumare
- Laboratoire Commun de Microbiologie (LCM, IRD/ISRA/UCAD), Dakar, Senegal
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, India
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11
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Monitoring Viable Cells of the Biological Control Agent Lactobacillus plantarum PM411 in Aerial Plant Surfaces by Means of a Strain-Specific Viability Quantitative PCR Method. Appl Environ Microbiol 2018. [PMID: 29523544 PMCID: PMC5930365 DOI: 10.1128/aem.00107-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A viability quantitative PCR (v-qPCR) assay was developed for the unambiguous detection and quantification of Lactobacillus plantarum PM411 viable cells in aerial plant surfaces. A 972-bp region of a PM411 predicted prophage with mosaic architecture enabled the identification of a PM411 strain-specific molecular marker. Three primer sets with different amplicon lengths (92, 188, and 317 bp) and one TaqMan probe were designed. All the qPCR assays showed good linearity over a 4-log range and good efficiencies but differed in sensitivity. The nucleic acid-binding dye PEMAX was used to selectively detect and enumerate viable bacteria by v-qPCR. The primer set amplifying a 188-bp DNA fragment was selected as the most suitable for v-qPCR. The performance of the method was assessed on apple blossoms, pear, strawberry, and kiwifruit leaves in potted plants under controlled environmental conditions, as well as pear and apple blossoms under field conditions, by comparing v-qPCR population estimations to those obtained by qPCR and specific plate counting on de Man-Rogosa-Sharpe (MRS)-rifampin. The population estimation did not differ significantly between methods when conditions were conducive to bacterial survival. However, under stressful conditions, differences between methods were observed due to cell death or viable-but-nonculturable state induction. While qPCR overestimated the population level, plate counting underestimated this value in comparison to v-qPCR. PM411 attained stable population levels of viable cells on the flower environment under high relative humidity. However, the unfavorable conditions on the leaf surface and the relatively dryness in the field caused an important decrease in the viable population. IMPORTANCE The v-qPCR method in combination with plate counting and qPCR is a powerful tool for studies of colonization and survival under field conditions, to improve formulations and delivery strategies of PM411, and to optimize the dose and timing of spray schedules. It is expected that PEMAX v-qPCR could also be developed for monitoring other strains on plant surfaces not only as biological control agents but also beneficial bacteria useful in the sustainable management of crop production.
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Reddy Priya P, Selastin Antony R, Gopalaswamy G, Balachandar D. Development of sequence-characterized amplified region (SCAR) markers as a quality standard of inoculants based on Azospirillum. Arch Microbiol 2016; 198:257-67. [PMID: 26792777 DOI: 10.1007/s00203-016-1187-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/05/2015] [Accepted: 01/08/2016] [Indexed: 11/28/2022]
Abstract
An attempt was made in this work to develop a strain-level molecular marker for unambiguous authentication of two Azospirillum inoculants, viz. A. lipoferum (strain Az204) and A. brasilense (strain Sp7). The sequence-characterized amplified region (SCAR) markers obtained from DNA fingerprints were designed for discrete detection of the strains. The SCAR primers could successfully amplify the target strain without cross-reaction with other Azospirillum strains, native isolates and other inoculants. The detection limit of SCAR primer for Az204 was 8.00 pg of DNA (approximately 10(5) cells per mL), and for Sp7, it was 0.49 pg of DNA (equal to 10(4) cells per mL). A simplified Sephadex G100-based crude DNA extraction protocol developed in this study was found suitable for SCAR marker-based strain authentication. Further, SCAR primers were assessed for simultaneous authentication as well as quantification of commercially prepared Azospirillum inoculants by quantitative real-time PCR (RT-PCR) and most-probable-number PCR (MPN-PCR). The RT-PCR assay can be able to quantify the commercial formulations as equal to culturable MPN method, while MPN-PCR failed for Az204. The SCAR marker-based strain authentication and presumptive quantification developed in the present work can contribute to improving the quality standard of commercial inoculants.
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Affiliation(s)
- Pasupuleti Reddy Priya
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Raju Selastin Antony
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Ganesan Gopalaswamy
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
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13
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Echeverria MC, Cardelli R, Bedini S, Colombini A, Incrocci L, Castagna A, Agnolucci M, Cristani C, Ranieri A, Saviozzi A, Nuti M. Microbially-enhanced composting of wet olive husks. BIORESOURCE TECHNOLOGY 2012; 104:509-517. [PMID: 22154749 DOI: 10.1016/j.biortech.2011.11.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/11/2011] [Accepted: 11/12/2011] [Indexed: 05/31/2023]
Abstract
The production of a compost from olive wet husks is described. The process is enhanced through the use of starters prepared with virgin husks enriched with selected microbial cultures. This approach, with respect to composting without the use of starters, allows to achieve faster start of the process (10 vs. 45 days), deeper humification (humification rate 19.2 vs. 12.2), shorter maturation time (2 vs. 4-5 months) and better detoxification of the starting material. Furthermore, the compost produced can effectively substitute for turf as a cultivation substrate in horticulture at greenhouse level, with beneficial effects on nutraceutical traits of tomato fruits.
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Affiliation(s)
- M C Echeverria
- Dipartimento di Biologia delle Piante Agrarie, Università di Pisa, via Del Borghetto 80, 56124 Pisa, Italy
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Huang B, Lv C, Zhuang P, Zhang H, Fan L. Endophytic colonisation of Bacillus subtilis in the roots of Robinia pseudoacacia L. PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:925-31. [PMID: 21972966 DOI: 10.1111/j.1438-8677.2011.00456.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The endophytic colonisation of Bacillus subtilis strain GXJM08, isolated from roots of Podocarpus imbricatus B1. Enum. P1. Jav., in roots of the leguminous plant Robinia pseudoacacia L. was investigated. Ultrastructure observations showed that B. subtilis caused morphological changes in the root hair and colonised the plant through infected root hairs. The structure of the infection thread was similar to that of rhizobia, but the structure of infected cells was different. B. subtilis is also different from rhizobia and plant pathogens in terms of the formation of a peribacteroid membrane and the mode of penetration through the host cell wall. Our results provide a basis for studying development of the mutualistic symbiotic relationship between B. subtilis and plants, and a basis for studying the mechanism of the B. subtilis-plant interaction.
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Affiliation(s)
- B Huang
- College of Forestry, Guangxi University, Nanning, Guangxi, China.
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15
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Development of a sequence-characterized amplified region marker-targeted quantitative PCR assay for strain-specific detection of Oenococcus oeni during wine malolactic fermentation. Appl Environ Microbiol 2010; 76:7765-74. [PMID: 20935116 DOI: 10.1128/aem.00929-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Control over malolactic fermentation (MLF) is a difficult goal in winemaking and needs rapid methods to monitor Oenococcus oeni malolactic starters (MLS) in a stressful environment such as wine. In this study, we describe a novel quantitative PCR (QPCR) assay enabling the detection of an O. oeni strain during MLF without culturing. O. oeni strain LB221 was used as a model to develop a strain-specific sequence-characterized amplified region (SCAR) marker derived from a discriminatory OPA20-based randomly amplified polymorphic DNA (RAPD) band. The 5' and 3' flanking regions and the copy number of the SCAR marker were characterized using inverse PCR and Southern blotting, respectively. Primer pairs targeting the SCAR sequence enabled strain-specific detection without cross amplification of other O. oeni strains or wine species of lactic acid bacteria (LAB), acetic acid bacteria (AAB), and yeasts. The SCAR-QPCR assay was linear over a range of cell concentrations (7 log units) and detected as few as 2.2 × 10(2) CFU per ml of red wine with good quantification effectiveness, as shown by the correlation of QPCR and plate counting results. Therefore, the cultivation-independent monitoring of a single O. oeni strain in wine based on a SCAR marker represents a rapid and effective strain-specific approach. This strategy can be adopted to develop easy and rapid detection techniques for monitoring the implantation of inoculated O. oeni MLS on the indigenous LAB population, reducing the risk of unsuccessful MLF.
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16
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Nijhuis E, Pastoor R, Postma J. Specific detection ofLysobacter enzymogenes(Christensen and Cook 1978) strain 3.1T8 with TaqMan®PCR. J Appl Microbiol 2010; 108:1155-66. [DOI: 10.1111/j.1365-2672.2009.04519.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Thenmozhi R, Balaji K, Kanagavel M, Karutha Pandian S. Development of species-specific primers for detection of Streptococcus pyogenes from throat swabs. FEMS Microbiol Lett 2010; 306:110-6. [PMID: 20337717 DOI: 10.1111/j.1574-6968.2010.01939.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A species-specific molecular marker has been developed to detect the human pathogen Streptococcus pyogenes from throat swabs. Streptococcus pyogenes is an important pathogen among Gram-positive organisms. A rapid and simple diagnostic tool is of utmost importance for the identification of this pathogen. The random amplified polymorphic DNA (RAPD) technique was used to differentiate the S. pyogenes strains. A differentially amplified fragment obtained from RAPD profiles was sequenced and characterized, which was developed into a sequence characterized amplified region (SCAR) marker to evaluate the specificity of S. pyogenes from other species of Streptococcus. The sensitivity of the SCAR primers was studied by qualitative PCR and the detection limit was found to be 10(-1) ng of genomic DNA or one to two cells of S. pyogenes. The specificity of the primers was assayed in 270 clinical throat swabs wherein 23 samples turned to be positive, which was highly significant over culture-based methods. This species-specific primer enables accurate detection of S. pyogenes from clinical samples and will be a useful tool in epidemiological studies.
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