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Keswani C, Prakash O, Bharti N, Vílchez JI, Sansinenea E, Lally RD, Borriss R, Singh SP, Gupta VK, Fraceto LF, de Lima R, Singh HB. Re-addressing the biosafety issues of plant growth promoting rhizobacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:841-852. [PMID: 31302549 DOI: 10.1016/j.scitotenv.2019.07.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 05/21/2023]
Abstract
To promote agronomic sustainability, extensive research is being carried out globally, investigating biofertilizer development. Recently, it has been realized that some microorganisms used as biofertilizers behave as opportunistic pathogens and belong to the biosafety level 2 (BSL-2) classification. This poses serious risk to the environmental and human health. Evidence presented in various scientific forums is increasingly favoring the merits of using BSL-2 microorganisms as biofertilizers. In this review, we emphasize that partial characterization based on traditional microbiological approaches and small subunit rRNA gene sequences/conserved regions are insufficient for the characterization of biofertilizer strains. It is advised herein, that research and industrial laboratories developing biofertilizers for commercialization or environmental release must characterize microorganisms of interest using a multilateral polyphasic approach of microbial systematics. This will determine their risk group and biosafety characteristics before proceeding with formulation development and environmental application. It has also been suggested that microorganisms belonging to risk-group-1 and BSL-1 category should be used for formulation development and for field scale applications. While, BSL-2 microorganisms should be restricted for research using containment practices compliant with strict regulations.
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Affiliation(s)
- Chetan Keswani
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India.
| | - Nidhi Bharti
- Department of Botany, Savitribai Phule Pune University, Pune 411007, India.
| | - Juan I Vílchez
- Department of Plant Growth Promotion Rhizobacteria, Plant Stress Centre for Biology (PSC), Chinese Academy of Sciences (CAS), Shanghai, China.
| | - Estibaliz Sansinenea
- Facultad de Ciencias Químicas, Benemerita Universidad Autonoma de Puebla, Puebla, Pue, Mexico.
| | - Richard D Lally
- Research Department, Alltech, 3031 Catnip Hill Road, Nicholasville, KY 40356, USA.
| | - Rainer Borriss
- Nord Reet UG Greifswald, Germany and Humboldt University, Berlin, Germany.
| | - Surya P Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | - Vijai K Gupta
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Leonardo F Fraceto
- São Paulo State University (UNESP), Institute of Science and Technology, Avenida Três de Março, 511, Alto da Boa Vista, Sorocaba, São Paulo, Brazil.
| | - Renata de Lima
- LABiToN - LaboratóriodeAvaliaçãodeBioatividadeeToxicologiade Nanomateriais, University of Sorocaba, Rodovia Raposo Tavares, Sorocaba, São Paulo, Brazil.
| | - Harikesh B Singh
- Department of Mycology and Plant Pathology, Institute of Agriculture Sciences, Banaras Hindu University, Varanasi 221005, India.
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Kuluev BR, Baymiev AK, Gerashchenkov GA, Chemeris DA, Zubov VV, Kuluev AR, Baymiev AK, Chemeris AV. Random Priming PCR Strategies for Identification of Multilocus DNA Polymorphism in Eukaryotes. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541805006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Saju JM, Németh S, Szűcs R, Sukumaran R, Lim Z, Wong L, Orbán L, Bercsényi M. PCR-based identification of adriatic specimen of three scorpionfish species (Scorpaenidae, Teleostei). ACTA BIOLOGICA HUNGARICA 2014; 65:132-43. [PMID: 24873907 DOI: 10.1556/abiol.65.2014.2.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The identification of three scorpionfish species, the black scorpionfish (Scorpaena porcus Linnaeus, 1758), the large-scaled scorpionfish (S. scrofa Linnaeus, 1758) and the small red scorpionfish (S. notata Rafinesque, 1810) is possible in adults by morphometry, but often problematic in juveniles due to their similar phenotypes. To develop a molecular species identification tool, first, we have analyzed the genetic similarity of the three species by a PCR-based 'blind method' that amplified bands from various locations of the genome. We found high levels of nucleotide similarity between S. porcus and S. scrofa, whereas S. notata showed a higher level of divergence from the other two species. Then, we have searched these patterns for differences between the genomes of Adriatic specimen of these three species and identified several species-specific products in two of them. For the third one a species-specific primer pair amplifying from the 16S ribosomal DNA was designed. One marker for each species was cloned, sequenced and converted into Sequence Characterized Amplified Region (SCAR) markers amplified by specific primer pairs. The SCAR markers amplified robust bands of limited variability from the target species, while no or only occasional weak products were obtained from the other two, proving that they can be used for molecular identification of these three species. These markers can help the conservation and future analysis of these three species as well as their possible selection programs for aquaculture purposes.
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Affiliation(s)
- J M Saju
- National University of Singapore Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, 1 Research Link Singapore 117604 Singapore
| | - Sz Németh
- University of Pannonia Department of Animal Sciences and Breeding, Georgikon Faculty Deák Ferenc u. 16 H-8230 Keszthely Hungary
| | - Réka Szűcs
- University of Pannonia Department of Animal Sciences and Breeding, Georgikon Faculty Deák Ferenc u. 16 H-8230 Keszthely Hungary
| | - Rashmi Sukumaran
- National University of Singapore Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, 1 Research Link Singapore 117604 Singapore National University of Singapore School of Computing Computing 1, 13 Computing Drive Singapore 117417 Singapore
| | - Z Lim
- National University of Singapore Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, 1 Research Link Singapore 117604 Singapore National University of Singapore Department of Biological Sciences 14 Science Drive 4 Singapore 117543 Singapore
| | - L Wong
- National University of Singapore School of Computing Computing 1, 13 Computing Drive Singapore 117417 Singapore
| | - L Orbán
- National University of Singapore Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, 1 Research Link Singapore 117604 Singapore University of Pannonia Department of Animal Sciences and Breeding, Georgikon Faculty Deák Ferenc u. 16 H-8230 Keszthely Hungary National University of Singapore Department of Biological Sciences 14 Science Drive 4 Singapore 117543 Singapore
| | - M Bercsényi
- University of Pannonia Department of Animal Sciences and Breeding, Georgikon Faculty Deák Ferenc u. 16 H-8230 Keszthely Hungary
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Abstract
In this review, we provide a detailed overview of studies on the elusive sex determination (SD) and gonad differentiation mechanisms of zebrafish (Danio rerio). We show that the data obtained from most studies are compatible with polygenic sex determination (PSD), where the decision is made by the allelic combinations of several loci. These loci are typically dispersed throughout the genome, but in some teleost species a few of them might be located on a preferential pair of (sex) chromosomes. The PSD system has a much higher level of variation of SD genotypes both at the level of gametes and the sexual genotype of individuals, than that of the chromosomal sex determination systems. The early sexual development of zebrafish males is a complicated process, as they first develop a ‘juvenile ovary’, that later undergoes a transformation to give way to a testis. To date, three major developmental pathways were shown to be involved with gonad differentiation through the modulation of programmed cell death. In our opinion, there are more pathways participating in the regulation of zebrafish gonad differentiation/transformation. Introduction of additional powerful large-scale genomic approaches into the analysis of zebrafish reproduction will result in further deepening of our knowledge as well as identification of additional pathways and genes associated with these processes in the near future.
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Affiliation(s)
- Woei Chang Liew
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
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Liew WC, Bartfai R, Lim Z, Sreenivasan R, Siegfried KR, Orban L. Polygenic sex determination system in zebrafish. PLoS One 2012; 7:e34397. [PMID: 22506019 PMCID: PMC3323597 DOI: 10.1371/journal.pone.0034397] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/27/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Despite the popularity of zebrafish as a research model, its sex determination (SD) mechanism is still unknown. Most cytogenetic studies failed to find dimorphic sex chromosomes and no primary sex determining switch has been identified even though the assembly of zebrafish genome sequence is near to completion and a high resolution genetic map is available. Recent publications suggest that environmental factors within the natural range have minimal impact on sex ratios of zebrafish populations. The primary aim of this study is to find out more about how sex is determined in zebrafish. METHODOLOGY/PRINCIPAL FINDINGS Using classical breeding experiments, we found that sex ratios across families were wide ranging (4.8% to 97.3% males). On the other hand, repeated single pair crossings produced broods of very similar sex ratios, indicating that parental genotypes have a role in the sex ratio of the offspring. Variation among family sex ratios was reduced after selection for breeding pairs with predominantly male or female offspring, another indication that zebrafish sex is regulated genetically. Further examinations by a PCR-based "blind assay" and array comparative genomic hybridization both failed to find universal sex-linked differences between the male and female genomes. Together with the ability to increase the sex bias of lines by selective breeding, these data suggest that zebrafish is unlikely to utilize a chromosomal sex determination (CSD) system. CONCLUSIONS/SIGNIFICANCE Taken together, our study suggests that zebrafish sex is genetically determined with limited, secondary influences from the environment. As we have not found any sign for CSD in the species, we propose that the zebrafish has a polygenic sex determination system.
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Affiliation(s)
- Woei Chang Liew
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Richard Bartfai
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zijie Lim
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rajini Sreenivasan
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Kellee R. Siegfried
- Department of Genetics, Max-Planck-Institut für Entwicklungsbiologie, Tübingen, Germany
| | - Laszlo Orban
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Animal Sciences and Animal Husbandry, University of Pannonia, Keszthely, Hungary
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Guan L, Shiraishi S. Improved AFLP protocol using dual-suppression PCR and its application to species with large genomes. Mol Ecol Resour 2011; 11:854-61. [PMID: 21676205 DOI: 10.1111/j.1755-0998.2011.03029.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To improve the amplified fragment length polymorphism assay, dual-suppression PCR was introduced into the preamplification step of the assay. The dual-suppression PCR blocked completely the amplification of fragments with the same sequence (Bsp1407I-Bsp1407I or NlaIII-NlaIII) at both ends and amplified selectively fragments with different adaptor sequences (Bsp1407I-NlaIII) at each end. Two protocols, referred to as A and B, were established for species with medium- and large-sized genomes, respectively. Both protocols incorporated the dual-suppression PCR. Protocol A resulted in high-quality electrophoretic profiles for black cottonwood and rice, which have medium-sized genomes. In protocol B, an intensely selective PCR step was added to protocol A. Protocol B yielded profiles for Japanese black pine and Japanese cedar that were improved significantly relative to protocol A: the number of strong peaks increased and that of low peaks decreased. Japanese black pine and Japanese cedar have large genomes. The optimal profiles were generated with a total of eight or nine selective nucleotides.
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Affiliation(s)
- Lanhua Guan
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan
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Research Spotlight: J. Sep. Sci. 10/2008. J Sep Sci 2008. [DOI: 10.1002/jssc.200890036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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