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Sun W, Shahrajabian MH, Soleymani A. The Roles of Plant-Growth-Promoting Rhizobacteria (PGPR)-Based Biostimulants for Agricultural Production Systems. PLANTS (BASEL, SWITZERLAND) 2024; 13:613. [PMID: 38475460 DOI: 10.3390/plants13050613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/17/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
The application of biostimulants has been proven to be an advantageous tool and an appropriate form of management towards the effective use of natural resources, food security, and the beneficial effects on plant growth and yield. Plant-growth-promoting rhizobacteria (PGPR) are microbes connected with plant roots that can increase plant growth by different methods such as producing plant hormones and molecules to improve plant growth or providing increased mineral nutrition. They can colonize all ecological niches of roots to all stages of crop development, and they can affect plant growth and development directly by modulating plant hormone levels and enhancing nutrient acquisition such as of potassium, phosphorus, nitrogen, and essential minerals, or indirectly via reducing the inhibitory impacts of different pathogens in the forms of biocontrol parameters. Many plant-associated species such as Pseudomonas, Acinetobacter, Streptomyces, Serratia, Arthrobacter, and Rhodococcus can increase plant growth by improving plant disease resistance, synthesizing growth-stimulating plant hormones, and suppressing pathogenic microorganisms. The application of biostimulants is both an environmentally friendly practice and a promising method that can enhance the sustainability of horticultural and agricultural production systems as well as promote the quantity and quality of foods. They can also reduce the global dependence on hazardous agricultural chemicals. Science Direct, Google Scholar, Springer Link, CAB Direct, Scopus, Springer Link, Taylor and Francis, Web of Science, and Wiley Online Library were checked, and the search was conducted on all manuscript sections in accordance with the terms Acinetobacter, Arthrobacter, Enterobacter, Ochrobactrum, Pseudomonas, Rhodococcus, Serratia, Streptomyces, Biostimulants, Plant growth promoting rhizobactera, and Stenotrophomonas. The aim of this manuscript is to survey the effects of plant-growth-promoting rhizobacteria by presenting case studies and successful paradigms in various agricultural and horticultural crops.
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Affiliation(s)
- Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ali Soleymani
- Department of Agronomy and Plant Breeding, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan 81551-39998, Iran
- Plant Improvement and Seed Production Research Center, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan 81551-39998, Iran
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Kavanat Beerahassan R, Vadavanath Prabhakaran V, Pillai D. Formulation of an exoskeleton degrading bacterial consortium from seafood processing effluent for the biocontrol of crustacean parasite Alitropus typus. Vet Parasitol 2021; 290:109348. [PMID: 33486459 DOI: 10.1016/j.vetpar.2021.109348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
Parasitic infestations on cultured fish due to the crustacean isopod Alitropus typus has been on the rise in recent years, causing large scale mortality, leading to significant economic loss to the farmer. Crustaceans are encased by an exoskeleton composed of chitin, protein and lipid microfibril frameworks, in which calcium carbonate is deposited. A strategy focused on the degradation of the exoskeletal framework utilizing nonpathogenic microorganisms that produce a wide variety of hydrolytic enzymes may be an environment-friendly and safe alternative to control these pests. The present study was aimed to formulate a microbial consortium having chitinase, protease, lipase and urease producing bacteria from seafood processing effluents that can potentially degrade the exoskeleton of A. typus. Based on the qualitative and quantitative assessment of the extracellular enzymes produced by the isolates, a novel consortium was prepared with three strains that were not antagonistic to each other and were nonpathogenic. The chitinase producing - Stenotrophomonas maltophilia and Bacillus altitudinis that produced protease and lipase as well; and non-chitinase producing Klebsiella pneumoniae were taken in the ratio of 1:1:2 respectively (109 CFU/mL). The result showed 100 % mortality of the isopods within five days when applied at a concentration of 2% (v/v) of 107 CFU/mL without any adverse effect on the fish host Oreochromis niloticus. Analysis of the ultrastructural alterations of the parasites by Environmental Scanning Electron microscopy (ESEM) showed noticeable exoskeletal damages. The microbial members of the consortium displayed remarkable chemotactic properties towards A. typus. The results suggest that the microbial consortium acts as a potential parasiticide that can be used for the control of A. typus infestation in aquaculture ponds., thus benefitting the aquaculture industry especially the small-scale farmers.
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Affiliation(s)
- Rajeena Kavanat Beerahassan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Panangad, Cochin, 682 506, Kerala, India; School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Panangad, Cochin, 682 506, Kerala, India
| | - Vineetha Vadavanath Prabhakaran
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Panangad, Cochin, 682 506, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Panangad, Cochin, 682 506, Kerala, India.
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Mapping Microbial Capacities for Bioremediation: Genes to Genomics. Indian J Microbiol 2019; 60:45-53. [PMID: 32089573 DOI: 10.1007/s12088-019-00842-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 12/15/2022] Open
Abstract
Bioremediation is a process wherein the decontamination strategies are designed so that a site could achieve the environmental abiotic and biotic parameters close to its baseline. In the process, the driving force is the available microbial genetic degradative capabilities, which are supported by required nutrients so that the desired expression of these capabilities could be exploited in favour of removal of pollutants. With genomics tools not only the available abilities could be estimated but their dynamic performance could also be established. These tools are now playing important role in bioprocess optimization, which not only derive the bio-stimulation plans but also could suggest possible genetic bio-augmentation options.
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Han Y, Yang K, Yang T, Zhang M, Li L. Bioaerosols emission and exposure risk of a wastewater treatment plant with A 2O treatment process. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 169:161-168. [PMID: 30445247 DOI: 10.1016/j.ecoenv.2018.11.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/08/2018] [Accepted: 11/06/2018] [Indexed: 05/11/2023]
Abstract
The characteristics of bioaerosol emissions from wastewater treatment plants (WWTPs) have attracted extensive attention. The anaerobic-anoxic-oxic (A2O) process, which uses the activated sludge approach to wastewater treatment, is the most widely used process in WWTPs. Concentration, size distribution, population, and exposure risk from bacteria and fungi in bioaerosols of WWTPs using the A2O process were studied in this work. The results showed that the maximum concentration of airborne bacteria (1.00 × 104 Colony Forming Units per cubic meter (CFU m-3)) and fungi (1.44 ×104 CFU m-3) occurred from the facility's aerobic tank, in summer. As one of the main factors affecting bioaerosol exposure risk, particle size distribution was related to season. The study found that particles larger than 3.3 µm in diameter were detected mainly in spring and summer, while particles less than 3.3 µm were detected mainly in autumn and winter, whether bacterial aerosol or fungal aerosol. In addition, pathogenic bacteria were observed in bioaerosols from WWTPs, with 18 of the 65 species of bacteria detected found to be potentially or opportunistically pathogenic, such as Chryseobacterium, Stenotrophomonas, Alcaligenes, Micrococcus, Pantoea, Enterobacter and Escherichia-Shigella. The presence of these pathogens further increased the exposure risk from bioaerosols. The results of an inhalation risk assessment for airborne bacteria and fungi indicated that potential adverse health risks for adults mainly occurred in spring, summer, and autumn. On this basis, it was concluded that WWTP operators should set up effective bioaerosol controls as soon as possible to protect the health of workers, and of residents near the plant.
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Affiliation(s)
- Yunping Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
| | - Kaixiong Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
| | - Tang Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
| | - Mengzhu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; CSD (Beijing) Water Service Co., Ltd., Beijing 100192, China.
| | - Lin Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, PR China.
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Genome-wide evolutionary characterization and expression analyses of major latex protein (MLP) family genes in Vitis vinifera. Mol Genet Genomics 2018; 293:1061-1075. [DOI: 10.1007/s00438-018-1440-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/19/2018] [Indexed: 12/17/2022]
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Purohit HJ, Kapley A, Khardenavis A, Qureshi A, Dafale NA. Insights in Waste Management Bioprocesses Using Genomic Tools. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:121-170. [PMID: 27926430 DOI: 10.1016/bs.aambs.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
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Affiliation(s)
- H J Purohit
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Kapley
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Khardenavis
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Qureshi
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - N A Dafale
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
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Tokdar P, Sanakal A, Ranadive P, Khora SS, George S, Deshmukh SK. Molecular, Physiological and Phenotypic Characterization of Paracoccus denitrificans ATCC 19367 Mutant Strain P-87 Producing Improved Coenzyme Q10. Indian J Microbiol 2015; 55:184-93. [PMID: 25805905 PMCID: PMC4363252 DOI: 10.1007/s12088-014-0506-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/24/2014] [Indexed: 10/24/2022] Open
Abstract
Coenzyme Q10 (CoQ10) is a blockbuster nutraceutical molecule which is often used as an oral supplement in the supportive therapy for cardiovascular diseases, cancer and neurodegenerative diseases. It is commercially produced by fermentation process, hence constructing the high yielding CoQ10 producing strains is a pre-requisite for cost effective production. Paracoccus denitrificans ATCC 19367, a biochemically versatile organism was selected to carry out the studies on CoQ10 yield improvement. The wild type strain was subjected to iterative rounds of mutagenesis using gamma rays and NTG, followed by selection on various inhibitors like CoQ10 structural analogues and antibiotics. The screening of mutants were carried out using cane molasses based optimized medium with feeding strategies at shake flask level. In the course of study, the mutant P-87 having marked resistance to gentamicin showed 1.25-fold improvements in specific CoQ10 content which was highest among all tested mutant strains. P-87 was phenotypically differentiated from the wild type strain on the basis of carbohydrate assimilation and FAME profile. Molecular differentiation technique based on AFLP profile showed intra specific polymorphism between wild type strain and P-87. This study demonstrated the beneficial outcome of induced mutations leading to gentamicin resistance for improvement of CoQ10 production in P. denitrificans mutant strain P-87. To investigate the cause of gentamicin resistance, rpIF gene from P-87 and wild type was sequenced. No mutations were detected on the rpIF partial sequence of P-87; hence gentamicin resistance in P-87 could not be conferred with rpIF gene. However, detecting the mutations responsible for gentamicin resistance in P-87 and correlating its role in CoQ10 overproduction is essential. Although only 1.25-fold improvement in specific CoQ10 content was achieved through mutant P-87, this mutant showed very interesting characteristic, differentiating it from its wild type parent strain P. denitrificans ATCC 19367, which are presented in this paper.
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Affiliation(s)
- Pradipta Tokdar
- />Fermentation Technology-Natural Products Department, Piramal Enterprises Ltd., 1 Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai, 400063 India
| | - Akshata Sanakal
- />Fermentation Technology-Natural Products Department, Piramal Enterprises Ltd., 1 Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai, 400063 India
| | - Prafull Ranadive
- />Fermentation Technology-Natural Products Department, Piramal Enterprises Ltd., 1 Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai, 400063 India
| | - Samanta Shekhar Khora
- />School of Bio Sciences and Technology, VIT University, Vellore, 632014 Tamil Nadu India
| | - Saji George
- />Fermentation Technology-Natural Products Department, Piramal Enterprises Ltd., 1 Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai, 400063 India
| | - Sunil Kumar Deshmukh
- />Fermentation Technology-Natural Products Department, Piramal Enterprises Ltd., 1 Nirlon Complex, Off Western Express Highway, Goregaon (East), Mumbai, 400063 India
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Genome Wide Analysis for Searching Novel Markers to Rapidly Identify Clostridium Strains. Indian J Microbiol 2015; 55:250-7. [PMID: 26063934 DOI: 10.1007/s12088-015-0535-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022] Open
Abstract
Microbial classification is based largely on the 16S rRNA (rrs) gene sequence, which is conserved throughout the prokaryotic domain. The Ribosomal Database Project (RDP) has become a reference point for almost all practical purposes. The use of this gene is limited by the fact that it can be used to identify only to the extent to what has been known and is available in the RDP. In order to identify an organism whose rrs is not present in the RDP database, we need to generate novel markers to place the unknown on the evolutionary map. Here, sequenced genomes of 27 Clostridium strains belonging to 9 species have been used to identify two sets of genes: (1) common to most of the species, and (2) unique to a species. Combinations of genes (recN, dnaJ, secA, mutS, and/or grpE) and their unique restriction endonuclease digestion (AluI, BfaI and/or Tru9I) patterns have been established to rapidly identify Clostridium species. This strategy for identifying novel markers can be extended to all other organisms and diagnostic applications.
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Bhushan A, Mukherjee T, Joshi J, Shankar P, Kalia VC. Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene). Indian J Microbiol 2015; 55:140-50. [PMID: 25805900 DOI: 10.1007/s12088-015-0514-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 01/12/2015] [Indexed: 11/26/2022] Open
Abstract
Diversity analysis of Clostridium botulinum strains is complicated by high microheterogeneity caused by the presence of 9-22 copies of rrs (16S rRNA gene). The need is to mine genetic markers to identify very closely related strains. Multiple alignments of the nucleotide sequences of the 212 rrs of 13 C. botulinum strains revealed intra- and inter-genomic heterogeneity. Low intragenomic heterogeneity in rrs was evident in strains 230613, Alaska E43, Okra, Eklund 17B, Langeland, 657, Kyoto, BKT015925, and Loch Maree. The most heterogenous rrs sequences were those of C. botulinum strains ATCC 19397, Hall, H04402065, and ATCC 3502. In silico restriction mapping of these rrs sequences was observable with 137 type II Restriction endonucleases (REs). Nucleotide changes (NC) at these RE sites resulted in appearance of distinct and additional sites, and loss in certain others. De novo appearances of RE sites due to NC were recorded at different positions in rrs gene. A nucleotide transition A>G in rrs of C. botulinum Loch Maree and 657 resulted in the generation of 4 and 10 distinct RE sites, respectively. Transitions A>G, G>A, and T>C led to the loss of RE sites. A perusal of the entire NC and in silico RE mapping of rrs of C. botulinum strains provided insights into their evolution. Segregation of strains on the basis of RE digestion patterns of rrs was validated by the cladistic analysis involving six house keeping genes: dnaN, gyrB, metG, prfA, pyrG, and Rho.
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Affiliation(s)
- Ashish Bhushan
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Tanmoy Mukherjee
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Jayadev Joshi
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Pratap Shankar
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
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de Smidt O, Smit NJ, Botes E. Bacterial diversity in soil from geophagic mining sites in the Qwa-Qwa region of South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2014; 25:184-195. [PMID: 24852929 DOI: 10.1080/09603123.2014.915019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Geophagia is practised in many parts of the world and can be associated with medicinal treatments, ceremonial events and spiritual behaviours/practices. This is the first report on a systematic investigation and description of the bacterial diversity in soil regularly ingested by geophagic individuals using a culture-independent method. Diversity in 17 different mining sites was investigated using denaturing gradient gel electrophoresis. Genetic material from Pantoea, Stenotrophomonas, Listeria, Rhodococcus and Sphingomonads was present in most of the soil samples. Species from these genera are recognised, potential or immerging human pathogens, and are of special interest in immune-compromised individuals. Other genera able to produce a variety of bacteriocins and antimicrobial/antifungal substances inhibitory towards food borne pathogens (Dactylosporangium and Bacillus) and able to degrade a range of environmental pollutants and toxins (Duganella and Massilia) were also present. These essential insights provide the platform for adjusting culturing strategies to isolate specific bacteria, further phylogenetic studies and microbial mining prospect for bacterial species of possible economic importance.
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Affiliation(s)
- Olga de Smidt
- a Life Sciences , Central University of Technology, Free State , Bloemfontein , South Africa
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Kumar P, Patel SK, Lee JK, Kalia VC. Extending the limits of Bacillus for novel biotechnological applications. Biotechnol Adv 2013; 31:1543-61. [DOI: 10.1016/j.biotechadv.2013.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 07/01/2013] [Accepted: 08/05/2013] [Indexed: 12/28/2022]
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Mazzucotelli CA, Ponce AG, Kotlar CE, Moreira MDR. Isolation and characterization of bacterial strains with a hydrolytic profile with potential use in bioconversion of agroindustial by-products and waste. FOOD SCIENCE AND TECHNOLOGY 2013. [DOI: 10.1590/s0101-20612013005000038] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Cintia Anabela Mazzucotelli
- Universidad Nacional de Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - Alejandra Graciela Ponce
- Universidad Nacional de Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - Catalina Elena Kotlar
- Universidad Nacional de Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - María del Rosario Moreira
- Universidad Nacional de Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
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Bhushan A, Joshi J, Shankar P, Kushwah J, Raju SC, Purohit HJ, Kalia VC. Development of Genomic Tools for the Identification of Certain Pseudomonas up to Species Level. Indian J Microbiol 2013; 53:253-63. [PMID: 24426119 DOI: 10.1007/s12088-013-0412-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/12/2013] [Indexed: 11/26/2022] Open
Abstract
Pseudomonas is a highly versatile bacterium at the species level with great ecological significance. These genetically and metabolically diverse species have undergone repeated taxonomic revisions. We propose a strategy to identify Pseudomonas up to species level, based on the unique features of their 16S rDNA (rrs) gene sequence, such as the frame work of sequences, sequence motifs and restriction endonuclease (RE) digestion patterns. A species specific phylogenetic framework composed of 31 different rrs sequences, allowed us to segregate 1,367 out of 2,985 rrs sequences of this genus, which have been classified at present only up to genus (Pseudomonas) level, as follows: P. aeruginosa (219 sequences), P. fluorescens (463 sequences), P. putida (347 sequences), P. stutzeri (197 sequences), and P. syringae (141 sequences). These segregations were validated by unique 30-50 nucleotide long motifs and RE digestion patterns in their rrs. A single gene thus provides multiple makers for identification and surveillance of Pseudomonas.
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Affiliation(s)
- Ashish Bhushan
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Jayadev Joshi
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Pratap Shankar
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Jyoti Kushwah
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Sajan C Raju
- Environmental Genomics Unit, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020 India
| | - Hemant J Purohit
- Environmental Genomics Unit, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
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Selvakumaran S, Kapley A, Kashyap SM, Daginawala HF, Kalia VC, Purohit HJ. Diversity of aromatic ring-hydroxylating dioxygenase gene in Citrobacter. BIORESOURCE TECHNOLOGY 2011; 102:4600-4609. [PMID: 21295975 DOI: 10.1016/j.biortech.2011.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/03/2011] [Accepted: 01/04/2011] [Indexed: 05/30/2023]
Abstract
Genetic and functional diversity of Citrobacter spp. for their abilities to degrade aromatic compounds was evaluated to develop mixed cultures or a consortium for bioremediation technology. Thirty Citrobacter strains isolated from various effluent treatment plants were found to degrade a range of aromatic compounds: phenol, benzoate, hydroxy benzoic acid and biotransform mono-chlorophenols and di-chlorophenol within 24 to 48 h of incubation at 30 °C. Sequence similarity and phylogeny of the ARHD gene transcripts (730 nucleotides) depicted their diversity within 9 Citrobacter strains: HPC255, HPC369, HPC560, HPC570, HPC784, HPC1196, HPC1216, HPC1276 and HPC1299. Here, the degree of associations varied up to 84% with (i) ARHD α-sub unit (SU), (ii) LSU of Phenylpropionate dioxygenase (PDO), (iii) Phenol hydroxylase α-SU, (iv) Benzoate 1,2-dioxygenase, α-SU, (v) Naphthalene dioxygenase LSU, etc. This study has provided basic information, which can be used to develop a consortium of bacteria with mutually beneficial characteristics.
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Affiliation(s)
- S Selvakumaran
- Environmental Genomics Division, National Environmental Engineering Research Institute (NEERI), CSIR, Nehru Marg, Nagpur 440 020, MH, India
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Verma V, Raju SC, Kapley A, Kalia VC, Kanade GS, Daginawala HF, Purohit HJ. Degradative potential of Stenotrophomonas strain HPC383 having genes homologous to dmp operon. BIORESOURCE TECHNOLOGY 2011; 102:3227-3233. [PMID: 21123060 DOI: 10.1016/j.biortech.2010.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 05/30/2023]
Abstract
A strain, Stenotrophomonas HPC383 is isolated from effluent treatment plant treating wastewater from pesticide industry; degrades various aromatic compounds (cresols, phenol, catechol, 4methyl-catechol and hydroquinone) and crude oil, as determined through HPLC and GC analysis. Culture HPC383 could degrade (%) various compounds (1 mM) from a mixture: phenol - 99, p-cresol - 100, 4-methylcatechol - 96 and hydroquinone - 43 within 48 h of incubation, whereas it took 7 days to degrade 94% of 0.5% crude oil. Gene locus dmpN, to identify phenol degrading capacity was determined by PCR followed by southern analysis. The sequenced DNA fragment exhibited 99% sequence similarity to phenol hydroxylase gene from Arthrobacter sp. W1 (FJ610336). Amino acid sequence analysis of phenol hydroxylase reveals it to belong to high-Ks (affinity constant) group. Application of HPC383 in bioremediation of aquatic and terrestrial sites contaminated with petrochemical has been suggested.
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Affiliation(s)
- Vinita Verma
- Environmental Genomics Unit, National Environmental Engineering Research Institute (NEERI), CSIR, Nehru Marg, Nagpur (MH), India
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Kalia VC, Mukherjee T, Bhushan A, Joshi J, Shankar P, Huma N. Analysis of the unexplored features of rrs (16S rDNA) of the Genus Clostridium. BMC Genomics 2011; 12:18. [PMID: 21223548 PMCID: PMC3024285 DOI: 10.1186/1471-2164-12-18] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Accepted: 01/11/2011] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Bacterial taxonomy and phylogeny based on rrs (16S rDNA) sequencing is being vigorously pursued. In fact, it has been stated that novel biological findings are driven by comparison and integration of massive data sets. In spite of a large reservoir of rrs sequencing data of 1,237,963 entries, this analysis invariably needs supplementation with other genes. The need is to divide the genetic variability within a taxa or genus at their rrs phylogenetic boundaries and to discover those fundamental features, which will enable the bacteria to naturally fall within them. Within the large bacterial community, Clostridium represents a large genus of around 110 species of significant biotechnological and medical importance. Certain Clostridium strains produce some of the deadliest toxins, which cause heavy economic losses. We have targeted this genus because of its high genetic diversity, which does not allow accurate typing with the available molecular methods. RESULTS Seven hundred sixty five rrs sequences (> 1200 nucleotides, nts) belonging to 110 Clostridium species were analyzed. On the basis of 404 rrs sequences belonging to 15 Clostridium species, we have developed species specific: (i) phylogenetic framework, (ii) signatures (30 nts) and (iii) in silico restriction enzyme (14 Type II REs) digestion patterns. These tools allowed: (i) species level identification of 95 Clostridium sp. which are presently classified up to genus level, (ii) identification of 84 novel Clostridium spp. and (iii) potential reduction in the number of Clostridium species represented by small populations. CONCLUSIONS This integrated approach is quite sensitive and can be easily extended as a molecular tool for diagnostic and taxonomic identification of any microbe of importance to food industries and health services. Since rapid and correct identification allows quicker diagnosis and consequently treatment as well, it is likely to lead to reduction in economic losses and mortality rates.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India
| | - Tanmoy Mukherjee
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India
| | - Ashish Bhushan
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India
| | - Jayadev Joshi
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India
| | - Pratap Shankar
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India
| | - Nusrat Huma
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India
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