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Li W, Yang M, Luo Y, Liu W, Wang Z, Ning Z. Effects of dietary rosemary ultrafine powder supplementation on aged hen health and productivity: a randomized controlled trial. Poult Sci 2024; 103:104133. [PMID: 39180778 PMCID: PMC11385426 DOI: 10.1016/j.psj.2024.104133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/26/2024] Open
Abstract
Recently, poultry industry has been seeking antibiotic residue-free poultry products and safe nutritious feed additives. Whether rosemary ultrafine powder (RUP) affects productive performance by regulating the intestinal microbiome of aged layers remains unclear. Here, we investigated the effects of dietary RUP supplementation on the production performance, egg quality, antioxidant capacity, intestinal microbial structure, and metabolome of aged hens. The results indicate that RUP had no significant effect on production performance but significantly enhanced Thick albumen height, Haugh unit, yolk color (P < 0.05), daily feed intake, and qualified egg rate. Serum content of non-esterified fatty acids, catalase, and glutathione peroxidase increased significantly (P < 0.05). Furthermore, the liver total protein content was significantly increased (P < 0.05). 16S rRNA sequence analysis revealed that RUP significantly impacted both α- and β-diversity of the caecum microbiota. Linear discriminant analysis of effect size and random forest identified Bacteroides, Muribaculum, Butyricimonas, Odoribacter, and Prevotella as biomarkers in groups A and B. In comparing groups A and C, Barnesiella, Turicibacter, and Acholeplasma were critical bacteria, while comparing groups A and D highlighted Barnesiella and Candidatus Saccharimonas as differential bacteria. FAPROTAX analysis of the caecum microbiota revealed that the functional genes associated with harmful substance biodegradation were significantly increased in the RUP-fed group. Based on Spearman correlation analysis, alterations in microbial genera were associated with divergent metabolites. In summary, dietary RUP can improve egg quality and antioxidant capacity and regulate the intestinal microbiome and metabolome in aged breeders. Therefore, RUP can potentially be used as a feed additive to extend breeder service life at an appropriate level of 1.0 g/kg.
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Affiliation(s)
- Wen Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Meixue Yang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuxing Luo
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wei Liu
- Zhuozhou Mufeng Poultry Company Limited, Zhuozhou 072750, China
| | - Zhong Wang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Shah BA, Malhotra H, Papade SE, Dhamale T, Ingale OP, Kasarlawar ST, Phale PS. Microbial degradation of contaminants of emerging concern: metabolic, genetic and omics insights for enhanced bioremediation. Front Bioeng Biotechnol 2024; 12:1470522. [PMID: 39364263 PMCID: PMC11446756 DOI: 10.3389/fbioe.2024.1470522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 09/05/2024] [Indexed: 10/05/2024] Open
Abstract
The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication etc., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. "Omics" and "Meta-omics" techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.
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Affiliation(s)
- Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sandesh E Papade
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Omkar P Ingale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sravanti T Kasarlawar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Malhotra H, Dhamale T, Kaur S, Kasarlawar ST, Phale PS. Metabolic engineering of Pseudomonas bharatica CSV86 T to degrade Carbaryl (1-naphthyl- N-methylcarbamate) via the salicylate-catechol route. Microbiol Spectr 2024; 12:e0028424. [PMID: 38869268 PMCID: PMC11302072 DOI: 10.1128/spectrum.00284-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 06/14/2024] Open
Abstract
Pseudomonas bharatica CSV86T displays the unique property of preferential utilization of aromatic compounds over simple carbon sources like glucose and glycerol and their co-metabolism with organic acids. Well-characterized growth conditions, aromatic compound metabolic pathways and their regulation, genome sequence, and advantageous eco-physiological traits (indole acetic acid production, alginate production, fusaric acid resistance, organic sulfur utilization, and siderophore production) make it an ideal host for metabolic engineering. Strain CSV86T was engineered for Carbaryl (1-naphthyl-N-methylcarbamate) degradation via salicylate-catechol route by expression of a Carbaryl hydrolase (CH) and a 1-naphthol 2-hydroxylase (1NH). Additionally, the engineered strain exhibited faster growth on Carbaryl upon expression of the McbT protein (encoded by the mcbT gene, a part of Carbaryl degradation upper operon of Pseudomonas sp. C5pp). Bioinformatic analyses predict McbT to be an outer membrane protein, and Carbaryl-dependent expression suggests its probable role in Carbaryl uptake. Enzyme activity and protein analyses suggested periplasmic localization of CH (carrying transmembrane domain plus signal peptide sequence at the N-terminus) and 1NH, enabling compartmentalization of the pathway. Enzyme activity, whole-cell oxygen uptake, spent media analyses, and qPCR results suggest that the engineered strain preferentially utilizes Carbaryl over glucose. The plasmid-encoded degradation property was stable for 75-90 generations even in the absence of selection pressure (kanamycin or Carbaryl). These results indicate the utility of P. bharatica CSV86T as a potential host for engineering various aromatic compound degradation pathways.IMPORTANCEThe current study describes engineering of Carbaryl metabolic pathway in Pseudomonas bharatica CSV86T. Carbaryl, a naphthalene-derived carbamate pesticide, is known to act as an endocrine disruptor, mutagen, cytotoxin, and carcinogen. Removal of xenobiotics from the environment using bioremediation faces challenges, such as slow degradation rates, instability of the degradation phenotype, and presence of simple carbon sources in the environment. The engineered CSV86-MEC2 overcomes these disadvantages as Carbaryl was degraded preferentially over glucose. Furthermore, the plasmid-borne degradation phenotype is stable, and presence of glucose and organic acids does not repress Carbaryl metabolism in the strain. The study suggests the role of outer membrane protein McbT in Carbaryl transport. This work highlights the suitability of P. bharatica CSV86T as an ideal host for engineering aromatic pollutant degradation pathways.
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Affiliation(s)
- Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sukhjeet Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sravanti T. Kasarlawar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Prashant S. Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Salter C, Westrick JA, Chaganti SR, Birbeck JA, Peraino NJ, Weisener CG. Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics. WATER RESEARCH 2023; 247:120816. [PMID: 37952399 DOI: 10.1016/j.watres.2023.120816] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/11/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023]
Abstract
As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.
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Affiliation(s)
- Chelsea Salter
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada.
| | - Judy A Westrick
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, School for Environment and Sustainability, University of Michigan, 440 Church Street, Ann Arbor, MI 48109, United States
| | - Johnna A Birbeck
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Nicholas J Peraino
- Lumigen Instrument Center, Department of Chemistry, Wayne State University, Detroit, MI 48202, United States
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada
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5
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Yesankar PJ, Patil A, Kapley A, Qureshi A. Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons. World J Microbiol Biotechnol 2023; 39:166. [PMID: 37076735 DOI: 10.1007/s11274-023-03617-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023]
Abstract
Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.
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Affiliation(s)
- Prerna J Yesankar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - Ayurshi Patil
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
| | - Asifa Qureshi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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6
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Ma XC, Wang K, Gao XL, Li XK, Liu GG, Chen HY, Piao CY, You SJ. Temperature-regulated and starvation-induced refractory para-toluic acid anaerobic biotransformation. CHEMOSPHERE 2023; 311:137008. [PMID: 36377119 DOI: 10.1016/j.chemosphere.2022.137008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/04/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Little research was focused on the anerobic degradation of refractory para-toluic acid at present. Thus, temperature-regulated anaerobic system of para-toluic acid fed as sole substrate was built and investigated via microbiota, metabolism intermediates, and function prediction in this study. Results showed that low methane yield was produced in para-toluic acid anaerobic system at alkaline condition. And the causes were owing to anaerobic methane oxidation and potentially H2S production at 37 °C, N2 production by denitrification before starvation and propionic acid occurrence after starvation at 27 °C, and production of N2 and free ammonia, and accumulation of acetic acid at 52 °C. Simultaneously, hydrogenotrophic methanogenesis dependent on syntrophic acetate oxidation (SAO) was predominant, facilitating the removal of para-toluic acid at 52 °C. Moreover, the key intermediate changed from phthalic acid of 37 °C and 27 °C before starvation to terephthalic acid of 52 °C. Starvation promoted removal of para-toluic acid through benzoyl-CoA pathway by Syntrophorhabdus, enrichment of syntrophic propionate degraders of Bacteroidetes and Ignavibacteriaceae, and increase of methylotrophic methanogens.
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Affiliation(s)
- Xiao-Chen Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ke Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; National Engineering Research Center for Safe Sludge Disposal and Resource Recovery, Harbin Institute of Technology, Harbin, 150090, China; Harbin Institute of Technology National Engineering Research Center of Water Resources Co., Ltd, Guangdong Yuehai Water Investment Co., Ltd, Harbin, 150090, China.
| | - Xin-Lei Gao
- Harbin Institute of Technology National Engineering Research Center of Water Resources Co., Ltd, Guangdong Yuehai Water Investment Co., Ltd, Harbin, 150090, China
| | - Xiang-Kun Li
- School of Civil and Transportation, Hebei University of Technology, Tianjin, 300401, China.
| | - Gai-Ge Liu
- School of Civil and Transportation, Hebei University of Technology, Tianjin, 300401, China
| | - Hong-Ying Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Chen-Yu Piao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Shi-Jie You
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
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Ren H, Deng Y, Ma L, Wei Z, Ma L, Yang D, Wang B, Luo ZY. Enhanced biodegradation of oil-contaminated soil oil in shale gas exploitation by biochar immobilization. Biodegradation 2022; 33:621-639. [PMID: 36214905 DOI: 10.1007/s10532-022-09999-6] [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: 04/24/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
Abstract
The enhanced biodegradation of oil-contaminated soil by fixing microorganisms with corn cob biochar was investigated. It was found that the components of oil in the test soil were mainly straight-chain alkanes and branched alkanes. When using corn cob biochar as a carrier to immobilize microorganisms, the best particle size of corn cob biochar as an immobilization carrier was 0.08 mm, and the best immobilization time was 18 h. SEM analysis confirmed that the microorganisms were immobilized on the corn cob biochar. Immobilized microorganisms exhibited high biodegradability under stress to high concentrations of petroleum pollutants, heavy metals, and organic pollutants. Infrared spectroscopy analysis showed that oxygen-containing groups such as hydroxyl, carboxyl, and methoxy on the surface of biochar were involved in the complexation of heavy metals. The mechanism of immobilization promoted microbial degradation of oil contamination was explained by gas chromatography mass. First, alkanes and aromatics were adsorbed by corn cob biochar and passed to immobilized microorganisms to promote their degradation. Their bioavailability increased, especially for aromatics. Second, biochar provided a more suitable environment for microorganisms to degrade. Third, the conversion of ketones to acids was accelerated during the biodegradation of alkanes, and the biodegradation of alkanes was accelerated by immobilization. The biodegradable efficiency of oil by immobilized microorganisms in soil was 70.10% within 60 days, 28.80% higher than that of free microorganisms. The degradation of immobilized microorganisms was highly correlated with the activities of catalase, urease, and polyphenol oxidase.
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Affiliation(s)
- Hongyang Ren
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China. .,State Environmental Protection Key Laboratory of Collaborative Control and Remediation of Soil and Water Pollution, Chengdu, 610059, China. .,Oil & Gas Field Applied Chemistry Key Laboratory of Sichuan Province, Chengdu, 610500, China.
| | - Yuanpeng Deng
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China
| | - Liang Ma
- Department of Quality, Health, Safety and Environmental Protection, PetroChina Zhejiang Oilfield Company, Hangzhou, 310000, People's Republic of China
| | - Zijing Wei
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China
| | - Lingli Ma
- Ecological and Environmental Monitoring Center of Chongqing, Chongqing, 401147, China
| | - Demin Yang
- National Joint Local Engineering Research Center for Shale Gas Exploration and Development, Chongqing Institute of Geology and Mineral Resources, Chongqing, 401120, China
| | - Bing Wang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, 610500, China
| | - Zheng-Yu Luo
- State Environmental Protection Key Laboratory of Collaborative Control and Remediation of Soil and Water Pollution, Chengdu, 610059, China
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8
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Geng S, Qin W, Cao W, Wang Y, Ding A, Zhu Y, Fan F, Dou J. Pilot-scale bioaugmentation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil using an indigenous bacterial consortium in soil-slurry bioreactors. CHEMOSPHERE 2022; 287:132183. [PMID: 34500332 DOI: 10.1016/j.chemosphere.2021.132183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/08/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Soil-slurry bioreactor based bioremediation of polycyclic aromatic hydrocarbons (PAHs) contaminated soil was studied through laboratory and pilot-scale trials, in which the degradation mechanism was explored. Indigenous PAH-degrading consortium was firstly screened out and it degraded 80.5% of total PAHs in lab-scale bioreactors. Then a pilot-scale trial lasting 410 days was conducted in two bioreactors of 1.5 m3 to examine the operating parameters and validate the optimum running conditions. During the initial 200 days, the crucial running parameters affecting PAH removal were evaluated and selected. Subsequently, an average PAH removal rate of 93.4% was achieved during 15 consecutive batches (210 days) under the optimum running conditions. The kinetic analysis showed that the reactor under optimum conditions achieved the highest PAH degradation rate of 0.1795 day-1 and the shortest half-life of 3.86 days. Notably, efficient mass transfer of PAHs and high biodegradation capability by bioaugmented consortia in soil-slurry bioreactors were two key mechanisms for appreciable PAH removal performance. Under the optimal operating conditions, the degradation rate of low-molecular-weight (LMW) PAHs was significantly higher than high-molecular-weight (HMW) PAHs; when the mass transfer was limited, there was no significant difference between their degradation behaviors. Both microbial co-metabolism and collaborative metabolism might occur when all PAHs demonstrated low degradation rates. The findings provide insightful guidance on the future assessment and remediation practices of PAH-contaminated sites.
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Affiliation(s)
- Shuying Geng
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Wei Qin
- School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Wei Cao
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Yingying Wang
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Aizhong Ding
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Yi Zhu
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China
| | - Fuqiang Fan
- Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, 519087, PR China.
| | - Junfeng Dou
- Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing, 100875, PR China.
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Mohapatra M, Yadav R, Rajput V, Dharne MS, Rastogi G. Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112738. [PMID: 34020306 DOI: 10.1016/j.jenvman.2021.112738] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 04/05/2021] [Accepted: 04/29/2021] [Indexed: 05/22/2023]
Abstract
Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.
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Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India
| | - Mahesh S Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India.
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Aksu D, Diallo MM, Şahar U, Uyaniker TA, Ozdemir G. High expression of ring-hydroxylating dioxygenase genes ensure efficient degradation of p-toluate, phthalate, and terephthalate by Comamonas testosteroni strain 3a2. Arch Microbiol 2021; 203:4101-4112. [PMID: 34057546 DOI: 10.1007/s00203-021-02395-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
Para-toluic acid, a major pollutant in industrial wastewater, is hazardous to human health. It has been demonstrated that Gram-negative bacteria are among the most effective degraders of para-toluic acid. In this study, the ability of Comamonas testosteroni strain 3a2, isolated from a petrochemical industry wastewater, to degrade para-toluic acid was investigated. The effect of different carbon (glucose and ethylene glycol) and nitrogen sources (urea, yeast extract, peptone, NaNO3, NH4NO3) on the biodegradation of para-toluic acid by the isolate 3a2 was evaluated. Furthermore, ring hydroxylating dioxygenase genes were amplified by PCR and their expression was evaluated during the biodegradation of para-toluic acid. The results indicated that strain 3a2 was able to degrade up to 1000 mg/L of para-toluic acid after 14 h. The highest degradation yield was recorded in the presence of yeast extract as nitrogen source. However, the formation of terephthalic acid and phthalic acid was noted during para-toluic acid degradation by the isolate 3a2. Toluate 1,2-dioxygenase, terephthalate 1,2 dioxygenase, and phthalate 4,5 dioxygenase genes were detected in the genomic DNA of 3a2. The induction of ring hydroxylating dioxygenase genes was proportional to the concentration of each hydrocarbon. This study showed that the isolate 3a2 can produce terephthalate and phthalate during the para-toluic acid biodegradation, which were also degraded after 24 h.
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Affiliation(s)
- Didem Aksu
- Application and Research Center for Testing and Analysis, Ege University, Izmir, Turkey.
| | | | - Umut Şahar
- Biology Department, Faculty of Science, Ege University, Izmir, Turkey
| | | | - Guven Ozdemir
- Biology Department, Faculty of Science, Ege University, Izmir, Turkey
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Chamberlain CA, Hatch M, Garrett TJ. Oxalobacter formigenes produces metabolites and lipids undetectable in oxalotrophic Bifidobacterium animalis. Metabolomics 2020; 16:122. [PMID: 33219444 DOI: 10.1007/s11306-020-01747-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/11/2020] [Indexed: 01/01/2023]
Abstract
INTRODUCTION In the search for new potential therapies for pathologies of oxalate, such as kidney stone disease and primary hyperoxaluria, the intestinal microbiome has generated significant interest. Resident oxalate-degrading bacteria inhabit the gastrointestinal tract and reduce absorption of dietary oxalate, thereby potentially lowering the potency of oxalate as a risk factor for kidney stone formation. Although several species of bacteria have been shown to degrade oxalate, select strains of Oxalobacter formigenes (O. formigenes) have thus far demonstrated the unique ability among oxalotrophs to initiate a net intestinal oxalate secretion into the lumen from the bloodstream, allowing them to feed on both dietary and endogenous metabolic oxalate. There is significant interest in this function as a potential therapeutic application for circulating oxalate reduction, although its mechanism of action is still poorly understood. Since this species-exclusive, oxalate-regulating function is reported to be dependent on the use of a currently unidentified secreted bioactive compound, there is much interest in whether O. formigenes produces unique biochemicals that are not expressed by other oxalotrophs which lack the ability to transport oxalate. Hence, this study sought to analyze and compare the metabolomes of O. formigenes and another oxalate degrader, Bifidobacterium animalis subsp. lactis (B. animalis), to determine whether O. formigenes could produce features undetectable in another oxalotroph, thus supporting the theory of a species-exclusive secretagogue compound. METHODS A comparative metabolomic analysis of O. formigenes strain HC1 (a human isolate) versus B. animalis, another oxalate-degrading human intestinal microbe, was performed by ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS). Bacteria were cultured independently in anaerobic conditions, harvested, lysed, and extracted by protein precipitation. Metabolite extracts were chromatographically separated and analyzed by UHPLC-HRMS using reverse phase gradient elution (ACE Excel 2 C18-Pentafluorophenyl column) paired with a Q Exactive™ mass spectrometer. OBJECTIVES The purpose of this study was to assess whether O. formigenes potentially produces unique biochemicals from other oxalate degraders to better understand its metabolic profile and provide support for the theoretical production of a species-exclusive secretagogue compound responsible for enhancing intestinal oxalate secretion. RESULTS We report a panel of metabolites and lipids detected in the O. formigenes metabolome which were undetectable in B. animalis, several of which were identified either by mass-to-charge ratio and retention time matching to our method-specific metabolite library or MS/MS fragmentation. Furthermore, re-examination of data from our previous work showed most of these features were also undetected in the metabolomes of Lactobacillus acidophilus and Lactobacillus gasseri, two other intestinal oxalate degraders. CONCLUSIONS Our observation of O. formigenes metabolites and lipids which were undetectable in other oxalotrophs suggests that this bacterium likely holds the ability to produce biochemicals not expressed by at least a selection of other oxalate degraders. These findings provide support for the hypothesized biosynthesis of a species-exclusive secretagogue responsible for the stimulation of net intestinal oxalate secretion.
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Affiliation(s)
- Casey A Chamberlain
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Marguerite Hatch
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA.
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Verma N, Kantiwal U, Nitika, Yadav YK, Teli S, Goyal D, Pandey J. Catalytic Promiscuity of Aromatic Ring-Hydroxylating Dioxygenases and Their Role in the Plasticity of Xenobiotic Compound Degradation. MICROORGANISMS FOR SUSTAINABILITY 2019. [DOI: 10.1007/978-981-13-7462-3_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Phenoxazinone synthase and antimicrobial activity by a bis(1,3-diamino-2-propanolate) cobalt(III) complex. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1562-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth. BMC Microbiol 2018; 18:12. [PMID: 29444636 PMCID: PMC5813417 DOI: 10.1186/s12866-018-1158-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/09/2018] [Indexed: 11/16/2022] Open
Abstract
Background The gene expression profile and metabolic pathways of Aspergillus oryzae underlying the anatomical and morphological differentiation across different growth stages have not been fully characterized. The rapid development of next-generation sequencing technologies provides advanced knowledge of the genomic organization of A. oryzae. Results In this study, we characterized the growth and development of A. oryzae at different growth stages, including the adaptive phase, logarithmic phase, and stationary phase. Our results revealed that A. oryzae undergoes physiological and morphological differentiation across the different stages. RNA-seq was employed to analyze the three stages of A. oryzae, which generated more than 27 million high-quality reads per sample. The analysis of differential gene expression showed more genes expressed differentially upon transition from the adaptive phase to the logarithmic and stationary phases, while relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase. GO classification of the differentially expressed genes among different growth stages revealed that most of these genes were enriched for single-organism process, metabolic process, and catalytic activity. These genes were then subjected to a clustering analysis. The results showed that the cluster with the majority of genes with increased expression upon transition from the adaptive phase to the logarithmic phase, and steady expression from the logarithmic phase to the stationary phase was mainly involved in the carbohydrate and amino acid metabolism. Conclusion Our results provide a foundation for identifying developmentally important genes and understanding the biological processes across various growth stages. Electronic supplementary material The online version of this article (10.1186/s12866-018-1158-z) contains supplementary material, which is available to authorized users.
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Michas A, Vestergaard G, Trautwein K, Avramidis P, Hatzinikolaou DG, Vorgias CE, Wilkes H, Rabus R, Schloter M, Schöler A. More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. MICROBIOME 2017; 5:118. [PMID: 28893308 PMCID: PMC5594585 DOI: 10.1186/s40168-017-0337-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/03/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods. RESULTS Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments. CONCLUSIONS The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.
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Affiliation(s)
- Antonios Michas
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Pavlos Avramidis
- Department of Geology, University of Patras, Panepistimioupoli Patron, 26504 Rio-Patras, Greece
| | - Dimitris G. Hatzinikolaou
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Constantinos E. Vorgias
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Heinz Wilkes
- Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
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Tarafdar A, Sinha A. Estimation of decrease in cancer risk by biodegradation of PAHs content from an urban traffic soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:10373-10380. [PMID: 28281056 DOI: 10.1007/s11356-017-8676-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
The role of preferential biodegradation in the reduction of cancer risk caused by polycyclic aromatic hydrocarbons (PAHs) has been studied. A consortium of microorganisms isolated from aged oil refinery exposed soil was used to degrade 13 PAHs content extracted from an urban traffic site soil. The biodegradation arranged in a batch process with a mineral salt broth, where PAHs were the sole carbon source. 70.46% biodegradation of the total PAHs occurred in an incubation period of 25 days. Sequential or preferential biodegradation took place as the lower molecular weight (LMW) PAHs were more prone to biodegradation than that of the higher molecular weight (HMW) PAHs. Microorganisms from the isolated consortia preferred the simpler carbon sources first. The relatively higher carcinogenicity of the HMW PAHs than that of the LMW PAHs leads to only 40.26% decrement in cancer risk. Initial cancer risk for children was 1.60E-05, which was decreased to 9.47E-06, whereas, for the adults, the risk decreased to 1.01E-05 from an initial value of 1.71E-05. The relative skin adherence factor for soil (AF) turned out to be the most influential parameter with 54.2% contributions to variance in total cancer risk followed by the exposure duration (ED) for children. For the adults, most contributions to the variance in total cancer risk were 58.5% by ED and followed by AF.
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Affiliation(s)
- Abhrajyoti Tarafdar
- Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, Jharkhand, 826004, India
| | - Alok Sinha
- Department of Environmental Science and Engineering, Indian Institute of Technology (ISM), Dhanbad, Jharkhand, 826004, India.
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Dellagnezze BM, Vasconcellos SP, Angelim AL, Melo VMM, Santisi S, Cappello S, Oliveira VM. Bioaugmentation strategy employing a microbial consortium immobilized in chitosan beads for oil degradation in mesocosm scale. MARINE POLLUTION BULLETIN 2016; 107:107-117. [PMID: 27158046 DOI: 10.1016/j.marpolbul.2016.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 05/22/2023]
Abstract
A bacterial consortium composed by four metagenomic clones and Bacillus subtilis strain CBMAI 707, all derived from petroleum reservoirs, was entrapped in chitosan beads and evaluated regarding hydrocarbon degradation capability. Experiments were carried out in mesocosm scale (3000L) with seawater artificially polluted with crude oil. At different time intervals, mesocosms were sampled and subjected to GC-FID and microbiological analyses, as total and heterotrophic culturable bacterial abundance (DAPI and CFU count), biological oxygen demand (BOD) and taxonomic diversity (massive sequencing of 16S rRNA genes). The results obtained showed that degradation of n-alkane hydrocarbons was similar between both treatments. However, aromatic compound degradation was more efficient in bioaugmentation treatment, with biodegradation percentages reaching up to 99% in 30days. Community dynamics was different between treatments and the consortium used in the bioaugmentation treatment contributed to a significant increase in aromatic hydrocarbon degradation.
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Affiliation(s)
- B M Dellagnezze
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil.
| | - S P Vasconcellos
- Federal University of São Paulo (UNIFESP), Rua Prof. Artur Riedel, 275, CEP 09972-270, Jd. Eldorado, Diadema, SP, Brazil
| | - A L Angelim
- Lembiotech (UFC), Federal University of Ceará, Av. Humberto Monte, 2977, Campus do Pici, Bloco 909, 60455-000, Fortaleza, CE, Brazil
| | - V M M Melo
- Lembiotech (UFC), Federal University of Ceará, Av. Humberto Monte, 2977, Campus do Pici, Bloco 909, 60455-000, Fortaleza, CE, Brazil
| | - S Santisi
- Institute for Coastal Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR) of Messina, Messina, Italy
| | - S Cappello
- Institute for Coastal Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR) of Messina, Messina, Italy
| | - V M Oliveira
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil
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Fuentes S, Ding GC, Cárdenas F, Smalla K, Seeger M. Assessing environmental drivers of microbial communities in estuarine soils of the Aconcagua River in Central Chile. FEMS Microbiol Ecol 2015; 91:fiv110. [PMID: 26362923 DOI: 10.1093/femsec/fiv110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2015] [Indexed: 11/14/2022] Open
Abstract
Aconcagua River basin (Central Chile) harbors diverse economic activities such as agriculture, mining and a crude oil refinery. The aim of this study was to assess environmental drivers of microbial communities in Aconcagua River estuarine soils, which may be influenced by anthropogenic activities taking place upstream and by natural processes such as tides and flood runoffs. Physicochemical parameters were measured in floodplain soils along the estuary. Bacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Pseudomonas, Bacillus and Fungi were studied by DGGE fingerprinting of 16S rRNA gene and ribosomal ITS-1 amplified from community DNA. Correlations between environment and communities were assessed by distance-based redundancy analysis. Mainly hydrocarbons, pH and the composed variable copper/arsenic/calcium but in less extent nitrogen and organic matter/phosphorous/magnesium correlated with community structures at different taxonomic levels. Aromatic hydrocarbons degradation potential by bacterial community was studied. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases genes were detected only at upstream sites. Naphthalene dioxygenase ndo genes were heterogeneously distributed along estuary, and related to Pseudomonas, Delftia, Comamonas and Ralstonia. IncP-1 plasmids were mainly present at downstream sites, whereas IncP-7 and IncP-9 plasmids showed a heterogeneous distribution. This study strongly suggests that pH, copper, arsenic and hydrocarbons are main drivers of microbial communities in Aconcagua River estuarine soils.
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Affiliation(s)
- Sebastián Fuentes
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Center of Nanotechnology and Systems Biology & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123 Valparaíso, Chile
| | - Guo-Chun Ding
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), 38116 Braunschweig, Germany College of Resources and Environmental Sciences, China Agricultural University, 100193 Beijing, China
| | - Franco Cárdenas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Center of Nanotechnology and Systems Biology & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123 Valparaíso, Chile
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), 38116 Braunschweig, Germany
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Center of Nanotechnology and Systems Biology & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123 Valparaíso, Chile
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Shifts in Microbial Community and Its Correlation with Degradative Efficiency in a Wastewater Treatment Plant. Appl Biochem Biotechnol 2015; 176:2131-43. [DOI: 10.1007/s12010-015-1703-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/01/2015] [Indexed: 11/26/2022]
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Johnson CW, Beckham GT. Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin. Metab Eng 2015; 28:240-247. [DOI: 10.1016/j.ymben.2015.01.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/08/2015] [Accepted: 01/13/2015] [Indexed: 10/24/2022]
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Dellagnezze BM, de Sousa GV, Martins LL, Domingos DF, Limache EEG, de Vasconcellos SP, da Cruz GF, de Oliveira VM. Bioremediation potential of microorganisms derived from petroleum reservoirs. MARINE POLLUTION BULLETIN 2014; 89:191-200. [PMID: 25457810 DOI: 10.1016/j.marpolbul.2014.10.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/03/2014] [Accepted: 10/04/2014] [Indexed: 06/04/2023]
Abstract
Bacterial strains and metagenomic clones, both obtained from petroleum reservoirs, were evaluated for petroleum degradation abilities either individually or in pools using seawater microcosms for 21 days. Gas Chromatography-Flame Ionization Detector (GC-FID) and Gas Chromatography-Mass Spectrometry (GC-MS) analyses were carried out to evaluate crude oil degradation. The results showed that metagenomic clones 1A and 2B were able to biodegrade n-alkanes (C14 to C33) and isoprenoids (phytane and pristane), with rates ranging from 31% to 47%, respectively. The bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 showed higher rates reaching 99% after 21 days. The metagenomic clone pool biodegraded these compounds at rates ranging from 11% to 45%. Regarding aromatic compound biodegradation, metagenomic clones 2B and 10A were able to biodegrade up to 94% of phenanthrene and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 55% to 70% after 21 days, while the bacteria Dietzia maris CBMAI 705 and Micrococcus sp. CBMAI 636 were able to biodegrade 63% and up to 99% of phenanthrene, respectively, and methylphenanthrenes (3-MP, 2-MP, 9-MP and 1-MP) with rates ranging from 23% to 99% after 21 days. In this work, isolated strains as well as metagenomic clones were capable of degrading several petroleum compounds, revealing an innovative strategy and a great potential for further biotechnological and bioremediation applications.
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Affiliation(s)
- Bruna Martins Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | - Gabriel Vasconcelos de Sousa
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Laercio Lopes Martins
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Daniela Ferreira Domingos
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | - Elmer E G Limache
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil
| | | | - Georgiana Feitosa da Cruz
- Laboratory of Engineering and Petroleum Exploration, Darcy Ribeiro North Fluminense State University - LENEP/UENF, POB 119562, 27910-970 Macaé, RJ, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, CEP 13148-218, Paulinia, Brazil.
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Jadeja NB, More RP, Purohit HJ, Kapley A. Metagenomic analysis of oxygenases from activated sludge. BIORESOURCE TECHNOLOGY 2014; 165:250-256. [PMID: 24631150 DOI: 10.1016/j.biortech.2014.02.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/13/2014] [Accepted: 02/15/2014] [Indexed: 06/03/2023]
Abstract
Oxygenases play a key role in degradation of the aromatic compounds in the wastewater. This study explores the oxygenase coding gene sequences from the metagenome of activated biomass. Based on these results, the catabolic capacity of the activated sludge was assessed towards degradation of naphthalene, anthracene, phenol, biphenyl and o-toluidine. Oxygenases found in this study were compared with oxygenases from three other metagenome datasets. Results demonstrate that despite different geographical locations and source, many genes coding for oxygenases were common between treatment plants. 1, 2 Homogentisate dioxygenase and phenylacetate CoA oxygenases were present in all four metagenomes. Metagenomics provides a vast amount of data that needs to be mined with specific targets to harness the potential of the microbial world.
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Affiliation(s)
- Niti B Jadeja
- Environmental Genomics Division, National Environmental Engineering Research Institute, (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India
| | - Ravi P More
- Environmental Genomics Division, National Environmental Engineering Research Institute, (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India
| | - Hemant J Purohit
- Environmental Genomics Division, National Environmental Engineering Research Institute, (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India
| | - Atya Kapley
- Environmental Genomics Division, National Environmental Engineering Research Institute, (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India.
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More RP, Mitra S, Raju SC, Kapley A, Purohit HJ. Mining and assessment of catabolic pathways in the metagenome of a common effluent treatment plant to induce the degradative capacity of biomass. BIORESOURCE TECHNOLOGY 2014; 153:137-146. [PMID: 24355504 DOI: 10.1016/j.biortech.2013.11.065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/19/2013] [Accepted: 11/24/2013] [Indexed: 06/03/2023]
Abstract
Metagenome analysis was used to understand the microbial community in activated sludge treating industrial wastewaters at a Common Effluent Treatment Plant (CETP) in South India. The taxonomic profile mapped onto National Center for Biotechnology Information (NCBI) taxonomy using MEtaGenome ANalyzer (MEGAN), demonstrated that the most abundant domain belonged to prokaryotes, dominated by bacteria. Bacteria representing nine phyla were identified from the sequence data including representatives from two new phyla, Synergistetes and Elusimicrobia. Functional analysis of the metagenome, with specific reference to the metabolism of aromatic compounds, revealed the dominance of genes of the central meta-cleavage pathway. This information was used to improve the degradative efficiency in the wastewater treatment plant. A pilot scale plant was set up with 200L of activated sludge using salicylate induced sludge and results demonstrated 52% removal in chemical oxygen demand (COD) against non-induced biomass.
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Affiliation(s)
- Ravi P More
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur 440020 (MH), India
| | - Suparna Mitra
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Sajan C Raju
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur 440020 (MH), India
| | - Atya Kapley
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur 440020 (MH), India.
| | - Hemant J Purohit
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur 440020 (MH), India
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The quest for a unified view of bacterial land colonization. ISME JOURNAL 2014; 8:1358-69. [PMID: 24451209 PMCID: PMC4069389 DOI: 10.1038/ismej.2013.247] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/15/2013] [Accepted: 12/12/2013] [Indexed: 12/13/2022]
Abstract
Exploring molecular mechanisms underlying bacterial water-to-land transition represents a critical start toward a better understanding of the functioning and stability of the terrestrial ecosystems. Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. We hypothesize that bacterial land colonization is dominated by a single-gene sweep, that is, the emergence of dnaE2 derived from an early duplication event of the primordial dnaE, followed by a series of niche-specific genomic adaptations, including GC content increase, intensive horizontal gene transfer and constant genome expansion. In addition, early bacterial radiation may be stimulated by an explosion of land-borne hosts (for example, plants and animals) after initial land colonization events.
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Pirog TP. MICROBIAL SURFACTANTS. II. LIPOPEPTIDES. BIOTECHNOLOGIA ACTA 2014. [DOI: 10.15407/biotech7.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Fan X, Liu X, Huang R, Liu Y. Identification and characterization of a novel thermostable pyrethroid-hydrolyzing enzyme isolated through metagenomic approach. Microb Cell Fact 2012; 11:33. [PMID: 22409882 PMCID: PMC3317823 DOI: 10.1186/1475-2859-11-33] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 03/13/2012] [Indexed: 11/21/2022] Open
Abstract
Background Pyrethroid pesticides are broad-spectrum pest control agents in agricultural production. Both agricultural and residential usage is continuing to grow, leading to the development of insecticide resistance in the pest and toxic effects on a number of nontarget organisms. Thus, it is necessary to hunt suitable enzymes including hydrolases for degrading pesticide residues, which is an efficient "green" solution to biodegrade polluting chemicals. Although many pyrethroid esterases have consistently been purified and characterized from various resources including metagenomes and organisms, the thermostable pyrethroid esterases have not been reported up to the present. Results In this study, we identified a novel pyrethroid-hydrolyzing enzyme Sys410 belonging to familyV esterases/lipases with activity-based functional screening from Turban Basin metagenomic library. Sys410 contained 280 amino acids with a predicted molecular mass (Mr) of 30.8 kDa and was overexpressed in Escherichia coli BL21 (DE3) in soluble form. The optimum pH and temperature of the recombinant Sys410 were 6.5 and 55°C, respectively. The enzyme was stable in the pH range of 4.5-8.5 and at temperatures below 50°C. The activity of Sys410 decreased a little when stored at 4°C for 10 weeks, and the residual activity reached 94.1%. Even after incubation at 25°C for 10 weeks, it kept 68.3% of its activity. The recombinant Sys410 could hydrolyze a wide range of ρ-nitrophenyl esters, but its best substrate is ρ-nitrophenyl acetate with the highest activity (772.9 U/mg). The enzyme efficiently degraded cyhalothrin, cypermethrin, sumicidin, and deltamethrin under assay conditions of 37°C for 15 min, with exceeding 95% hydrolysis rate. Conclusion This is the first report to construct metagenomic libraries from Turban Basin to obtain the thermostable pyrethroid-hydrolyzing enzyme. The recombinant Sys410 with broad substrate specificities and high activity was the most thermostable one of the pyrethroid-hydrolyzing esterases studied before, which made it an ideal candidate for the detoxification of pyrethroids.
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Affiliation(s)
- Xinjiong Fan
- School of life sciences, Sun Yat-sen University, Guangzhou 510275, P R China
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Paissé S, Goñi-Urriza M, Stadler T, Budzinski H, Duran R. Ring-hydroxylating dioxygenase (RHD) expression in a microbial community during the early response to oil pollution. FEMS Microbiol Ecol 2012; 80:77-86. [DOI: 10.1111/j.1574-6941.2011.01270.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 11/08/2011] [Accepted: 11/24/2011] [Indexed: 11/27/2022] Open
Affiliation(s)
- Sandrine Paissé
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Thibault Stadler
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Hélène Budzinski
- Institut des Sciences Moléculaires; UMR CNRS 5255; Université Bordeaux; Talence; France
| | - Robert Duran
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
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Montersino S, van Berkel WJH. Functional annotation and characterization of 3-hydroxybenzoate 6-hydroxylase from Rhodococcus jostii RHA1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:433-42. [PMID: 22207056 DOI: 10.1016/j.bbapap.2011.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/09/2011] [Accepted: 12/14/2011] [Indexed: 12/11/2022]
Abstract
The genome of Rhodococcus jostii RHA1 contains an unusually large number of oxygenase encoding genes. Many of these genes have yet an unknown function, implying that a notable part of the biochemical and catabolic biodiversity of this Gram-positive soil actinomycete is still elusive. Here we present a multiple sequence alignment and phylogenetic analysis of putative R. jostii RHA1 flavoprotein hydroxylases. Out of 18 candidate sequences, three hydroxylases are absent in other available Rhodococcus genomes. In addition, we report the biochemical characterization of 3-hydroxybenzoate 6-hydroxylase (3HB6H), a gentisate-producing enzyme originally mis-annotated as salicylate hydroxylase. R. jostii RHA1 3HB6H expressed in Escherichia coli is a homodimer with each 47kDa subunit containing a non-covalently bound FAD cofactor. The enzyme has a pH optimum around pH 8.3 and prefers NADH as external electron donor. 3HB6H is active with a series of 3-hydroxybenzoate analogues, bearing substituents in ortho- or meta-position of the aromatic ring. Gentisate, the physiological product, is a non-substrate effector of 3HB6H. This compound is not hydroxylated but strongly stimulates the NADH oxidase activity of the enzyme.
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Pinto UM, Flores-Mireles AL, Costa ED, Winans SC. RepC protein of the octopine-type Ti plasmid binds to the probable origin of replication within repC and functions only in cis. Mol Microbiol 2011; 81:1593-606. [PMID: 21883520 DOI: 10.1111/j.1365-2958.2011.07789.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Vegetative replication and partitioning of many plasmids and some chromosomes of alphaproteobacteria are directed by their repABC operons. RepA and RepB proteins direct the partitioning of replicons to daughter cells, while RepC proteins are replication initiators, although they do not resemble any characterized replication initiation protein. Here we show that the replication origin of an Agrobacterium tumefaciens Ti plasmid resides fully within its repC gene. Purified RepC bound to a site within repC with moderate affinity, high specificity and with twofold cooperativity. The binding site was localized to an AT-rich region that contains a large number of GANTC sites, which have been implicated in replication regulation in related organisms. A fragment of RepC containing residues 26-158 was sufficient to bind DNA, although with limited sequence specificity. This portion of RepC is predicted to have structural homology to members of the MarR family of transcription factors. Overexpression of RepC in A. tumefaciens caused large increases in copy number in cis but did not change the copy number of plasmids containing the same oriV sequence in trans, confirming other observations that RepC functions only in cis.
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Affiliation(s)
- Uelinton M Pinto
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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Djokic L, Narancic T, Nikodinovic-Runic J, Savic M, Vasiljevic B. Isolation and characterization of four novel Gram-positive bacteria associated with the rhizosphere of two endemorelict plants capable of degrading a broad range of aromatic substrates. Appl Microbiol Biotechnol 2011; 91:1227-38. [PMID: 21706169 DOI: 10.1007/s00253-011-3426-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/31/2011] [Accepted: 06/01/2011] [Indexed: 01/12/2023]
Abstract
Four new Gram-positive, phenol-degrading strains were isolated from the rhizospheres of endemorelict plants Ramonda serbica and Ramonda nathaliae known to exude high amounts of phenolics in the soil. Isolates were designated Bacillus sp. PS1, Bacillus sp. PS11, Streptomyces sp. PS12, and Streptomyces sp. PN1 based on 16S rDNA sequence and biochemical analysis. In addition to their ability to tolerate and utilize high amounts of phenol of either up to 800 or up to 1,400 mg l(-1) without apparent inhibition in growth, all four strains were also able to degrade a broad range of aromatic substrates including benzene, toluene, ethylbenzene, xylenes, styrene, halogenated benzenes, and naphthalene. Isolates were able to grow in pure culture and in defined mixed culture on phenol and on the mixture of BTEX (benzene, toluene, ethylbenzene, and xylenes) compounds as a sole source of carbon and energy. Pure culture of Bacillus sp. PS11 yielded 1.5-fold higher biomass amounts in comparison to mixed culture, under all conditions. Strains successfully degraded phenol in the soil model system (2 g kg(-1)) within 6 days. Activities of phenol hydroxylase, catechol 1,2-dioxygenase, and catechol 2,3-dioxygenase were detected and analyzed from the crude cell extract of the isolates. While all four strains use ortho degradation pathway, enzyme indicative of meta degradation pathway (catechol 2,3-dioxygenase) was also detected in Bacillus sp. PS11 and Streptomyces sp. PN1. Phenol degradation activities were induced 2 h after supplementation by phenol, but not by catechol. Catechol slightly inhibited activity of catechol 2,3-dioxygenase in strains PS11 and PN1.
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Affiliation(s)
- Lidija Djokic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, PO Box 23, 11010, Belgrade, Serbia
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Purification and characterization of benzyl alcohol- and benzaldehyde- dehydrogenase from Pseudomonas putida CSV86. Arch Microbiol 2011; 193:553-63. [PMID: 21448720 DOI: 10.1007/s00203-011-0697-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 03/05/2011] [Accepted: 03/13/2011] [Indexed: 10/18/2022]
Abstract
Pseudomonas putida CSV86 utilizes benzyl alcohol via catechol and methylnaphthalenes through detoxification pathway via hydroxymethylnaphthalenes and naphthaldehydes. Based on metabolic studies, benzyl alcohol dehydrogenase (BADH) and benzaldehyde dehydrogenase (BZDH) were hypothesized to be involved in the detoxification pathway. BADH and BZDH were purified to apparent homogeneity and were (1) homodimers with subunit molecular mass of 38 and 57 kDa, respectively, (2) NAD(+) dependent, (3) broad substrate specific accepting mono- and di-aromatic alcohols and aldehydes but not aliphatic compounds, and (4) BADH contained iron and magnesium, while BZDH contained magnesium. BADH in the forward reaction converted alcohol to aldehyde and required NAD(+), while in the reverse reaction it reduced aldehyde to alcohol in NADH-dependent manner. BZDH showed low K (m) value for benzaldehyde as compared to BADH reverse reaction. Chemical cross-linking studies revealed that BADH and BZDH do not form multi-enzyme complex. Thus, the conversion of aromatic alcohol to acid is due to low K (m) and high catalytic efficiency of BZDH. Phylogenetic analysis revealed that BADH is a novel enzyme and diverged during the evolution to gain the ability to utilize mono- and di-aromatic compounds. The wide substrate specificity of these enzymes enables strain to detoxify methylnaphthalenes to naphthoic acids efficiently.
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Silva-Rocha R, Tamames J, dos Santos VM, de Lorenzo V. The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol 2011; 13:2389-402. [PMID: 21410625 DOI: 10.1111/j.1462-2920.2011.02455.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The regulatory and metabolic networks that rule biodegradation of pollutants by environmental bacteria are wired to the rest of the cellular physiology through both transcriptional factors and intermediary signal molecules. In this review, we examine some formalisms for describing catalytic/regulatory circuits of this sort and advocate the adoption of Boolean logic for combining transcriptional and enzymatic occurrences in the same biological system. As an example, we show how known regulatory and metabolic actions that bring about biodegradation of m-xylene by Pseudomonas putida mt-2 can be represented as clusters of binary operations and then reconstructed as a digital network. Despite the many simplifications, Boolean tools still capture the gross behaviour of the system even in the absence of kinetic constants determined experimentally. On this basis, we argue that still with a limited volume of data binary formalisms allow us to penetrate the raison d'être of extant regulatory and metabolic architectures.
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Affiliation(s)
- Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, 28049, Spain
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Raaijmakers JM, De Bruijn I, Nybroe O, Ongena M. Natural functions of lipopeptides fromBacillusandPseudomonas: more than surfactants and antibiotics. FEMS Microbiol Rev 2010; 34:1037-62. [DOI: 10.1111/j.1574-6976.2010.00221.x] [Citation(s) in RCA: 719] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Deveryshetty J, Phale PS. Biodegradation of phenanthrene by Alcaligenes sp. strain PPH: partial purification and characterization of 1-hydroxy-2-naphthoic acid hydroxylase. FEMS Microbiol Lett 2010; 311:93-101. [PMID: 20727010 DOI: 10.1111/j.1574-6968.2010.02079.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Alcaligenes sp. strain PPH degrades phenanthrene via 1-hydroxy-2-naphthoic acid (1-H2NA), 1,2-dihydroxynaphthalene (1,2-DHN), salicylic acid and catechol. Enzyme activity versus growth profile and heat stability studies suggested the presence of two distinct hydroxylases, namely 1-hydroxy-2-naphthoic acid hydroxylase and salicylate hydroxylase. 1-Hydroxy-2-naphthoic acid hydroxylase was partially purified (yield 48%, fold 81) and found to be a homodimer with a subunit molecular weight of ∼34 kDa. The enzyme was yellow in color, showed UV-visible absorption maxima at 274, 375 and 445 nm, and fluorescence emission maxima at 527 nm suggested it to be a flavoprotein. The apoenzyme prepared by the acid-ammonium sulfate (2 M) dialysis method was colorless, inactive and lost the characteristic flavin absorption spectra but regained ∼90% activity when reconstituted with FAD. Extraction of the prosthetic group and its analysis by HPLC suggests that the holoenzyme contained FAD. The enzyme was specific for 1-H2NA and failed to show activity with any other hydroxynaphthoic acid analogs or salicylic acid. The K(m) for 1-H2NA in the presence of either NADPH or NADH remained unaltered (72 and 75 μM, respectively), suggesting dual specificity for the coenzyme. The K(m) for FAD was determined to be 4.7 μM. The enzyme catalyzed the conversion of 1-H2NA to 1,2-DHN only under aerobic conditions. These results suggested that 1-hydroxy-2-naphthoic acid hydroxylase is a flavoprotein monooxygenase specific for 1-H2NA and different from salicylate-1-hydroxylase.
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Affiliation(s)
- Jaigeeth Deveryshetty
- Department of Biosciences and Bioengineering, Indian Institute Technology Bombay, Mumbai, Maharashtra, India
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Chauhan A, Islam Z, Jain RK, Karthikeyan S. Expression, purification, crystallization and preliminary X-ray analysis of maleylacetate reductase from Burkholderia sp. strain SJ98. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1313-1316. [PMID: 20054138 PMCID: PMC2802890 DOI: 10.1107/s1744309109047319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 11/09/2009] [Indexed: 05/28/2023]
Abstract
Maleylacetate reductase (EC 1.3.1.32) is an important enzyme that is involved in the degradation pathway of aromatic compounds and catalyzes the reduction of maleylacetate to 3-oxoadipate. The gene pnpD encoding maleylacetate reductase in Burkholderia sp. strain SJ98 was cloned, expressed in Escherichia coli and purified by affinity chromatography. The enzyme was crystallized in both native and SeMet-derivative forms by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant at 293 K. The crystals belonged to space group P2(1)2(1)2, with unit-cell parameters a = 72.91, b = 85.94, c = 53.07 A. X-ray diffraction data for the native and SeMet-derivative crystal were collected to 2.7 and 2.9 A resolution, respectively.
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Affiliation(s)
- Archana Chauhan
- Institute of Microbial Technology (CSIR), Sector 39-A, Chandigarh 160 036, India
| | - Zeyaul Islam
- Institute of Microbial Technology (CSIR), Sector 39-A, Chandigarh 160 036, India
| | - Rakesh Kumar Jain
- Institute of Microbial Technology (CSIR), Sector 39-A, Chandigarh 160 036, India
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Bypassing isophthalate inhibition by modulating glutamate dehydrogenase (GDH): purification and kinetic characterization of NADP-GDHs from isophthalate-degrading Pseudomonas aeruginosa strain PP4 and Acinetobacter lwoffii strain ISP4. J Bacteriol 2009; 192:801-6. [PMID: 19933355 DOI: 10.1128/jb.01365-09] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa strain PP4 and Acinetobacter lwoffii strain ISP4 metabolize isophthalate as a sole source of carbon and energy. Isophthalate is known to be a competitive inhibitor of glutamate dehydrogenase (GDH), which is involved in C and N metabolism. Strain PP4 showed carbon source-dependent modulation of NADP-GDH; GDH(I) was produced when cells were grown on isophthalate, while GDH(II) was produced when cells were grown on glucose. Strain ISP4 produced a single form of NADP-GDH, GDH(P), when it was grown on either isophthalate or rich medium (2YT). All of the forms of GDH were purified to homogeneity and characterized. GDH(I) and GDH(II) were found to be homotetramers, while GDH(P) was found to be a homohexamer. GDH(II) was more sensitive to inhibition by isophthalate (2.5- and 5.5-fold more sensitive for amination and deamination reactions, respectively) than GDH(I). Differences in the N-terminal sequences and electrophoretic mobilities in an activity-staining gel confirmed the presence of two forms of GDH, GDH(I) and GDH(II), in strain PP4. In strain ISP4, irrespective of the carbon source, the GDH(P) produced showed similar levels of inhibition with isophthalate. However, the specific activity of GDH(P) from isophthalate-grown cells was 2.5- to 3-fold higher than that of GDH(P) from 2YT-grown cells. Identical N-terminal sequences and electrophoretic mobilities in the activity-staining gel suggested the presence of a single form of GDH(P) in strain ISP4. These results demonstrate the ability of organisms to modulate GDH either by producing an entirely different form or by increasing the level of the enzyme, thus enabling strains to utilize isophthalate more efficiently as a sole source of carbon and energy.
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Deveryshetty J, Phale PS. Biodegradation of phenanthrene by Pseudomonas sp. strain PPD: purification and characterization of 1-hydroxy-2-naphthoic acid dioxygenase. MICROBIOLOGY-SGM 2009; 155:3083-3091. [PMID: 19574301 DOI: 10.1099/mic.0.030460-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonas sp. strain PPD can metabolize phenanthrene as the sole source of carbon and energy via the 'phthalic acid' route. The key enzyme, 1-hydroxy-2-naphthoic acid dioxygenase (1-HNDO, EC 1.13.11.38), was purified to homogeneity using a 3-hydroxy-2-naphthoic acid (3-H2NA)-affinity matrix. The enzyme was a homotetramer with a native molecular mass of 160 kDa and subunit molecular mass of approximately 39 kDa. It required Fe(II) as the cofactor and was specific for 1-hydroxy-2-naphthoic acid (1-H2NA), with K(m) 13.5 microM and V(max) 114 micromol min(-1) mg(-1). 1-HNDO failed to show activity with gentisic acid, salicylic acid and other hydroxynaphthoic acids tested. Interestingly, the enzyme showed substrate inhibition with a K(i) of 116 microM. 1-HNDO was found to be competitively inhibited by 3-H2NA with a K(i) of 24 microM. Based on the pH-dependent spectral changes, the enzyme reaction product was identified as 2-carboxybenzalpyruvic acid. Under anaerobic conditions, the enzyme failed to convert 1-H2NA to 2-carboxybenzalpyruvic acid. Stoichiometric studies showed the incorporation of 1 mol O(2) into the substrate to yield 1 mol product. These results suggest that 1-HNDO from Pseudomonas sp. strain PPD is an extradiol-type ring-cleaving dioxygenase.
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Affiliation(s)
- Jaigeeth Deveryshetty
- Biotechnology Group, Department of Biosciences and Bioengineering, Indian Institute of Technology - Bombay, Powai, Mumbai 400 076, India
| | - Prashant S Phale
- Biotechnology Group, Department of Biosciences and Bioengineering, Indian Institute of Technology - Bombay, Powai, Mumbai 400 076, India
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Pandey J, Chauhan A, Jain RK. Integrative approaches for assessing the ecological sustainability ofin situbioremediation. FEMS Microbiol Rev 2009; 33:324-75. [PMID: 19178567 DOI: 10.1111/j.1574-6976.2008.00133.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Vamsee-Krishna C, Phale PS. Carbon source-dependent modulation of NADP-glutamate dehydrogenases in isophthalate-degrading Pseudomonas aeruginosa strain PP4, Pseudomonas strain PPD and Acinetobacter lwoffii strain ISP4. MICROBIOLOGY-SGM 2008; 154:3329-3337. [PMID: 18957586 DOI: 10.1099/mic.0.2008/022087-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Acinetobacter lwoffii strain ISP4 metabolizes isophthalate rapidly compared with Pseudomonas aeruginosa strain PP4 and Pseudomonas strain PPD. Isophthalate has been reported to be a potent competitive inhibitor of glutamate dehydrogenase (GDH). Exogenous supplementation of isophthalate with glutamate or alpha-ketoglutarate at 1 mM concentration caused strains PP4 and PPD to grow faster than in the presence of isophthalate alone; however, no such effect was observed in strain ISP4. When grown on isophthalate, all strains showed activity of NADP-dependent GDH (NADP-GDH), while cells grown on glucose, 2x yeast extract-tryptone broth (2YT) or glutamate showed activities of both NAD-dependent GDH (NAD-GDH) and NADP-GDH. Activity staining, inhibition and thermal stability studies indicated the carbon source-dependent presence of two (GDH(I) and GDH(II)), three (GDH(A), GDH(B) and GDH(C)) and one (GDH(P)) forms of NADP-GDH in strains PP4, PPD and ISP4, respectively. The results demonstrate the carbon source-dependent modulation of different forms of NADP-GDH in these bacterial strains. This modulation may help the efficient utilization of isophthalate as a carbon source by overcoming the inhibitory effect on GDH.
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Affiliation(s)
- C Vamsee-Krishna
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology - Bombay, Powai, Mumbai 400 076, India
| | - Prashant S Phale
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology - Bombay, Powai, Mumbai 400 076, India
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Abstract
Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.
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Affiliation(s)
- Paul Keese
- Office of the Gene Technology Regulator, GPO Box 9848 Canberra, ACT 2601 [corrected] Australia.
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