1
|
Ashesh A, Singh S, Linthoingambi Devi N, Chandra Yadav I. Organochlorine pesticides in multi-environmental matrices of India: A comprehensive review on characteristics, occurrence, and analytical methods. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
2
|
Kaminski MA, Sobczak A, Dziembowski A, Lipinski L. Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis. Genes (Basel) 2019; 10:E688. [PMID: 31500174 PMCID: PMC6771000 DOI: 10.3390/genes10090688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 11/29/2022] Open
Abstract
Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxislindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.
Collapse
Affiliation(s)
- Michal A Kaminski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
| |
Collapse
|
3
|
Regar RK, Gaur VK, Bajaj A, Tambat S, Manickam N. Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:413-423. [PMID: 31108361 DOI: 10.1016/j.scitotenv.2019.05.090] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 05/17/2023]
Abstract
Microbial communities play a crucial role in bioremediation of pollutants in contaminated ecosystem. In addition to pure culture isolation and bacterial 16S rRNA based community studies, the focus has now shifted employing the omics technologies enormously for understanding the microbial diversity and functional potential of soil samples. Our previous report on two pesticide-contaminated sites revealed the diversity of both culturable and unculturable bacteria. In the present study, we have observed distinct taxonomic and functional communities in contaminated soil with respect to an uncontaminated soil as control by using shotgun metagenomic sequencing method. Our data demonstrated that Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria significantly dominated the microbial diversity with their cumulative abundance percentage in the range of 98.61, 87.38, and 80.52 for Hindustan Insecticides Limited (HIL), India Pesticides Limited (IPL), and control respectively. Functional gene analysis demonstrated the presence of large number of both substrate specific upper pathway and common lower pathway degradative genes. Relatively lower number of genes was found encoding the degradation of styrene, atrazine, bisphenol, dioxin, and naphthalene. When three bacteria were augumentated with rhamnolipid (20-100 μM) and Triton X-100 (84-417 μM) surfactants in HIL soil, an enhanced degradation to 76%, 70%, and 58% of HCH, Endosulfan, and DDT respectively was achieved. The overall data obtained from two heavily contaminated soil suggest the versatility of the microbial communities for the xenobiotic pollutant degradation which may help in exploiting their potential applications in bioremediation.
Collapse
Affiliation(s)
- Raj Kumar Regar
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India; Department of Biochemistry, School of Dental Sciences, Babu Banarsi Das University, Lucknow, Uttar Pradesh, India
| | - Vivek Kumar Gaur
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Subodh Tambat
- Bionivid Technology Pvt. Ltd., Bengaluru, Karnataka, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India.
| |
Collapse
|
4
|
Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water. Ecol Modell 2019. [DOI: 10.1016/j.ecolmodel.2019.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
5
|
Gaur VK, Bajaj A, Regar RK, Kamthan M, Jha RR, Srivastava JK, Manickam N. Rhamnolipid from a Lysinibacillus sphaericus strain IITR51 and its potential application for dissolution of hydrophobic pesticides. BIORESOURCE TECHNOLOGY 2019; 272:19-25. [PMID: 30296609 DOI: 10.1016/j.biortech.2018.09.144] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/28/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Abstract
Rhamnolipid produced from a Lysinibacillus sphaericus IITR51 was characterized and its ability for dissolution of hydrophobic pesticides were evaluated. L. sphaericus produced 1.6 g/L of an anionic biosurfactant that reduced surface tension from 72 N/m to 52 N/m with 48% emulsification index. The biosurfactant was found stable over a wide range of pH (4.0-10.0), temperature (4-100 °C), salt concentration (2-14%) and was identified as rhamnolipid. At the concentration of 90 mg/L rhamnolipid showed enhanced dissolution of α-, β-endosulfan, and γ-hexachlorocyclohexane up to 7.2, 2.9, and 1.8 folds, respectively. The bacterium utilized benzoic acid, chlorobenzene, 3- and 4-chlorobenzoic acid as sole source of carbon and was found resistant to arsenic, lead and cadmium. Furthermore, the isolated biosurfactant showed antimicrobial activities against different pathogenic bacteria. The results obtained indicate the usefulness of rhamnolipid for enhanced dissolution and thereby increasing the bioavailability.
Collapse
Affiliation(s)
- Vivek Kumar Gaur
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Raj Kumar Regar
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Department of Biochemistry, School of Dental Sciences, Babu Banarsi Das University, Lucknow 226028, Uttar Pradesh, India
| | - Mohan Kamthan
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Rakesh Roshan Jha
- Analytical Chemistry Laboratory, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Janmejai Kumar Srivastava
- Department of Biochemistry, School of Dental Sciences, Babu Banarsi Das University, Lucknow 226028, Uttar Pradesh, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India.
| |
Collapse
|
6
|
Kumar D, Pannu R. Perspectives of lindane (γ-hexachlorocyclohexane) biodegradation from the environment: a review. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0213-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
7
|
de Lima e Silva MR, Correa RC, Sakamoto IK, Varesche MBA. Microbial Characterization of Methanogenic and Iron-reducing Consortium in Reactors with Polychlorinated Biphenyls. Curr Microbiol 2018; 75:666-676. [DOI: 10.1007/s00284-018-1431-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
|
8
|
Xu B, Xiong C, Deng M, Li J, Tang X, Wu Q, Zhou J, Yang Y, Ding J, Han N, Huang Z. Genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome. J Basic Microbiol 2017; 57:883-895. [PMID: 28745827 DOI: 10.1002/jobm.201700106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/25/2017] [Accepted: 06/06/2017] [Indexed: 11/07/2022]
Abstract
Catechol 1,2-dioxygenase is the key enzyme that catalyzes the cleavage of the aromatic ring of catechol. We explored the genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome by PCR with degenerate primers. A total of 35 gene fragments of C12O were retrieved from microbial DNA in the feces of pygmy loris. Based on phylogenetic analysis, most sequences were closely related to C12O sequences from Acinetobacter. A full-length C12O gene was directly cloned, heterologously expressed in Escherichia coli, and biochemically characterized. Purified catPL12 had optimum pH and temperature pH 8.0 and 25 °C and retained 31 and 50% of its maximum activity when assayed at 0 and 35 °C, respectively. The enzyme was stable at 25 and 37 °C, retaining 100% activity after pre-incubation for 1 h. The kinetic parameters of catPL12 were determined. The enzyme had apparent Km of 67 µM, Vmax of 7.3 U/mg, and kcat of 4.2 s-1 for catechol, and the cleavage activities for 3-methylcatechol, 4-methylcatechol, and 4-chlorocatechol were much less than for catechol, and no activity with hydroquinone or protocatechuate was detected. This study is the first to report the molecular and biochemical characterizations of a cold-adapted catechol 1,2-dioxygenase from a fecal microbial metagenome.
Collapse
Affiliation(s)
- Bo Xu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Caiyun Xiong
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Meng Deng
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junjun Li
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Yunjuan Yang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junmei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| |
Collapse
|
9
|
Nanasato Y, Namiki S, Oshima M, Moriuchi R, Konagaya KI, Seike N, Otani T, Nagata Y, Tsuda M, Tabei Y. Biodegradation of γ-hexachlorocyclohexane by transgenic hairy root cultures of Cucurbita moschata that accumulate recombinant bacterial LinA. PLANT CELL REPORTS 2016; 35:1963-1974. [PMID: 27295266 DOI: 10.1007/s00299-016-2011-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 06/04/2016] [Indexed: 06/06/2023]
Abstract
γ-HCH was successfully degraded using LinA-expressed transgenic hairy root cultures of Cucurbita moschata . Fusing an endoplasmic reticulum-targeting signal peptide to LinA was essential for stable accumulation in the hairy roots. The pesticide γ-hexachlorocyclohexane (γ-HCH) is a persistent organic pollutant (POP) that raises public health and environmental pollution concerns worldwide. Although several isolates of γ-HCH-degrading bacteria are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the bacterial survival rate. Cucurbita species incorporate significant amounts of POPs from soils compared with other plant species. Here, we describe a novel bioremediation strategy that combines the bacterial degradation of γ-HCH and the efficient uptake of γ-HCH by Cucurbita species. We produced transgenic hairy root cultures of Cucurbita moschata that expressed recombinant bacterial linA, isolated from the bacterium Sphingobium japonicum UT26. The LinA protein was accumulated stably in the hairy root cultures by fusing an endoplasmic reticulum (ER)-targeting signal peptide to LinA. Then, we demonstrated that the cultures degraded more than 90 % of γ-HCH (1 ppm) overnight and produced the γ-HCH metabolite 1,2,4-trichlorobenzene, indicating that LinA degraded γ-HCH. These results indicate that the gene linA has high potential for phytoremediation of environmental γ-HCH.
Collapse
Affiliation(s)
- Yoshihiko Nanasato
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan.
| | - Sayuri Namiki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Masao Oshima
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Ryota Moriuchi
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi, 980-8577, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, Gifu, 501-1193, Japan
| | - Ken-Ichi Konagaya
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Nobuyasu Seike
- Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Takashi Otani
- Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yuji Nagata
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi, 980-8577, Japan
| | - Masataka Tsuda
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi, 980-8577, Japan
| | - Yutaka Tabei
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| |
Collapse
|
10
|
Abstract
ABSTRACT
Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity. While applications of some of these techniques in the field of soil microbial forensics are still in early stages, we are still gaining insight into how microorganisms may be more robustly used in forensic investigations.
Collapse
|
11
|
Kumari S, Regar RK, Bajaj A, Ch R, Satyanarayana GNV, Mudiam MKR, Manickam N. Simultaneous Biodegradation of Polyaromatic Hydrocarbons by a Stenotrophomonas sp: Characterization of nid Genes and Effect of Surfactants on Degradation. Indian J Microbiol 2016; 57:60-67. [PMID: 28148980 DOI: 10.1007/s12088-016-0612-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/21/2016] [Indexed: 11/25/2022] Open
Abstract
A polyaromatic hydrocarbon degrading bacterium was isolated from a petroleum contaminated site and designated as Stenotrophomonas sp. strain IITR87. It was found to utilize pyrene, phenanthrene and benzo(a)pyrene as sole carbon source, but not anthracene, chrysene and fluoranthene. Gas chromatography and mass spectroscopy analysis resulted in identification of pyrene metabolites namely monohydroxypyrene, 4-oxa-pyrene-5-one, dimethoxypyrene and monohydroxyphenanthrene. Southern hybridization using naphthalene dioxygenase gene (nidA) as probe against the DNA of strain IITR87 revealed the presence of nidA gene. PCR analysis suggests dispersed occurrence of nid genes in the genome instead of a cluster as reported in a PAH-degrading Mycobacterium vanbaalenii PYR-1. The nid genes in strain IITR87, dioxygenase large subunit (nidA), naphthalene dioxygenase small subunit (nidB) and aldehyde dehydrogenase gene (nidD) showed more than 97 % identity to the reported nid genes from Mycobacterium vanbaalenii PYR-1. Most significantly, the biodegradation of PAHs was enhanced 25-60 % in the presence of surfactants rhamnolipid and Triton X-100 due to increased solubilization and bioavailability. These results could be useful for the improved biodegradation of high-molecular-weight PAHs in contaminated habitats.
Collapse
Affiliation(s)
- Smita Kumari
- Environmental Biotechnology Laboratory, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
| | - Raj Kumar Regar
- Environmental Biotechnology Laboratory, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
- Department of Biochemistry, Babu Banarsi Das University, Lucknow, 226028 India
| | - Abhay Bajaj
- Environmental Biotechnology Laboratory, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Ratnasekhar Ch
- Analytical Chemistry Laboratory, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
| | - Gubbala Naga Venkata Satyanarayana
- Analytical Chemistry Laboratory, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
| | - Mohana Krishna Reddy Mudiam
- Analytical Chemistry Laboratory, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
| | - Natesan Manickam
- Environmental Biotechnology Laboratory, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001 India
| |
Collapse
|
12
|
Wu Q, Hu Y, Li S, Peng S, Zhao H. Microbial mechanisms of using enhanced ecological floating beds for eutrophic water improvement. BIORESOURCE TECHNOLOGY 2016; 211:451-456. [PMID: 27035477 DOI: 10.1016/j.biortech.2016.03.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 06/05/2023]
Abstract
Enhanced ecological floating beds were implemented to reduce nutrient quantity and improve the water quality of a eutrophic lake. The results showed that average removal efficiencies of CODCr, total nitrogen, NH3-N and total phosphorus for Canna indica L. set-up were 23.1%, 15.3%, 18.1% and 19.4% higher, respectively, than that of the setup with only substrate, and 14.2%, 12.8%, 7.9% and 11.9% higher than Iris pseudacorus L. ecological floating bed. The microbial community structure had obvious differences between devices and low similarity; bacteria were mainly attached on the fiber filling. The microbial population was abundant at the start and end of the experiment. Shannon index of samples selected ranged from 0.85 to 1.05. The sequencing results showed that fiber filling collected most uncultured bacteria species and the majority of bacteria on the plant roots were β-Proteobacteria and α-Proteobacteria. The co-dominant species attaching to the filling and plant was Nitrosomonadaceae.
Collapse
Affiliation(s)
- Qing Wu
- School of Environmental Science and Engineering, Tianjin University, 300072, China; Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, Logistics University of Chinese People's Armed Police Forces, Tianjin 300162, China
| | - Yue Hu
- School of Environmental Science and Engineering, Tianjin University, 300072, China
| | - Shuqun Li
- School of Environmental Science and Engineering, Tianjin University, 300072, China
| | - Sen Peng
- School of Environmental Science and Engineering, Tianjin University, 300072, China.
| | - Huabing Zhao
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, Logistics University of Chinese People's Armed Police Forces, Tianjin 300162, China
| |
Collapse
|
13
|
Degenerate primers as biomarker for gene-targeted metagenomics of the catechol 1, 2-dioxygenase-encoding gene in microbial populations of petroleum-contaminated environments. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1197-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
14
|
Coleman NV. Primers: Functional Genes for Aerobic Chlorinated Hydrocarbon-Degrading Microbes. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_91] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
15
|
The treatment of PPCP-containing sewage in an anoxic/aerobic reactor coupled with a novel design of solid plain graphite-plates microbial fuel cell. BIOMED RESEARCH INTERNATIONAL 2014; 2014:765652. [PMID: 25197659 PMCID: PMC4150452 DOI: 10.1155/2014/765652] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 07/16/2014] [Indexed: 11/18/2022]
Abstract
Synthetic sewage containing high concentrations of pharmaceuticals and personal care products (PPCPs, mg/L level) was treated using an anoxic/aerobic (A/O) reactor coupled with a microbial fuel cell (MFC) at hydraulic retention time (HRT) of 8 h. A novel design of solid plain graphite plates (SPGRPs) was used for the high surface area biodegradation of the PPCP-containing sewage and for the generation of electricity. The average CODCr and total nitrogen removal efficiencies achieved were 97.20% and 83.75%, respectively. High removal efficiencies of pharmaceuticals, including acetaminophen, ibuprofen, and sulfamethoxazole, were also obtained and ranged from 98.21% to 99.89%. A maximum power density of 532.61 mW/cm2 and a maximum coulombic efficiency of 25.20% were measured for the SPGRP MFC at the anode. Distinct differences in the bacterial community were presented at various locations including the mixed liquor suspended solids and biofilms. The bacterial groups involved in PPCP biodegradation were identified as Dechloromonas spp., Sphingomonas sp., and Pseudomonas aeruginosa. This design, which couples an A/O reactor with a novel design of SPGRP MFC, allows the simultaneous removal of PPCPs and successful electricity production.
Collapse
|
16
|
Jacobsen CS, Hjelmsø MH. Agricultural soils, pesticides and microbial diversity. Curr Opin Biotechnol 2014; 27:15-20. [DOI: 10.1016/j.copbio.2013.09.003] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/05/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022]
|
17
|
Manickam N, Singh NK, Bajaj A, Kumar RM, Kaur G, Kaur N, Bala M, Kumar A, Mayilraj S. Bacillus mesophilum sp. nov., strain IITR-54T, a novel 4-chlorobiphenyl dechlorinating bacterium. Arch Microbiol 2014; 196:517-23. [PMID: 24807729 DOI: 10.1007/s00203-014-0988-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/02/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
Abstract
The taxonomic position of a Gram-positive, endospore-forming bacterium isolated from soil sample collected from an industrial site was analyzed by a polyphasic approach. The strain designated as IITR-54T matched most of the phenotypic and chemical characteristics of the genus Bacillus and represents a novel species. It was found to biodegrade 4-chlorobiphenyl through dechlorination and was isolated through enrichment procedure from an aged polychlorinated biphenyl-contaminated soil. Both resting cell assay and growth under aerobic liquid conditions using 4-chlorobiphenyl as sole source of carbon along with 0.01% yeast extract, formation of chloride ions was measured. 16S rRNA (1,489 bases) nucleotide sequence of isolated strain was compared with those of closely related Bacillus type strains and confirmed that the strain belongs to the genus Bacillus. Strain IITR-54T differs from all other species of Bacillus by at least 2.1% at the 16S rRNA level, and the moderately related species are Bacillus oceanisediminis (97.9%) followed by Bacillus infantis (97.7%), Bacillus firmus (97.4%), Bacillus drentensis (97.3%), Bacillus circulans (97.2%), Bacillus soli (97.1%), Bacillus horneckiae (97.1%), Bacillus pocheonensis (97.1%) and Bacillus bataviensis (97.1%), respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Major fatty acids are iso-C15:0 (32.4%) and anteiso-C15:0 (27.4%). Predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The results of physiological and biochemical tests allowed the genotypic and phenotypic distinctiveness of strain IITR-54T with its phylogenetic relatives and suggest that the strain IITR-54T should be recognized as a novel species, for which the name Bacillus mesophilum sp. nov. is proposed. The type strain is IITR-54T (=MTCC 11060T=JCM 19208T).
Collapse
Affiliation(s)
- Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Khedkar S, Shanker R. Degradation of dibenzothiophene and its metabolite 3-hydroxy-2-formylbenzothiophene by an environmental isolate. Biodegradation 2014; 25:643-54. [DOI: 10.1007/s10532-014-9688-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/19/2014] [Indexed: 11/29/2022]
|
19
|
Gupta SK, Lal D, Lata P, Sangwan N, Garg N, Holliger C, Lal R. Changes in the bacterial community and lin genes diversity during biostimulation of indigenous bacterial community of hexachlorocyclohexane (HCH) dumpsite soil. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713020185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
20
|
Manickam N, Pareek S, Kaur I, Singh NK, Mayilraj S. Nitratireductor lucknowense sp. nov., a novel bacterium isolated from a pesticide contaminated soil. Antonie van Leeuwenhoek 2011; 101:125-31. [DOI: 10.1007/s10482-011-9623-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 07/06/2011] [Indexed: 11/29/2022]
|
21
|
Pathak A, Shanker R, Garg SK, Manickam N. Profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems using 60-mer oligonucleotide microarray. Appl Microbiol Biotechnol 2011; 90:1739-54. [DOI: 10.1007/s00253-011-3268-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 03/16/2011] [Accepted: 03/16/2011] [Indexed: 12/01/2022]
|
22
|
Lovley DR, Ueki T, Zhang T, Malvankar NS, Shrestha PM, Flanagan KA, Aklujkar M, Butler JE, Giloteaux L, Rotaru AE, Holmes DE, Franks AE, Orellana R, Risso C, Nevin KP. Geobacter: the microbe electric's physiology, ecology, and practical applications. Adv Microb Physiol 2011; 59:1-100. [PMID: 22114840 DOI: 10.1016/b978-0-12-387661-4.00004-5] [Citation(s) in RCA: 384] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.
Collapse
Affiliation(s)
- Derek R Lovley
- Department of Microbiology and Environmental Biotechnology Center, University of Massachusetts, Amherst, Massachusetts, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|