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Dinh MTN, Nguyen VT, Nguyen LTH. The potential application of carbazole-degrading bacteria for dioxin bioremediation. BIORESOUR BIOPROCESS 2023; 10:56. [PMID: 38647625 PMCID: PMC10992316 DOI: 10.1186/s40643-023-00680-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/17/2023] [Indexed: 04/25/2024] Open
Abstract
Extensive research has been conducted over the years on the bacterial degradation of dioxins and their related compounds including carbazole, because these chemicals are highly toxic and has been widely distributed in the environment. There is a pressing need to explore and develop more bacterial strains with unique catabolic features to effectively remediate dioxin-polluted sites. Carbazole has a chemical structure similar to dioxins, and the degradation pathways of these two chemicals are highly homologous. Some carbazole-degrading bacterial strains have been demonstrated to have the ability to degrade dioxins, such as Pseudomonas sp. strain CA10 và Sphingomonas sp. KA1. The introduction of strain KA1 into dioxin-contaminated model soil resulted in the degradation of 96% and 70% of 2-chlorodibenzo-p-dioxin (2-CDD) and 2,3-dichlorodibenzo-p-dioxin (2,3-DCDD), respectively, after 7-day incubation period. These degradation rates were similar to those achieved with strain CA10, which removed 96% of 2-CDD and 80% of 2,3-DCDD from the same model soil. Therefore, carbazole-degrading bacteria hold significant promise as potential candidates for dioxin bioremediation. This paper overviews the connection between the bacterial degradation of dioxins and carbazole, highlighting the potential for dioxin biodegradation by carbazole-degrading bacterial strains.
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Affiliation(s)
- Mai Thi Ngoc Dinh
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, A9 Building, Nguyen Van Trac Street, Ha Dong District, Hanoi, Vietnam.
- Bioresource Research Center, Phenikaa University, Hanoi, Vietnam.
| | - Van Thi Nguyen
- VNU Institute of Microbiology and Biotechnology, Vietnam National University, E2 Building, 144 Xuan Thuy Street, Cau Giay District, Hanoi, Vietnam
| | - Ly Thi Huong Nguyen
- Department of Physiology, College of Korean Medicine, Dongguk University, Gyeongju, Republic of Korea
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Nguyen TLA, Dang HTC, Dat TTH, Brandt BW, Röling WFM, Brouwer A, van Spanning RJM. Correlating biodegradation kinetics of 2,3,7,8-tetrachlorodibenzo-p-dioxin to the dynamics of microbial communities originating from soil in Vietnam contaminated with herbicides and dioxins. Front Microbiol 2022; 13:923432. [PMID: 36033897 PMCID: PMC9404497 DOI: 10.3389/fmicb.2022.923432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/12/2022] [Indexed: 12/02/2022] Open
Abstract
We studied the succession of bacterial communities during the biodegradation of 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD). The communities originated from a mesocosm with soil from Bien Hoa airbase in Vietnam heavily contaminated with herbicides and dioxins. They were grown in defined media with different carbon and Gibbs energy sources and 2,3,7,8-TCDD. Cultures with dimethyl sulfoxide (DMSO) as the sole carbon and energy source degraded about 95% of 2,3,7,8-TCDD within 60 days of cultivation. Those with an additional 1 mM of vanillin did that in roughly 90 days. Further 16S rRNA gene amplicon sequencing showed that the increase in relative abundance of members belonging to the genera Bordetella, Sphingomonas, Proteiniphilum, and Rhizobium correlated to increased biodegradation of 2,3,7,8-TCDD in these cultures. A higher concentration of vanillin slowed down the biodegradation rate. Addition of alternative carbon and Gibbs energy sources, such as amino acids, sodium lactate and sodium acetate, even stopped the degradation of 2,3,7,8-TCDD completely. Bacteria from the genera Bordetella, Achromobacter, Sphingomonas and Pseudomonas dominated most of the cultures, but the microbial profiles also significantly differed between cultures as judged by non-metric multidimensional scaling (NMDS) analyses. Our study indicates that 2,3,7,8-TCDD degradation may be stimulated by bacterial communities preadapted to a certain degree of starvation with respect to the carbon and energy source. It also reveals the succession and abundance of defined bacterial genera in the degradation process.
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Affiliation(s)
- Thi Lan Anh Nguyen
- Department of Molecular Cell Biology, Vrije Universiteit, Amsterdam, Netherlands
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- *Correspondence: Thi Lan Anh Nguyen,
| | - Ha Thi Cam Dang
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Thua Thien Hue, Vietnam
| | - Bernd W. Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Wilfred F. M. Röling
- Department of Molecular Cell Biology, Vrije Universiteit, Amsterdam, Netherlands
| | - Abraham Brouwer
- BioDetection Systems, Amsterdam, Netherlands
- Department of Ecological Science, Vrije Universiteit, Amsterdam, Netherlands
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Ghosh P, Mukherji S. Environmental contamination by heterocyclic Polynuclear aromatic hydrocarbons and their microbial degradation. BIORESOURCE TECHNOLOGY 2021; 341:125860. [PMID: 34614557 DOI: 10.1016/j.biortech.2021.125860] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Heterocyclic polynuclear aromatic hydrocarbons (PAHs) have been detected in all environmental matrices at few ppb to several ppm concentrations and they are characterized by high polarity. Some heterocyclic PAHs are mutagenic and carcinogenic to humans and various organisms. Despite being potent environmental pollutants, these compounds have received less attention. This paper focuses on the sources and occurrence of these compounds and their microbial degradation using diverse species of bacteria, fungi, and algae. Complete removal of 1.8 to 2614 mg/L of nitrogen heterocyclic PAH (PANH), 0.27 to 184 mg/L of sulfur heterocyclic PAH (PASH), and 0.6 to 120 mg/L of oxygen heterocyclic PAH (PAOH) compounds by various microbial species was observed between 3 h and 18 days, 8 h to 6 days, and 4 h to 250 h, respectively under aerobic condition. Strategies for enhancing the removal of heterocyclic PAHs from aquatic systems are also discussed along with the challenges.
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Affiliation(s)
- Prasenjit Ghosh
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Department of Civil Engineering, NIT Tiruchirappalli, Tiruchirappalli, Tamil Nadu 620015, India
| | - Suparna Mukherji
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Ghosh P, Mukherji S. Elucidation of substrate interaction effects in multicomponent systems containing 3-ring homocyclic and heterocyclic polynuclear aromatic hydrocarbons. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:1394-1404. [PMID: 34382630 DOI: 10.1039/d1em00140j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial growth and degradation experiments were conducted on carbazole (CBZ), fluorene (FLU) and dibenzothiophene (DBT) individually and in various mixture combinations using an efficient polynuclear aromatic hydrocarbon (PAH) degrading bacterial strain, Pseudomonas aeruginosa RS1. In single component systems, bacterial growth on CBZ (specific growth rate, μ = 0.99 day-1) was much higher compared to that on FLU (μ = 0.38 day-1) and DBT (μ = 0.33 day-1) and bacterial growth was inhibited in the presence of FLU and DBT in binary (μ = 0.64 day-1) and ternary (μ = 0.75 day-1) mixtures. Multisubstrate additive modelling indicated growth inhibition in all the systems. The degradation of the compounds was significantly inhibited in binary mixtures. While the degradation of the compounds in binary mixtures varied from 35 ± 4% to 73 ± 3%, their degradation varied from 61 ± 5% to 91 ± 4%, when applied as sole substrates and from 77 ± 3% to 96 ± 3%, when applied in a ternary mixture. Degradation experiments were also conducted in ternary mixtures using a 23 full factorial design and the results were examined using analysis of variance (ANOVA) and Tukey's honest significant difference (HSD) tests. At a low concentration of the heterocyclics, CBZ and DBT (5 mg L-1 each), the degradation of the PAH, FLU, was significantly enhanced (from 81 ± 1% to 93 ± 0.3%) when its concentration was increased from 5 to 30 mg L-1. The full factorial design can provide valuable insights into substrate interaction effects in mixtures.
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Affiliation(s)
- Prasenjit Ghosh
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Department of Civil Engineering, National Institute of Technology Goa, Farmagudi, Ponda, Goa 403401, India.
| | - Suparna Mukherji
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Delamuta JRM, Scherer AJ, Ribeiro RA, Hungria M. Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. Int J Syst Evol Microbiol 2020; 70:4233-4244. [PMID: 32568030 DOI: 10.1099/ijsem.0.004278] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense, Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Anderson José Scherer
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
| | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C and D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
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Saibu S, Adebusoye SA, Oyetibo GO, Rodrigues DF. Aerobic degradation of dichlorinated dibenzo-p-dioxin and dichlorinated dibenzofuran by bacteria strains obtained from tropical contaminated soil. Biodegradation 2020; 31:123-137. [PMID: 32342243 DOI: 10.1007/s10532-020-09898-8] [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] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/07/2020] [Indexed: 11/26/2022]
Abstract
Bacterial diversity and aerobic catabolic competence of dioxin-degrading bacterial strains isolated from a polluted soil in the tropics were explored. Isolation of bacteria occurred after 12 months of consecutive enrichment, with dioxin congeners serving as the only sources of carbon and energy. Seventeen strains that were isolated were subsequently screened for dioxin metabolic competence. Among these isolates, five had unique amplified ribosomal DNA restriction analysis (ARDRA) patterns out of which two exhibiting good metabolic competence were selected for further investigation. The two strains were identified as Bacillus sp. SS2 and Serratia sp. SSA1, based on their 16S rRNA gene sequences. Bacterial growth co-occurred with dioxin disappearance and near stoichiometric release of chloride for one ring of the chlorinated congeners. The overall percentage removal of dibenzofuran (DF) by strain SS2 was 93.87%; while corresponding values for 2,8-dichlorodibenzofuran (2,8-diCDF) and 2,7-dichlorodibenzo-p-dioxin (2,7-diCDD) were 86.22% and 82.30% respectively. In the case of strain SSA1, percentage removal for DF, 2,8-diCDF and 2,7-diCDD were respectively 98.9%, 80.97% and 70.80%. The presence of two dioxin dioxygenase catabolic genes (dxnA1 and dbfA1) was investigated. Only the dbfA1 gene could be amplified in SS2 strain. Results further revealed that strain SS2 presented higher expression levels for the alpha-subunit of DF dioxygenase (dbfA1) gene during growth with dioxins. The expression level for dbfA1 gene was higher when growing on DF than on the other chlorinated analogs. This study gives an insight into dioxin degradation, with the catabolic potential of strains SS2 and SSA1 (an enteric bacterium) within the sub-Sahara Africa. It further shows that dioxin catabolic potential might be more prevalent in different groups of microorganisms than previously believed. Few reports have demonstrated the degradation of chlorinated congeners of dioxins, particularly from sub-Saharan African contaminated systems.
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Affiliation(s)
- Salametu Saibu
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos, Nigeria
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77204-4003, USA
| | - Sunday A Adebusoye
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos, Nigeria.
| | - Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos, Nigeria
| | - Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77204-4003, USA
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Saibu S, Adebusoye SA, Oyetibo GO. Aerobic bacterial transformation and biodegradation of dioxins: a review. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-0294-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractWaste generation tends to surge in quantum as the population and living conditions grow. A group of structurally related chemicals of dibenzofurans and dibenzo-p-dioxins including their chlorinated congeners collectively known as dioxins are among the most lethal environmental pollutants formed during different anthropogenic activities. Removal of dioxins from the environment is challenging due to their persistence, recalcitrance to biodegradation, and prevalent nature. Dioxin elimination through the biological approach is considered both economically and environmentally as a better substitute to physicochemical conventional approaches. Bacterial aerobic degradation of these compounds is through two major catabolic routes: lateral and angular dioxygenation pathways. Information on the diversity of bacteria with aerobic dioxin degradation capability has accumulated over the years and efforts have been made to harness this fundamental knowledge to cleanup dioxin-polluted soils. This paper covers the previous decades and recent developments on bacterial diversity and aerobic bacterial transformation, degradation, and bioremediation of dioxins in contaminated systems.
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Thanh LTH, Thi TVN, Shintani M, Moriuchi R, Dohra H, Loc NH, Kimbara K. Isolation and characterization of a moderate thermophilic Paenibacillus naphthalenovorans strain 4B1 capable of degrading dibenzofuran from dioxin-contaminated soil in Vietnam. J Biosci Bioeng 2019; 128:571-577. [DOI: 10.1016/j.jbiosc.2019.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/19/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
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Rathna R, Varjani S, Nakkeeran E. Recent developments and prospects of dioxins and furans remediation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 223:797-806. [PMID: 29986327 DOI: 10.1016/j.jenvman.2018.06.095] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/10/2018] [Accepted: 06/30/2018] [Indexed: 05/18/2023]
Abstract
Rapid urbanization and industrialization of anthropogenic activities have exerted immense pressure on the environment. Polyhalogenated organic compounds, especially dioxins and furans are regarded as ubiquitously persistent environmental pollutants in the ecosystem. The recalcitrant nature of dioxins and furans induce toxicity in both humans and wildlife. Dioxins and furans are generated by defective technological chemical processes that occur during the manufacture of herbicides and pesticides, use of fertilizers, bleaching of paper and wood pulp and incomplete combustion process. However, incineration and incomplete combustion of solid waste are the main cause for the discharge of dioxins and furans to the environment. During incineration and incomplete combustion, noxious flue gas and ashes are released into the atmosphere and contaminate the soil and water systems; thereby affecting the ecology. According to World Health Organization fact sheet 2016, more than 90% of human exposure to dioxins is through the food chain, especially from dairy products, seafood and meat. These pollutants are mutagenic, carcinogenic, immunotoxic and teratogenic for lower and higher forms of life i.e. microorganisms to humans. This review describes the sources of dioxins and furans pollution, hazardous effects on the ecosystem and recent techniques to minimize and treat dioxins and furans contaminants in the environment. This paper also previews the significance of conventional and latest remediation techniques prevailing around the globe for treating dioxins and furans entry into the ecosystem.
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Affiliation(s)
- Ravichandran Rathna
- Research Laboratory, Department of Biotechnology, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur Tk, 602 117, Tamil Nadu, India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Sector-10A, Gandhinagar, 382 010, Gujarat, India
| | - Ekambaram Nakkeeran
- Research Laboratory, Department of Biotechnology, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur Tk, 602 117, Tamil Nadu, India.
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Liu X, Wang W, Hu H, Lu X, Zhang L, Xu P, Tang H. 2-Hydroxy-4-(3′-oxo-3′H-benzofuran-2′-yliden)but-2-enoic acid biosynthesis from dibenzofuran using lateral dioxygenation in a Pseudomonas putida strain B6-2 (DSM 28064). BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0209-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Pourfakhraei E, Badraghi J, Mamashli F, Nazari M, Saboury AA. Biodegradation of asphaltene and petroleum compounds by a highly potent Daedaleopsis sp. J Basic Microbiol 2018; 58:609-622. [PMID: 29775208 DOI: 10.1002/jobm.201800080] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/15/2018] [Accepted: 04/22/2018] [Indexed: 11/11/2022]
Abstract
Petroleum, as the major energy source, is indispensable from our lives. Presence of compounds resistant to degradation can pose risks for human health and environment. Basidiomycetes have been considered as powerful candidates in biodegradation of petroleum compounds via secreting ligninolytic enzymes. In this study a wood-decaying fungus was isolated by significant degradation ability that was identified as Daedaleopsis sp. by morphological and molecular identification methods. According to GC/MS studies, incubation of heavy crude oil with Daedaleopsis sp. resulted in increased amounts of <C24 hydrocarbons and decreased amounts of >C24 compounds. Degradation of asphaltene, anthracene, and dibenzofuran by the identified fungal strain was determined to evaluate its potential in biodegradation. After 14 days of incubation, Daedaleopsis sp. could degrade 93.7% and 91.2% of anthracene and dibenzofuran, respectively, in pH 5 and 40 °C in optimized medium, as revealed by GC/FID. Notably, analysis of saturates, aromatics, resins, and asphaltenes showed a reduction of 88.7% and 38% in asphaletene and aromatic fractions. Laccase, lignin peroxidase, and manganese peroxidase activities were enhanced from 51.3, 145.2, 214.5 U ml-1 in the absence to 121.5, 231.4, and 352.5 U ml-1 in the presence of heavy crude oil, respectively. This is the first report that Daedaleopsis sp. can degrade asphaltene and dibenzofuran. Moreover, compared to the reported results of asphaltene biodegradation, this strain was the most successful. Thus, Daedaleopsis sp. could be a promising candidate for biotransformation of heavy crude oil and biodegradation of recalcitrant toxic compounds.
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Affiliation(s)
- Elaheh Pourfakhraei
- Research Institute of Applied Sciences, Academic Center of Education, Culture and Research (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Jalil Badraghi
- Research Institute of Applied Sciences, Academic Center of Education, Culture and Research (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Fatemeh Mamashli
- Research Institute of Applied Sciences, Academic Center of Education, Culture and Research (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Mahboobeh Nazari
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Zahradník J, Nunvar J, Pařízková H, Kolářová L, Palyzová A, Marešová H, Grulich M, Kyslíková E, Kyslík P. Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia. Syst Appl Microbiol 2018; 41:184-190. [PMID: 29402492 DOI: 10.1016/j.syapm.2018.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/11/2018] [Accepted: 01/17/2018] [Indexed: 10/18/2022]
Abstract
Two non-pathogenic strains R89-1 and R90T isolated from poppy seed (Papaver somniferum L.) wastes were phenotypically and genotypically characterized. Multilocus sequence analysis (MLSA) was conducted with six genes (atpD, glnA, gyrB, recA, rpoB, 16S rRNA). The strains represented a new species which clustered with Agrobacterium rubi NBRC 13261T and Agrobacterium skierniewicense Ch11T type strains. MLSA was further accompanied by whole-genome phylogeny, in silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses for both strains. ANI and dDDH values were deep below the species delineation threshold. Phenotypic features of the novel strains unequivocally allowed their differentiation from all other Agrobacterium species. Unlike other agrobacteria, the strains were salt sensitive and were able to biotransform morphine alkaloids. The dominant cellular fatty acids are 18:1 w7c, 16:0 and 12:0 aldehyde/16:1 iso I/14:0 3OH summed in feature 2 and the major respiratory quinine is Q-10 (87%). The DNA G+C content is 56mol%. Microbial community analysis indicated probable association with P. somniferum plant material. Altogether, these characteristics showed that strains R90T and R89-1 represent a new species of the genus Agrobacterium which we propose to name Agrobacterium bohemicum. The type strain of A. bohemicum is R90T (=CCM 8736T=DSM 104667T).
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Affiliation(s)
- Jiří Zahradník
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic; Faculty of Science, Charles University Prague, Viničná 5, CZ-128 44 Prague 2, Czech Republic.
| | - Jaroslav Nunvar
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, V Uvalu 84, CZ-150 06 Prague 5, Czech Republic
| | - Hana Pařízková
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic
| | - Lucie Kolářová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic
| | - Andrea Palyzová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Helena Marešová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Michal Grulich
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Eva Kyslíková
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Pavel Kyslík
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic.
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Effects of inorganic nanoparticles on viability and catabolic activities of Agrobacterium sp. PH-08 during biodegradation of dibenzofuran. Biodegradation 2014; 25:655-68. [DOI: 10.1007/s10532-014-9689-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
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