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Gao T, Tian H, Xiang L, Wang Z, Fu Y, Shi J, Wen X, Jiang X, He W, Hashsham SA, Wang F. Characteristics of bacterial community and extracellular enzymes in response to atrazine application in black soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123286. [PMID: 38171425 DOI: 10.1016/j.envpol.2023.123286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/04/2023] [Accepted: 12/31/2023] [Indexed: 01/05/2024]
Abstract
The ecological functioning of black soil largely depends on the activities of various groups of microorganisms. However, little is known about how atrazine, a widely used herbicide with known harmful effects on the environment, influences the microbial ecology of black soil, and the extracellular enzymes related to the carbon, nitrogen and phosphorus cycles. Here, we evaluated the change in extracellular enzymes and bacterial community characteristics in black soil after exposure to various concentrations of atrazine. Low concentrations of applied atrazine (10 - 20 mg kg-1) were almost completely degraded after 120 days. At high concentrations (80 - 100 mg kg-1), about 95% of the applied atrazine was degraded over the same period. Additionally, linear fitting of data indicated that the total enzymatic activity index (TEI) and bacterial α-diversity index were negatively correlated with atrazine applied concentration. The atrazine had a greater effect on bacterial beta diversity after 120 days, which differentiated species clusters treated with low and high atrazine concentrations. Soil bacterial community structure and function were affected by atrazine, especially at high atrazine concentrations (80 - 100 mg kg-1). Key microorganisms such as Sphingomonas and Nocardioides were identified as biomarkers for atrazine dissipation. Functional prediction indicated that most metabolic pathways might be involved in atrazine dissipation. Overall, the findings enhance our understanding of the factors driving atrazine degradation in black soil and supports the use of biomarkers as indicators of atrazine dissipation.
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Affiliation(s)
- Tiancong Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Leilei Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziqi Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Shi
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Xin Wen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Center for Microbial Ecology, Michigan State University, USA
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Nguyen TTT, Foysal MJ, Gupta SK, Tay A, Fotedar R, Gagnon MM. Effects of carbon source addition in rearing water on sediment characteristics, growth and health of cultured marron (Cherax cainii). Sci Rep 2024; 14:1349. [PMID: 38228662 DOI: 10.1038/s41598-024-51585-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/07/2024] [Indexed: 01/18/2024] Open
Abstract
Carbon sources are considered as critical input for the health and immunity of aquatic animals. The present study investigated the impact of different carbon sources on water quality parameters, carbon to nitrogen (C/N) ratio and microbial community in sediments, and health responses of marron (Cherax cainii) under laboratory conditions. Following one week of acclimation, 120 marron were randomly assigned to 12 experimental tanks. There were four treatments including one untreated control and three groups with carbon addition to maintain a C/N ratio of 12 maintained in culture water. Carbon supplementation groups included corn flour (CBC12), molasses (MBC12) and wheat flour (WBC12). At the end of the 60-day trial, MBC12 resulted in the highest sediment C/N ratio, followed by CBC12. Weight gain and specific growth rate were higher in MBC12, compared to control. The protease activity in marron hepatopancreas, total haemocyte count and lysozyme activity in haemolymph were highest in MBC12. Analysis of 16S rRNA sequence data of tank sediments revealed increased bacterial alpha diversity in MBC12 and WBC12. Proteobacteria was the most abundant phylum in MBC12 (88.6%), followed by control (82.4%) and CBC12 (72.8%). Sphingobium and Novosphingobium were the most abundant genera in control and MBC12 groups, respectively. Higher Aeromonas abundance in CBC12 and Flavobacterium in WBC12 were observed. Overall results indicated that MBC12 led to improved water quality, retaining high C/N ratio and enriched the bacterial populations in sediments resulting in improved growth and immune performance of marron.
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Affiliation(s)
- Thi Thu Thuy Nguyen
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.
- Department of Experimental Biology, Research Institute for Aquaculture No.2, Ho Chi Minh City, Vietnam.
| | - Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia.
| | - Sanjay Kumar Gupta
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Alfred Tay
- Helicobacter Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Perth, WA, Australia
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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Liu L, Zhang Y, Chen Q, Shen Q, Li L, Cao C, Li R, Jiang J, Liu J. Nocardioides potassii sp. nov., isolated from weathered potash tailings soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486345 DOI: 10.1099/ijsem.0.005967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
A Gram-positive, aerobic actinomycete, designated strain KLBMP 9356T, was isolated from weathered potash tailings soil sampled in Xuzhou, Jiangsu Province, PR China. The colonies were cream-coloured, convex and rounded. The optimal growth conditions of strain KLBMP 9356T were 1 % (w/v) NaCl, 28 °C and pH 7. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KLBMP 9356T showed the highest similarity to Nocardioides zhouii CGMCC 1.11084T (98.9 %) and Nocardioides glacieisoli CGMCC 1.11097T (98.7 %). Results from two tree-making algorithms supported the position that strain KLBMP 9356T forms a stable clade with N. zhouii CGMCC 1.11084T and N. glacieisoli CGMCC 1.11097T. Strain KLBMP 9356T exhibited low digital DNA-DNA hybridization values with N. zhouii CGMCC 1.11084T (27.6 %) and N. glacieisoli CGMCC 1.11097T (31.4 %). The average nucleotide identity values between strain KLBMP 9356T and N. zhouii CGMCC 1.11084T and N. glacieisoli CGMCC 1.11097T were 83.8% and 85.9%, respectively. The peptidoglycan in the cell wall of the novel strain was ll-2,6-diaminopimelic acid and the predominant menaquinone was MK-8(H4). The major fatty acids (>10 %) were C17:1ω8c and C18:1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, lyso-phospatidylglycerol and phosphatidylinositol. The genomic DNA G+C content was 71.6 mol%. Based on its morphological, chemotaxonomic and phylogenetic characteristics, strain KLBMP 9356T represents a novel species of the genus Nocardioides, for which the name Nocardioides potassii sp. nov. is proposed. The type strain is KLBMP 9356T (=CGMCC 4.7738T=NBRC 115493T).
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Affiliation(s)
- Lingxiao Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Ya Zhang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Qiuyu Chen
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Qi Shen
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Ludan Li
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
- The Key Laboratory of Microbial Resources of Xuzhou City, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Chengliang Cao
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
- The Key Laboratory of Microbial Resources of Xuzhou City, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Rongpeng Li
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
- The Key Laboratory of Microbial Resources of Xuzhou City, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
- The Key Laboratory of Microbial Resources of Xuzhou City, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Jinjuan Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
- The Key Laboratory of Microbial Resources of Xuzhou City, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
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4
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Aldas-Vargas A, Poursat BAJ, Sutton NB. Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil. World J Microbiol Biotechnol 2022; 38:240. [PMID: 36261779 PMCID: PMC9581840 DOI: 10.1007/s11274-022-03426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022]
Abstract
Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.
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Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Baptiste A J Poursat
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands.
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Nocardioides carbamazepini sp. nov., an ibuprofen degrader isolated from a biofilm bacterial community enriched on carbamazepine. Syst Appl Microbiol 2022; 45:126339. [PMID: 35714383 DOI: 10.1016/j.syapm.2022.126339] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/11/2022] [Accepted: 05/31/2022] [Indexed: 11/23/2022]
Abstract
From the metagenome of a carbamazepine amended selective enrichment culture the genome of a new to science bacterial species affiliating with the genus Nocardioides was reconstructed. From the same enrichment an aerobic actinobacterium, strain CBZ_1T, sharing 99.4% whole-genome sequence similarity with the reconstructed Nocardioides sp. bin genome was isolated. On the basis of 16S rRNA gene sequence similarity the novel isolate affiliated to the genus Nocardioides, with the closest relatives Nocardioides kongjuensis DSM19082T (98.4%), Nocardioides daeguensis JCM17460T (98.4%) and Nocardioides nitrophenolicus DSM15529T (98.2%). Using a polyphasic approach it was confirmed that the isolate CBZ_1T represents a new phyletic lineage within the genus Nocardioides. According to metagenomic, metatranscriptomic studies and metabolic analyses strain CZB_1T was abundant in both carbamazepine and ibuprofen enrichments, and harbors biodegradative genes involved in the biodegradation of pharmaceutical compounds. Biodegradation studies supported that the new species was capable of ibuprofen biodegradation. After 7 weeks of incubation, in mineral salts solution supplemented with glucose (3 g l-1) as co-substrate, 70% of ibuprofen was eliminated by strain CBZ_1T at an initial conc. of 1.5 mg l-1. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of strain CBZ_1T to the genus Nocardioides, for which the name Nocardioides carbamazepini sp. nov. (CBZ_1T = NCAIM B.0.2663 = LMG 32395) is proposed. To the best of our knowledge, this is the first study that reports simultaneous genome reconstruction of a new to science bacterial species using metagenome binning and at the same time the isolation of the same novel bacterial species.
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6
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Malla MA, Dubey A, Kumar A, Yadav S. Metagenomic analysis displays the potential predictive biodegradation pathways of the persistent pesticides in agricultural soil with a long record of pesticide usage. Microbiol Res 2022; 261:127081. [DOI: 10.1016/j.micres.2022.127081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 12/29/2022]
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7
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Mitzscherling J, MacLean J, Lipus D, Bartholomäus A, Mangelsdorf K, Lipski A, Roddatis V, Liebner S, Wagner D. Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005319] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain NGK65T, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65T hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0–1% NaCl and at pH 7.5–8.0. Glycerol, d-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C16:0 followed by iso-C17:0 and C18:1
ω9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65T belongs to the genus
Nocardioides
(phylum
Actinobacteria
), appearing most closely related to
Nocardioides daejeonensis
MJ31T (98.6%) and
Nocardioides dubius
KSL-104T (98.3%). The genomic DNA G+C content of strain NGK65T was 68.2%. Strain NGK65T and the type strains of species involved in the analysis had average nucleotide identity values of 78.3–71.9% as well as digital DNA–DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus
Nocardioides
. Based on phenotypic and molecular characterization, strain NGK65T can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65T (=DSM 113112T=NCCB 100846T).
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Affiliation(s)
- Julia Mitzscherling
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Joana MacLean
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | | | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Potsdam, Germany
| | - André Lipski
- University of Bonn, Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, Bonn, Germany
| | - Vladimir Roddatis
- GFZ German Research Centre for Geosciences, Section Interface Geochemistry, Potsdam, Germany
| | - Susanne Liebner
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Dirk Wagner
- University of Potsdam, Institute of Geoscience, Potsdam, Germany
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
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8
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Luo S, Ren L, Wu W, Chen Y, Li G, Zhang W, Wei T, Liang YQ, Zhang D, Wang X, Zhen Z, Lin Z. Impacts of earthworm casts on atrazine catabolism and bacterial community structure in laterite soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127778. [PMID: 34823960 DOI: 10.1016/j.jhazmat.2021.127778] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Atrazine accumulation in agricultural soil is prone to cause serious environmental problems and pose risks to human health. Vermicomposting is an eco-friendly approach to accelerating atrazine biodegradation, but the roles of earthworm cast in the accelerated atrazine removal remains unclear. This work aimed to investigate the roles of earthworm cast in promoting atrazine degradation performance by comprehensively exploring the change in atrazine metabolites and bacterial communities. Our results showed that earthworm cast amendment significantly increased soil pH, organic matters, humic acid, fulvic acid and humin, and achieved a significantly higher atrazine removal efficiency. Earthworm cast addition also remarkably changed soil microbial communities by enriching potential soil atrazine degraders (Pseudomonadaceae, Streptomycetaceae, and Thermomonosporaceae) and introducing cast microbial degraders (Saccharimonadaceae). Particularly, earthworm casts increased the production of metabolites deethylatrazine and deisopropylatrazine, but not hydroxyatrazine. Some bacterial taxa (Gaiellaceaea and Micromonosporaceae) and humus (humic acid, fulvic acid and humin) were strongly correlated with atrazine metabolism into deisopropylatrazine and deethylatrazine, whereas hydroxyatrazine production was benefited by higher pH. Our findings verified the accelerated atrazine degradation with earthworm cast supplement, providing new insights into the influential factors on atrazine bioremediation in vermicomposting.
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Affiliation(s)
- Shuwen Luo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Weijian Wu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Yijie Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Gaoyang Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Weijian Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Ting Wei
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Yan-Qiu Liang
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China
| | - Xinzi Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Zhen Zhen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China.
| | - Zhong Lin
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang 524088, PR China; Shenzhen Institute of Guangdong Ocean University, Shenzhen 518114, PR China.
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9
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Jia W, Li N, Yang T, Dai W, Jiang J, Chen K, Xu X. Bioaugmentation of Atrazine-Contaminated Soil With Paenarthrobacter sp. Strain AT-5 and Its Effect on the Soil Microbiome. Front Microbiol 2021; 12:771463. [PMID: 34956132 PMCID: PMC8692732 DOI: 10.3389/fmicb.2021.771463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022] Open
Abstract
Atrazine, a triazine herbicide, is widely used around the world. The residue of atrazine due to its application in the fore-rotating crop maize has caused phytotoxicity to the following crop sweet potato in China. Bioaugmentation of atrazine-contaminated soil with atrazine-degrading strains is considered as the most potential method to remove atrazine from soil. Nevertheless, the feasibility of bioaugmentation and its effect on soil microbiome still need investigation. In this study, Paenarthrobacter sp. AT-5, an atrazine-degrading strain, was inoculated into agricultural soils contaminated with atrazine to investigate the bioaugmentation process and the reassembly of the soil microbiome. It was found that 95.9% of 5 mg kg−1 atrazine was removed from the soils when inoculated with strain AT-5 with 7 days, and the phytotoxicity of sweet potato caused by atrazine was significantly alleviated. qRT-PCR analysis revealed that the inoculated strain AT-5 survived well in the soils and maintained a relatively high abundance. The inoculation of strain AT-5 significantly affected the community structure of the soil microbiome, and the abundances of bacteria associated with atrazine degradation were improved.
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Affiliation(s)
- Weibin Jia
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ning Li
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Tunan Yang
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Weixian Dai
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Kai Chen
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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10
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Luo S, Zhen Z, Zhu X, Ren L, Wu W, Zhang W, Chen Y, Zhang D, Song Z, Lin Z, Liang YQ. Accelerated atrazine degradation and altered metabolic pathways in goat manure assisted soil bioremediation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 221:112432. [PMID: 34166937 DOI: 10.1016/j.ecoenv.2021.112432] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The intensive and long-term use of atrazine in agriculture has resulted in serious environmental pollution and consequently endangered ecosystem and human health. Soil microorganisms play an important role in atrazine degradation. However, their degradation efficiencies are relatively low due to their slow growth and low abundance, and manure amendment as a practice to improve soil nutrients and microbial activities can solve these problems. This study investigated the roles of goat manure in atrazine degradation performance, metabolites and bacterial community structure. Our results showed that atrazine degradation efficiencies in un-amended soils were 26.9-35.7% and increased to 60.9-84.3% in goat manure amended treatments. Hydroxyatrazine pathway was not significantly altered, whereas deethylatrazine and deisopropylatrazine pathways were remarkably enhanced in treatments amended with manure by encouraging the N-dealkylation of atrazine side chains. In addition, goat manure significantly increased soil pH and contents of organic matters and humus, explaining the change of atrazine metabolic pathway. Nocardioides, Sphingomonas and Massilia were positively correlated with atrazine degradation efficiency and three metabolites, suggesting their preference in atrazine contaminated soils and potential roles in atrazine degradation. Our findings suggested that goat manure acts as both bacterial inoculum and nutrients to improve soil microenvironment, and its amendment is a potential practice in accelerating atrazine degradation at contaminated sites, offering an efficient, cheap, and eco-friendly strategy for herbicide polluted soil remediation.
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Affiliation(s)
- Shuwen Luo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Zhen Zhen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Xiaoping Zhu
- The Pearl River Hydraulic Research Institute, Guangzhou 510000, PR China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Weijian Wu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Weijian Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Yijie Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Zhiguang Song
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang 524088, PR China; Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, PR China
| | - Zhong Lin
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang 524088, PR China; Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, PR China.
| | - Yan-Qiu Liang
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang 524088, PR China.
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11
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Hyun DW, Jeong YS, Lee JY, Sung H, Lee SY, Choi JW, Kim HS, Kim PS, Bae JW. Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish). J Microbiol 2021; 59:552-562. [PMID: 33877575 DOI: 10.1007/s12275-021-1036-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022]
Abstract
A polyphasic taxonomic approach was used to characterize three novel bacterial strains, designated as HDW12AT, HDW-15BT, and HDW15CT, isolated from the intestine of fish species Odontobutis interrupta or Siniperca scherzeri. All isolates were obligate aerobic, non-motile bacteria, and grew optimally at 30°C. Phylogenetic analysis based on 16S rRNA sequences revealed that strain HDW12AT was a member of the genus Nocardioides, and closely related to Nocardioides allogilvus CFH 30205T (98.9% sequence identities). Furthermore, strains HDW15BT and HDW15CT were members of the genus Sphingomonas, and closely related to Sphingomonas lutea JS5T and Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence identities), respectively. Strain HDW12AT contained MK-8 (H4), and strains HDW15BT and HDW15CT contained Q-10 as the respiratory quinone. Major polar lipid components of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and those of strains HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The G + C content of strains HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and 65.5%, respectively. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggest that strain HDW12AT represents a novel species within the genus Nocardioides, and strains HDW15BT and HDW15CT represent two novel species within the genus Sphingomonas. We propose the names Nocardioides piscis for strain HDW12AT (= KACC 21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM 33738T), and Sphingomonas sinipercae for strain HDW15CT (= KACC 21342T = KCTC 72589T = JCM 33739T).
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Affiliation(s)
- Dong-Wook Hyun
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Yun-Seok Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jae-Yun Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hojun Sung
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - So-Yeon Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jee-Won Choi
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hyun Sik Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea.
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12
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Liu Y, Fan X, Zhang T, He W, Song F. Effects of the long-term application of atrazine on soil enzyme activity and bacterial community structure in farmlands in China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114264. [PMID: 32142977 DOI: 10.1016/j.envpol.2020.114264] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/23/2020] [Accepted: 02/22/2020] [Indexed: 05/25/2023]
Abstract
Atrazine has been used on Chinese farmlands for a long time and over a wide range. The concentration of atrazine (1.86-1100 mg kg-1) has exceeded the allowable limit in the soil (1.0 mg kg-1), and concern is increasing about the potential harm to farmland soil. Four treatments (AT0, AT6, AT10, AT16) were established to reveal the effects of the long-term application of atrazine on soil health. The results showed a nonlinear regulation of the atrazine residue concentrations in the four treatments. The highest concentration of atrazine residue was in AT6, at 167 mg kg-1, and the lowest concentration of atrazine residue was in AT16, at 102 mg kg-1, but there was no significant difference between AT10 and AT16. The soil urease activity decreased significantly with the increase in the years of atrazine application, the saccharase and cellulase activities in the AT6 were significantly higher than those observed in the other three treatments, the catalase activity gradually decreased with the increase in atrazine application years, and the activity in AT6 was significantly higher than that in AT16. A total of 238 genera were identified by Illumina MiSeq sequencing, and 28 dominant genera were screened. Atrazine significantly increased the relative abundance of Actinobacteria and contributed to the relative abundance of Rubrobacter, Blastococcus, Promicromonospora, Jiangella, Psychroglaciecola and Acetobacteraceae_uncultured, which exhibited significantly higher abundance in AT16 than in AT0. Although there were atrazine-degrading bacteria in the soil, and the atrazine residue decreased with the increase in application years, the concentration of the atrazine residue was still nearly 100 times higher than the allowable limit in the soil, which is a great threat to the soil health.
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Affiliation(s)
- Yufei Liu
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China
| | - Xiaoxu Fan
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China
| | - Tong Zhang
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China
| | - Wenyuan He
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China
| | - Fuqiang Song
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China.
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13
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Brereton NJB, Gonzalez E, Desjardins D, Labrecque M, Pitre FE. Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:135067. [PMID: 31818595 DOI: 10.1016/j.scitotenv.2019.135067] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.
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Affiliation(s)
- N J B Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada.
| | - E Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC H3A 0G1, Canada; Department of Human Genetics, McGill University, Montreal H3A 1B1, Canada
| | - D Desjardins
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada
| | - M Labrecque
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada; Montreal Botanical Garden, Montreal, QC H1X 2B2, Canada
| | - F E Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC H1X 2B2, Canada; Montreal Botanical Garden, Montreal, QC H1X 2B2, Canada
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14
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Esquirol L, Peat TS, Sugrue E, Balotra S, Rottet S, Warden AC, Wilding M, Hartley CJ, Jackson CJ, Newman J, Scott C. Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application. Adv Microb Physiol 2020; 76:129-186. [PMID: 32408946 DOI: 10.1016/bs.ampbs.2020.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.
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Affiliation(s)
- Lygie Esquirol
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing, Parkville, VIC, Australia
| | - Elena Sugrue
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Sahil Balotra
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Sarah Rottet
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Andrew C Warden
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Matthew Wilding
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia; CSIRO Biomedical Manufacturing, Parkville, VIC, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Carol J Hartley
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Janet Newman
- CSIRO Biomedical Manufacturing, Parkville, VIC, Australia
| | - Colin Scott
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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15
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Kanazawa H, Ozaki S, Doi Y, Masuo S, Takaya N. Symbiotic riboflavin degradation by Microbacterium and Nocardioides bacteria. Biosci Biotechnol Biochem 2020; 84:1056-1061. [PMID: 31959067 DOI: 10.1080/09168451.2020.1715783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Unlike its biosynthetic mechanisms and physiological function, current understanding of riboflavin degradation in soil is limited to a few bacteria that decompose it to lumichrome. Here, we isolated six Microbacterium and three Nocardioides strains. These strains utilized riboflavin and lumichrome, respectively, as carbon sources. Among these strains, we identified Microbacterium paraoxydans R16 (R16) and Nocardioides nitrophenolicus L16 (L16), which were isolated form the same enrichment culture. Co-cultured R16 and L16 reconstituted a riboflavin-degrading interspecies consortium, in which the R16 strain degraded riboflavin to lumichrome and ᴅ-ribose. The L16 strain utilized the lumichrome as a carbon source, indicating that R16 is required for L16 to grow in the consortium. Notably, rates of riboflavin degradation and growth were increased in co-cultured, compared with monocultured R16 cells. These results indicated that a beneficial symbiotic interaction between M. paraoxydans R16 and N. nitrophenolicus L16 results in the ability to degrade riboflavin.
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Affiliation(s)
- Hiroshi Kanazawa
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Sayoko Ozaki
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Yuki Doi
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
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Biodegradation of Atrazine by the Novel Klebsiella variicola Strain FH-1. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4756579. [PMID: 31467894 PMCID: PMC6699352 DOI: 10.1155/2019/4756579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/16/2019] [Indexed: 12/04/2022]
Abstract
Bacterial strain FH-1 with high efficiency of degrading Atrazine is separated by means of enrichment culture from the soil applied with Atrazine for many years. FH-1, recognized as Klebsiella variicola based on phylogenetic analysis of 16S rDNA sequences, can grow with Atrazine which is the sole nitrogen source. In fluid inorganic salt medium, the optimal degradation temperature, pH value, and initial concentration of Atrazine are 25°C, 9.0, and 50 mg L–1, respectively, and the degradation rate of Atrazine by strain FH-1 reached 81.5% in 11 d of culture. The degrading process conforms to the kinetics equation of pesticide degradation. Among the metal ions tested, Zn2+ (0.2 mM) has the most significant effect of facilitation on the degradation of Atrazine. In the fluid medium with Zn2+, the degradation rate of Atrazine is increased to 72.5%, while the Cu2+ (0.2 mM) inhibits the degradation of Atrazine. The degradation products of Atrazine by strain FH-1 were identified as HEIT (2-hydroxyl-4-ethylamino-6-isopropylamino-1,3,5-triazine), MEET (2-hydroxyl-4,6-bis(ethylamino)-1,3,5-triazine), and AEEO (4,6-bis(ethylamino)-1,3,5-triazin-2(1H)-one) by HPLC-MS/MS. Three genes (atzC, trzN, and trzD) encoding for Atrazine degrading enzymes were identified by PCR and sequencing in strain FH-1. This study provides additional theoretical support for the application of strain FH-1 in bioremediation of fields polluted by Atrazine.
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17
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Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YH. Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China. Int J Syst Evol Microbiol 2019; 69:2329-2334. [PMID: 31135330 DOI: 10.1099/ijsem.0.003471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, non-motile, rod-shaped, non-spore-forming bacterium, designated HLT2-9T, was isolated from the ice tongue surface of Hailuogou Glacier in Sichuan Province, PR China. Colonies of cells were cream yellow, convex and round. Growth occurred at 0-27 °C (optimum, 20 °C), pH 7.0-10.0 (pH 7.0) and in the presence of 0-2.0 % (w/v) NaCl (0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HLT2-9T belonged to the genus Nocardioides. The highest level of sequence similarities were found to Nocardioides glacieisoli CGMCC1.11097T (99.24 %), Nocardioides oleivorans CGMCC 4.6882T (98.54 %) and Nocardioides ganghwensis CGMCC 4.6875T (98.54 %). However, the low average nucleotide identity (85.6-87.9 %) and digital DNA-DNA hybridization values (26.4-30.2 %) of strain HLT2-9T to its three closest relatives demonstrated that it represents a novel species of the genus Nocardioides. The major cellular fatty acids of strain HLT2-9T were C17 : 1ω8c and iso-C16 : 0. Strain HLT2-9T contained ll-2,6-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinone is MK-8(H4). The G+C content of the genomic DNA was 70.65 mol%. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species Nocardioideszhouii sp. nov. is proposed, with HLT2-9T (=CGMCC 1.11084T=NBRC 109783T) as the type strain.
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Affiliation(s)
- Guo-Qing Zhang
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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18
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Romdhane S, Devers-Lamrani M, Martin-Laurent F, Jrad AB, Raviglione D, Salvia MV, Besse-Hoggan P, Dayan FE, Bertrand C, Barthelmebs L. Evidence for photolytic and microbial degradation processes in the dissipation of leptospermone, a natural β-triketone herbicide. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29848-29859. [PMID: 28718021 DOI: 10.1007/s11356-017-9728-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/06/2017] [Indexed: 06/07/2023]
Abstract
Bioherbicides appear as an ecofriendly alternative to synthetic herbicides, generally used for weed management, because they are supposed to have low side on human health and ecosystems. In this context, our work aims to study abiotic (i.e., photolysis) and biotic (i.e,. biodegradation) processes involved in the fate of leptospermone, a natural β-triketone herbicide, by combining chemical and microbiological approaches. Under controlled conditions, the photolysis of leptospermone was sensitive to pH. Leptospermone has a half-life of 72 h under simulated solar light irradiations. Several transformation products, including hydroxy-leptospermone, were identified. For the first time, a bacterial strain able to degrade leptospermone was isolated from an arable soil. Based on its 16S ribosomal RNA (rRNA) gene sequence, it was affiliated to the Methylophilus group and was accordingly named as Methylophilus sp. LS1. Interestingly, we report that the abundance of OTUs, similar to the 16S rRNA gene sequence of Methylophilus sp. LS1, was strongly increased in soil treated with leptospermone. The leptospermone was completely dissipated by this bacteria, with a half-life time of 6 days, allowing concomitantly its growth. Hydroxy-leptospermone was identified in the bacterial culture as a major transformation product, allowing us to propose a pathway of transformation of leptospermone including both abiotic and biotic processes.
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Affiliation(s)
- Sana Romdhane
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls sur-Mer, France
- AgroSup Dijon, INRA, Univ. Bourgogne-Franche-Comté, Agroécologie, Dijon, France
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, Université Perpignan via Domitia, Perpignan, France
| | | | | | - Amani Ben Jrad
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls sur-Mer, France
| | - Delphine Raviglione
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, Université Perpignan via Domitia, Perpignan, France
| | - Marie-Virginie Salvia
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, Université Perpignan via Domitia, Perpignan, France
| | - Pascale Besse-Hoggan
- Université Clermont Auvergne, CNRS, Sigma Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), 63000, Clermont-Ferrand, France
| | - Franck E Dayan
- Bioagricultural Sciences and Pest Management Department, Colorado State University, Fort Collins, CO, USA
| | - Cédric Bertrand
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, Université Perpignan via Domitia, Perpignan, France
| | - Lise Barthelmebs
- Univ. Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860, Perpignan, France.
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls sur-Mer, France.
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19
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Yang X, Wei H, Zhu C, Geng B. Biodegradation of atrazine by the novel Citricoccus sp. strain TT3. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:144-150. [PMID: 28841530 DOI: 10.1016/j.ecoenv.2017.08.046] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 06/07/2023]
Abstract
A previously undescribed atrazine-degrading bacterial strain TT3 capable of growing with atrazine as its sole nitrogen source was isolated from soil at the wastewater outfall of a pesticide factory in China. Phenotypic characterization and 16S rRNA gene sequencing indicated that the isolate belonged to the genus Citricoccus. Polymerase chain reaction (PCR) analysis revealed that TT3 contained the atrazine-degrading genes trzN, atzB, and atzC. The range for growth and atrazine degradation of TT3 was found to be pH 6.0-11.0, with a preference for alkaline conditions. At 30°C and pH 7.0, the strain removed 50mg/L atrazine in 66h with 1% inoculum. These results demonstrate that Citricoccus sp. TT3 has great potential for bioremediation of atrazine-contaminated sites, particularly in alkaline environments. To the best of our knowledge, there are no previous reports of Citricoccus strains that degrade atrazine, and therefore this work provides a novel candidate for atrazine bioremediation.
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Affiliation(s)
- Xiaoyan Yang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Huanyu Wei
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Bing Geng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China.
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Huang X, He J, Yan X, Hong Q, Chen K, He Q, Zhang L, Liu X, Chuang S, Li S, Jiang J. Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2017; 143:272-297. [PMID: 29183604 DOI: 10.1016/j.pestbp.2016.11.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 06/07/2023]
Abstract
Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.
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Affiliation(s)
- Xing Huang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Jian He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Xin Yan
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Qing Hong
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Kai Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Qin He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Long Zhang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Xiaowei Liu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Shaochuang Chuang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Shunpeng Li
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China.
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Háhn J, Szoboszlay S, Tóth G, Kriszt B. Assessment of bacterial biodetoxification of herbicide atrazine using Aliivibrio fischeri cytotoxicity assay with prolonged contact time. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:648-657. [PMID: 28466204 DOI: 10.1007/s10646-017-1797-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
In our study, we determined and compared the atrazine-biodetoxification ability of 41 bacterial strains and 21 consortia created of those with over 50% degradation rate in pure cultures. Biodegradation capacity was measured with GC-MS. Detoxification was assessed based on the cytotoxic effect of end-products to Aliivibrio fischeri in chronic bioluminescence inhibition assay with 25 h contact time. Chronic A. fischeri assay adapted to a microplate, which is suitable for examine numerous residues simultaneously, also appeared to be significantly more sensitive to atrazine compared to the standard acute (30 min) test. Due to its sensitivity, the chronic assay could be a valuable tool to provide a more comprehensive view of the ecological risks of atrazine and other chemicals. Thirteen strains were able to degrade more than 50% of 50 ppm atrazine. Four of these belong to Rhodococcus aetherivorans, R. qingshengii, Serratia fonticola and Olivibacter oleidegradans which species' atrazine degrading ability has never been reported before. Four consortia degrading ability was more effective than that of the creating individual strains; moreover, their residues did not show cytotoxic effects to A. fischeri. However, in several cases, the degradation products of sole strains and consortia resulted in significant bioluminescence inhibition. Thus high biodegradation (>90%) does not certainly mean the reduction or cessation of toxicity highlighting the importance of the evaluation of biological effects of degradation residues to improve the efficiency and abate the ecological risks of bioremediation techniques.
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Affiliation(s)
- Judit Háhn
- Szent István University, Regional University Center of Excellence, 1 Páter Károly Street, Gödöllő, 2100, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Safety and Ecotoxicology, Szent István University, 1 Páter Károly Street, Gödöllő, 2100, Hungary.
| | - Gergő Tóth
- Department of Environmental Safety and Ecotoxicology, Szent István University, 1 Páter Károly Street, Gödöllő, 2100, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety and Ecotoxicology, Szent István University, 1 Páter Károly Street, Gödöllő, 2100, Hungary
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Bazhanov DP, Li C, Li H, Li J, Zhang X, Chen X, Yang H. Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China. BMC Microbiol 2016; 16:265. [PMID: 27821056 PMCID: PMC5100194 DOI: 10.1186/s12866-016-0868-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 10/26/2016] [Indexed: 11/10/2022] Open
Abstract
Background Soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation. Methods Atrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA. Results A total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins. Conclusions Direct plating on SM agar enabled rapid isolation of atrazine-degrading bacteria and analysis of their natural diversity in soil. The results obtained provided evidence that contaminated soils harbored communities of genetically distinct bacteria capable of individually degrading and utilizing atrazine. The community structures of culturable atrazine degraders were habitat-specific. Bacteria belonging to the genus Arthrobacter were the predominant degraders of atrazine in the plant rhizosphere. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0868-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dmitry P Bazhanov
- Key Laboratory for Applied Microbiology of Shandong Province, Ecology Institute (Biotechnology Center) of Shandong Academy of Sciences, Jinan, Shandong Province, People's Republic of China.
| | - Chengyun Li
- Biology Institute of Shandong Academy of Sciences, Jinan, Shandong Province, People's Republic of China
| | - Hongmei Li
- Biology Institute of Shandong Academy of Sciences, Jinan, Shandong Province, People's Republic of China
| | - Jishun Li
- Biology Institute of Shandong Academy of Sciences, Jinan, Shandong Province, People's Republic of China
| | - Xinjian Zhang
- Key Laboratory for Applied Microbiology of Shandong Province, Ecology Institute (Biotechnology Center) of Shandong Academy of Sciences, Jinan, Shandong Province, People's Republic of China
| | - Xiangfeng Chen
- Shandong Provincial Analysis and Test Center of Shandong Academy of Sciences, Jinan, Shandong Province, People's Republic of China
| | - Hetong Yang
- Biology Institute of Shandong Academy of Sciences, Jinan, Shandong Province, People's Republic of China
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Romdhane S, Devers-Lamrani M, Barthelmebs L, Calvayrac C, Bertrand C, Cooper JF, Dayan FE, Martin-Laurent F. Ecotoxicological Impact of the Bioherbicide Leptospermone on the Microbial Community of Two Arable Soils. Front Microbiol 2016; 7:775. [PMID: 27252691 PMCID: PMC4877392 DOI: 10.3389/fmicb.2016.00775] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
The ecotoxicological impact of leptospermone, a β-triketone bioherbicide, on the bacterial community of two arable soils was investigated. Soil microcosms were exposed to 0 × (control), 1 × or 10 × recommended dose of leptospermone. The β-triketone was moderately adsorbed to both soils (i.e.,: Kfa ~ 1.2 and Koc ~ 140 mL g−1). Its dissipation was lower in sterilized than in unsterilized soils suggesting that it was mainly influenced by biotic factors. Within 45 days, leptospermone disappeared almost entirely from one of the two soils (i.e., DT50 < 10 days), while 25% remained in the other. The composition of the microbial community assessed by qPCR targeting 11 microbial groups was found to be significantly modified in soil microcosms exposed to leptospermone. Pyrosequencing of 16S rRNA gene amplicons showed a shift in the bacterial community structure and a significant impact of leptospermone on the diversity of the soil bacterial community. Changes in the composition, and in the α- and β-diversity of microbial community were transient in the soil able to fully dissipate the leptospermone, but were persistent in the soil where β-triketone remained. To conclude the bacterial community of the two soils was sensitive to leptospermone and its resilience was observed only when leptospermone was fully dissipated.
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Affiliation(s)
- Sana Romdhane
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via DomitiaPerpignan, France; Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via DomitiaPerpignan, France; Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDurDijon, France
| | - Marion Devers-Lamrani
- Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDur Dijon, France
| | - Lise Barthelmebs
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via Domitia Perpignan, France
| | - Christophe Calvayrac
- Biocapteurs Analyse Environnement, EA 4218, University of Perpignan via Domitia Perpignan, France
| | - Cédric Bertrand
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia Perpignan, France
| | - Jean-François Cooper
- Centre de Recherches Insulaires et Observatoire de l'Environnement, USR 3278 EPHE-Centre National de la Recherche Scientifique, University of Perpignan via Domitia Perpignan, France
| | - Franck E Dayan
- Bioagricultural Sciences and Pest Management Department, Colorado State University Fort Collins, CO, USA
| | - Fabrice Martin-Laurent
- Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, EcolDur Dijon, France
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Nordenholt RM, Goyne KW, Kremer RJ, Lin CH, Lerch RN, Veum KS. Veterinary Antibiotic Effects on Atrazine Degradation and Soil Microorganisms. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:565-575. [PMID: 27065404 DOI: 10.2134/jeq2015.05.0235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Veterinary antibiotics (VAs) in manure applied to agricultural lands may change agrichemical degradation by altering soil microbial community structure or function. The objectives of this study were to investigate the influence of two VAs, sulfamethazine (SMZ) and oxytetracycline (OTC), on atrazine (ATZ) degradation, soil microbial enzymatic activity, and phospholipid fatty acid (PLFA) markers. Sandy loam soil with and without 5% swine manure (w/w) was amended with 0 or 500 μg kgC radiolabeled ATZ and with 0, 100, or 1000 μg kg SMZ or OTC and incubated at 25°C in the dark for 96 d. The half-life of ATZ was not significantly affected by VA treatment in the presence or absence of manure; however, the VAs significantly ( < 0.05) inhibited ATZ mineralization in soil without manure (25-50% reduction). Manure amendment decreased ATZ degradation by 22%, reduced ATZ mineralization by 50%, and increased the half-life of ATZ by >10 d. The VAs had limited adverse effects on the microbial enzymes β-glucosidase and dehydrogenase in soils with and without manure. In contrast, manure application stimulated dehydrogenase activity and altered chlorinated ATZ metabolite profiles. Concentrations of PLFA markers were reduced by additions of ATZ, manure, OTC, and SMZ; adverse additive effects of combined treatments were noted for arbuscular mycorrhizal fungi and actinobacteria. In this work, the VAs did not influence persistence of the ATZ parent compound or chlorinated ATZ metabolite formation and degradation. However, reduced CO evolved from VA-treated soil suggests an inhibition to the degradation of other ATZ metabolites due to an altered soil microbial community structure.
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Sagarkar S, Bhardwaj P, Storck V, Devers-Lamrani M, Martin-Laurent F, Kapley A. s-triazine degrading bacterial isolate Arthrobacter sp. AK-YN10, a candidate for bioaugmentation of atrazine contaminated soil. Appl Microbiol Biotechnol 2015; 100:903-13. [PMID: 26403923 DOI: 10.1007/s00253-015-6975-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/20/2015] [Accepted: 09/01/2015] [Indexed: 12/13/2022]
Abstract
The Arthrobacter sp. strain AK-YN10 is an s-triazine pesticide degrading bacterium isolated from a sugarcane field in Central India with history of repeated atrazine use. AK-YN10 was shown to degrade 99 % of atrazine in 30 h from media supplemented with 1000 mg L(-1) of the herbicide. Draft genome sequencing revealed similarity to pAO1, TC1, and TC2 catabolic plasmids of the Arthrobacter taxon. Plasmid profiling analyses revealed the presence of four catabolic plasmids. The trzN, atzB, and atzC atrazine-degrading genes were located on a plasmid of approximately 113 kb.The flagellar operon found in the AK-YN10 draft genome suggests motility, an interesting trait for a bioremediation agent, and was homologous to that of Arthrobacter chlorophenolicus. The multiple s-triazines degradation property of this isolate makes it a good candidate for bioremediation of soils contaminated by s-triazine pesticides.
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Affiliation(s)
- Sneha Sagarkar
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440 020, India
| | - Pooja Bhardwaj
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440 020, India
| | - Veronika Storck
- INRA, UMR 1347 Agroécologie, 17 rue Sully, B.P. 86510, 21065, Dijon Cedex, France
| | | | | | - Atya Kapley
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440 020, India.
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Wang J, Zhu L, Wang Q, Wang J, Xie H. Isolation and characterization of atrazine mineralizing Bacillus subtilis strain HB-6. PLoS One 2014; 9:e107270. [PMID: 25238246 PMCID: PMC4169520 DOI: 10.1371/journal.pone.0107270] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 08/14/2014] [Indexed: 12/03/2022] Open
Abstract
Atrazine is a widely used herbicide with great environmental concern due to its high potential to contaminate soil and waters. An atrazine-degrading bacterial strain HB-6 was isolated from industrial wastewater and the 16S rRNA gene sequencing identified HB-6 as a Bacillus subtilis. PCR assays indicated that HB-6 contained atrazine-degrading genes trzN, atzB and atzC. The strain HB-6 was capable of utilizing atrazine and cyanuric acid as a sole nitrogen source for growth and even cleaved the s-triazine ring and mineralized atrazine. The strain demonstrated a very high efficiency of atrazine biodegradation with a broad optimum pH and temperature ranges and could be enhanced by cooperating with other bacteria, suggesting its huge potential for remediation of atrazine-contaminated sites. To our knowledge, there are few Bacillus subtilis strains reported that can mineralize atrazine, therefore, the present work might provide some new insights on atrazine remediation.
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Affiliation(s)
- Jinhua Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agriculture University, People's Republic of China
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, People's Republic of China
| | - Lusheng Zhu
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agriculture University, People's Republic of China
- * E-mail:
| | - Qi Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agriculture University, People's Republic of China
| | - Jun Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agriculture University, People's Republic of China
| | - Hui Xie
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agriculture University, People's Republic of China
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Solomon RDJ, Kumar A, Satheeja Santhi V. Atrazine biodegradation efficiency, metabolite detection, and trzD gene expression by enrichment bacterial cultures from agricultural soil. J Zhejiang Univ Sci B 2014; 14:1162-72. [PMID: 24302716 DOI: 10.1631/jzus.b1300001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Atrazine is a selective herbicide used in agricultural fields to control the emergence of broadleaf and grassy weeds. The persistence of this herbicide is influenced by the metabolic action of habituated native microorganisms. This study provides information on the occurrence of atrazine mineralizing bacterial strains with faster metabolizing ability. The enrichment cultures were tested for the biodegradation of atrazine by high-performance liquid chromatography (HPLC) and mass spectrometry. Nine cultures JS01.Deg01 to JS09.Deg01 were identified as the degrader of atrazine in the enrichment culture. The three isolates JS04.Deg01, JS07.Deg01, and JS08.Deg01 were identified as efficient atrazine metabolizers. Isolates JS04.Deg01 and JS07.Deg01 produced hydroxyatrazine (HA) N-isopropylammelide and cyanuric acid by dealkylation reaction. The isolate JS08.Deg01 generated deethylatrazine (DEA), deisopropylatrazine (DIA), and cyanuric acid by N-dealkylation in the upper degradation pathway and later it incorporated cyanuric acid in their biomass by the lower degradation pathway. The optimum pH for degrading atrazine by JS08.Deg01 was 7.0 and 16S rDNA phylogenetic typing identified it as Enterobacter cloacae strain JS08.Deg01. The highest atrazine mineralization was observed in case of isolate JS08.Deg01, where an ample amount of trzD mRNA was quantified at 72 h of incubation with atrazine. Atrazine bioremediating isolate E. cloacae strain JS08.Deg01 could be the better environmental remediator of agricultural soils and the crop fields contaminated with atrazine could be the source of the efficient biodegrading microbial strains for the environmental cleanup process.
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Guo Q, Wan R, Xie S. Simazine degradation in bioaugmented soil: urea impact and response of ammonia-oxidizing bacteria and other soil bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:337-343. [PMID: 23771408 DOI: 10.1007/s11356-013-1914-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 06/05/2013] [Indexed: 06/02/2023]
Abstract
The objective of this study was to investigate the impact of exogenous urea nitrogen on ammonia-oxidizing bacteria (AOB) and other soil bacterial communities in soil bioaugmented for simazine remediation. The previously isolated simazine-degrading Arthrobacter sp. strain SD1 was used to degrade the herbicide. The effect of urea on the simazine degradation capacity of the soil bioaugmented with Arthrobacter strain SD1 was assessed using quantitative PCR targeting the s-triazine-degrading trzN and atzC genes. Structures of bacterial and AOB communities were characterized using terminal restriction fragment length polymorphism. Urea fertilizer could affect simazine biodegradation and decreased the proportion of its trzN and atzC genes in soil augmented with Arthrobacter strain SD1. Bioaugmentation process could significantly alter the structures of both bacterial and AOB communities, which were strongly affected by urea amendment, depending on the dosage. This study could provide some new insights towards s-triazine bioremediation and microbial ecology in a bioaugmented system. However, further studies are necessary in order to elucidate the impact of different types and levels of nitrogen sources on s-triazine-degraders and bacterial and AOB communities in bioaugmented soil.
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Affiliation(s)
- Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
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Xie S, Wan R, Wang Z, Wang Q. Atrazine biodegradation by Arthrobacter strain DAT1: effect of glucose supplementation and change of the soil microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:4078-4084. [PMID: 23224504 DOI: 10.1007/s11356-012-1356-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/21/2012] [Indexed: 06/01/2023]
Abstract
The objective of this study was to investigate the impact of glucose supplementation on the soil microbiota inoculated with the atrazine-degrading Arthrobacter strain DAT1. Soil microcosms with different treatments were constructed for biodegradation tests. The impact of glucose supplementation on atrazine degradation capacity of the strain DAT1 and the strain's survival and growth were assessed. The densities of the 16S rRNA gene and the atrazine-metabolic trzN gene were determined using quantitative PCR. The growth of the strain DAT1 and the bacterial community structure were characterized using terminal restriction fragment length polymorphism. Glucose supplementation could affect atrazine degradation by the strain DAT1 and the strain's trzN gene density and growth. The density of the16S rRNA gene decreased during the incubation period. Glucose supplementation could alter the bacterial community structure during the bioaugmentation process. Glucose supplementation could promote the growth of the autochthonous soil degraders that harbored novel functional genes transforming atrazine. Further study will be necessary in order to elucidate the impact of exogenous carbon on autochthonous and inoculated degraders. This study could add some new insights on atrazine bioremediation.
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Affiliation(s)
- Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing, 100871, China.
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Godoi I, Sene L, Barra Caracciolo A. Assessment of the bacterial community structure in a Brazilian clay soil treated with atrazine. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0665-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Tyler HL, Khalid S, Jackson CR, Moore MT. Determining potential for microbial atrazine degradation in agricultural drainage ditches. JOURNAL OF ENVIRONMENTAL QUALITY 2013; 42:828-834. [PMID: 23673950 DOI: 10.2134/jeq2012.0388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Passage of agricultural runoff through vegetated drainage ditches has been shown to reduce the amount of pesticides, such as atrazine, exiting out of agricultural watersheds. Previous studies have found that microbial communities in soil from fields treated with atrazine display enhanced rates of atrazine degradation. However, no studies have examined the potential for atrazine degradation in ditches used to drain these lands. The purpose of the current study was to determine the potential of the drainage ditch soil microbial community for atrazine degradation. Soil samples were collected from fields and adjacent drainage ditches and from nonagricultural land with no previous exposure to atrazine. Polymerase chain reaction analysis indicated widespread presence of atrazine degradation genes in fields and ditches. Potential for degradation was determined by following the decrease of atrazine in spiked soil samples over a 28-d incubation period. Greater than 95% of atrazine was degraded in field and ditch soils, whereas only 68.5 ± 1.3% was degraded in the nonagricultural control. Comparison with autoclaved soil samples indicated the primary mechanism of atrazine degradation in agricultural soils was microbially mediated, whereas its breakdown in nonagricultural soil appeared to be the byproduct of abiotic processes. Therefore, microbial communities in drainage ditch sediments have the potential to play a role in atrazine removal from agricultural runoff by breaking down atrazine deposited in sediments and limiting the amount of this herbicide carried into downstream ecosystems.
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Zhou X, Wang Q, Wang Z, Xie S. Nitrogen impacts on atrazine-degrading Arthrobacter strain and bacterial community structure in soil microcosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:2484-2491. [PMID: 22961491 DOI: 10.1007/s11356-012-1168-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 08/27/2012] [Indexed: 06/01/2023]
Abstract
The objective of this study was to investigate the impacts of exogenous nitrogen on a microbial community inoculated with the atrazine-degrading Arthrobacter sp. in soil amended with a high concentration of atrazine. Inoculated and uninoculated microcosms for biodegradation tests were constructed. Atrazine degradation capacity of the strain DAT1 and the strain's atrazine-metabolic potential and survival were assessed. The relative abundance of the strain DAT1 and the bacterial community structure in soils were characterized using quantitative PCR in combination with terminal restriction fragment length polymorphism. Atrazine degradation by the strain DAT1 and the strain's atrazine-metabolic potential and survival were not affected by addition of a medium level of nitrate, but these processes were inhibited by addition of a high level of nitrate. Microbial community structure changed in both inoculated and uninoculated microcosms, dependent on the level of added nitrate. Bioaugmentation with the strain DAT1 could be a very efficient biotechnology for bioremediation of soils with high concentrations of atrazine.
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Affiliation(s)
- Xiaode Zhou
- State Key Laboratory of Ecohydraulic Engineering in Shaanxi, Xi'an University of Technology, Xi'an 710048, China
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Udiković-Kolić N, Scott C, Martin-Laurent F. Evolution of atrazine-degrading capabilities in the environment. Appl Microbiol Biotechnol 2012; 96:1175-89. [DOI: 10.1007/s00253-012-4495-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/02/2012] [Accepted: 10/03/2012] [Indexed: 11/30/2022]
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Fernández LA, Valverde C, Gómez MA. Isolation and characterization of atrazine-degrading Arthrobacter sp. strains from Argentine agricultural soils. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0463-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Cheyns K, Martin-Laurent F, Bru D, Aamand J, Vanhaecke L, Diels J, Merckx R, Smolders E, Springael D. Long-term dynamics of the atrazine mineralization potential in surface and subsurface soil in an agricultural field as a response to atrazine applications. CHEMOSPHERE 2012; 86:1028-34. [PMID: 22176786 DOI: 10.1016/j.chemosphere.2011.11.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/23/2011] [Accepted: 11/23/2011] [Indexed: 05/25/2023]
Abstract
The dynamics of the atrazine mineralization potential in agricultural soil was studied in two soil layers (topsoil and at 35-45 cm depth) in a 3 years field trial to examine the long term response of atrazine mineralizing soil populations to atrazine application and intermittent periods without atrazine and the effect of manure treatment on those processes. In topsoil samples, (14)C-atrazine mineralization lag times decreased after atrazine application and increased with increasing time after atrazine application, suggesting that atrazine application resulted into the proliferation of atrazine mineralizing microbial populations which decayed when atrazine application stopped. Decay rates appeared however much slower than growth rates. Atrazine application also resulted into the increase of the atrazine mineralization potential in deeper layers which was explained by the growth on leached atrazine as measured in soil leachates recovered from that depth. However, no decay was observed during intermittent periods without atrazine application in the deeper soil layer. atzA and trzN gene quantification confirmed partly the growth and decay of the atrazine degrading populations in the soil and suggested that especially trzN bearing populations are the dominant atrazine degrading populations in both topsoil and deeper soil. Manure treatment only improved the atrazine mineralization rate in deeper soil layers. Our results point to the importance of the atrazine application history on a field and suggests that the long term survival of atrazine degrading populations after atrazine application enables them to rapidly proliferate once atrazine is again applied.
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Affiliation(s)
- K Cheyns
- Division Soil and Water Management, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium.
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Changey F, Devers-Lamrani M, Rouard N, Martin-Laurent F. In vitro evolution of an atrazine-degrading population under cyanuric acid selection pressure: evidence for the selective loss of a 47 kb region on the plasmid ADP1 containing the atzA, B and C genes. Gene 2011; 490:18-25. [PMID: 21959051 DOI: 10.1016/j.gene.2011.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 09/05/2011] [Accepted: 09/09/2011] [Indexed: 02/02/2023]
Abstract
The adaptation of microorganisms to pesticide biodegradation relies on the recruitment of catabolic genes by horizontal gene transfer and homologous recombination mediated by insertion sequences (IS). This environment-friendly function is maintained in the degrading population but it has a cost which could diminish its fitness. The loss of genes in the course of evolution being a major mechanism of ecological specialization, we mimicked evolution in vitro by sub-culturing the atrazine-degrading Pseudomonas sp. ADP in a liquid medium containing cyanuric acid as the sole source of nitrogen. After 120 generations, a new population evolved, which replaced the original one. This new population grew faster on cyanuric acid but showed a similar cyanuric acid degrading ability. Plasmid profiles and Southern blot analyses revealed the deletion of a 47 kb region from pADP1 containing the atzABC genes coding for the enzymes that turn atrazine into cyanuric acid. Long PCR and sequencing analyses revealed that this deletion resulted from a homologous recombination between two direct repeats of a 110-bp, identical to ISPps1 of Pseudomonas huttiensis, flanking the deleted 47 kb region. The loss of a region containing three functional genes constitutively expressed thereby constituting a genetic burden under cyanuric acid selection pressure was responsible for the gain in fitness of the new population. It highlights the IS-mediated plasticity of the pesticide-degrading potential and shows that IS not only favours the expansion of the degrading genetic potential thanks to dispersion and duplication events but also contribute to its reduction thanks to deletion events.
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Affiliation(s)
- F Changey
- INRA, Université de Bourgogne, Microbiologie du Sol et de l'Environnement, 17 Rue Sully, 21065 Dijon Cedex, France
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Allaby RG, Woodwark M. Phylogenetics in the bioinformatics culture of understanding. Comp Funct Genomics 2011; 5:128-46. [PMID: 18629061 PMCID: PMC2447345 DOI: 10.1002/cfg.381] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2003] [Revised: 12/07/2003] [Accepted: 12/22/2003] [Indexed: 11/29/2022] Open
Abstract
Bioinformatics, as a relatively young discipline, has grown up in a world of high-throughput
large volume data that requires automatic analysis to enable us to
stay on top of it all. As a response, the bioinformatics discipline has developed
strategies to find patterns in a ‘low signal : noise ratio’ environment. While the need
to process large amounts of information and extract hypotheses is both laudable
and inescapable, the pressures that such requirements have introduced can lead
to short cuts and misapprehensions. This is particularly the case with reference to
assumptions about the underlying evolutionary theories that are implicitly invoked
by the algorithms utilised in the analysis pipelines. The classic example is the misuse
of the term ‘homologous’ to mean ‘similar’ or even ‘functionally similar’, rather
than the correct definition of ‘having the same evolutionary origin’, which may
or may not imply similarity of function. In this review, we outline some of the
common phylogenetic questions from a bioinformatics perspective that can be better
addressed with a deeper understanding of evolutionary principles and show, with
examples from the amidohydrolase and Toll families, that quite different conclusions
can be drawn if such approaches are taken. This review focuses on the importance
of the underlying evolutionary biology, rather than assessing the merits of different
phylogenetic techniques. The relative merits of a priori and a posteriori inclusion of
biological information are discussed.
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Affiliation(s)
- Robin G Allaby
- EST Bioinformatics, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
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Udiković-Kolić N, Devers-Lamrani M, Petrić I, Hršak D, Martin-Laurent F. Evidence for taxonomic and functional drift of an atrazine-degrading culture in response to high atrazine input. Appl Microbiol Biotechnol 2011; 90:1547-54. [DOI: 10.1007/s00253-011-3198-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 02/28/2011] [Accepted: 03/01/2011] [Indexed: 10/18/2022]
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Wang H, Chen X, Xing X, Hao X, Chen D. Transgenic tobacco plants expressing atzA exhibit resistance and strong ability to degrade atrazine. PLANT CELL REPORTS 2010; 29:1391-9. [PMID: 20960204 DOI: 10.1007/s00299-010-0924-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Revised: 08/11/2010] [Accepted: 09/12/2010] [Indexed: 05/30/2023]
Abstract
Atrazine chlorohydrolase (AtzA) catalyzes hydrolytic dechlorination and can be used in detoxification of atrazine, a herbicide widely employed in the control of broadleaf weeds. In this study, to investigate the potential use of transgenic tobacco plants for phytoremediation of atrazine, atzA genes from Pseudomonas sp. strain ADP and Arthrobacter strain AD1 were transferred into tobacco. Three and four transgenic lines, expressing atzA-ADP and atzA-AD1, respectively, were produced by Agrobacterium-mediated transformation. Molecular characterization including PCR, RT-PCR and Southern blot revealed that atzA was inserted into the tobacco genome and stably inherited by and expressed in the progenies. Seeds of the T(1) transgenic lines had a higher germination percentage and longer roots than the untransformed plants in the presence of 40-150 mg/l atrazine. The T(2) transgenic lines grew taller, gained more dry biomass, and had higher total chlorophyll content than the untransformed plants after growing in soil containing 1 or 2 mg/kg atrazine for 90 days. No atrazine residue remained in the soil in which the T(2) transgenic lines were grown (except 401), while, in the case of the untransformed plants, 0.91 mg (81.3%) and 1.66 mg (74.1%) of the atrazine still remained in the soil containing 1 and 2 mg/kg of atrazine, respectively, indicating that the transgenic lines could degrade atrazine effectively. The transgenic tobacco lines developed could be useful for phytoremediation of atrazine-contaminated soil and water.
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Affiliation(s)
- Huizhuan Wang
- Laboratory of Molecular Genetics, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
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Nocardioides sp. strain WSN05-2, isolated from a wheat field, degrades deoxynivalenol, producing the novel intermediate 3-epi-deoxynivalenol. Appl Microbiol Biotechnol 2010; 89:419-27. [PMID: 20857291 PMCID: PMC3291841 DOI: 10.1007/s00253-010-2857-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 08/01/2010] [Accepted: 08/31/2010] [Indexed: 11/15/2022]
Abstract
The mycotoxin deoxynivalenol (DON) causes serious problems worldwide in the production of crops such as wheat and barley because of its toxicity toward humans and livestock. A bacterial culture capable of degrading DON was obtained from soil samples collected in wheat fields using an enrichment culture procedure. The isolated bacterium, designated strain WSN05-2, completely removed 1,000 μg/mL of DON from the culture medium after incubation for 10 days. On the basis of phylogenetic studies, WSN05-2 was classified as a bacterium belonging to the genus Nocardioides. WSN05-2 showed significant growth in culture medium with DON as the sole carbon source. High-performance liquid chromatography analysis indicated the presence of a major initial metabolite of DON in the culture supernatant. The metabolite was identified as 3-epi-deoxynivalenol (3-epi-DON) by mass spectrometry and 1H and 13C nuclear magnetic resonance analysis. The amount of DON on wheat grain was reduced by about 90% at 7 days after inoculation with WSN05-2. This is the first report of a Nocardioides sp. strain able to degrade DON and of the yet unknown 3-epi-DON as an intermediate in the degradation of DON by a microorganism.
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Seffernick JL, Reynolds E, Fedorov AA, Fedorov E, Almo SC, Sadowsky MJ, Wackett LP. X-ray structure and mutational analysis of the atrazine Chlorohydrolase TrzN. J Biol Chem 2010; 285:30606-14. [PMID: 20659898 DOI: 10.1074/jbc.m110.138677] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Atrazine chlorohydrolase, TrzN (triazine hydrolase or atrazine chlorohydrolase 2), initiates bacterial metabolism of the herbicide atrazine by hydrolytic displacement of a chlorine substituent from the s-triazine ring. The present study describes crystal structures and reactivity of wild-type and active site mutant TrzN enzymes. The homodimer native enzyme structure, solved to 1.40 Å resolution, is a (βα)(8) barrel, characteristic of members of the amidohydrolase superfamily. TrzN uniquely positions threonine 325 in place of a conserved aspartate that ligates the metal in most mononuclear amidohydrolases superfamily members. The threonine side chain oxygen atom is 3.3 Å from the zinc atom and 2.6 Å from the oxygen atom of zinc-coordinated water. Mutation of the threonine to a serine resulted in a 12-fold decrease in k(cat)/K(m), largely due to k(cat), whereas the T325D and T325E mutants had immeasurable activity. The structure and kinetics of TrzN are reminiscent of carbonic anhydrase, which uses a threonine to assist in positioning water for reaction with carbon dioxide. An isosteric substitution in the active site glutamate, E241Q, showed a large diminution in activity with ametryn, no detectable activity with atratone, and a 10-fold decrease with atrazine, when compared with wild-type TrzN. Activity with the E241Q mutant was nearly constant from pH 6.0 to 10.0, consistent with the loss of a proton-donating group. Structures for TrzN-E241Q were solved with bound ametryn and atratone to 1.93 and 1.64 Å resolution, respectively. Both structure and kinetic determinations suggest that the Glu(241) side chain provides a proton to N-1 of the s-triazine substrate to facilitate nucleophilic displacement at the adjacent C-2.
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Arbeli Z, Fuentes C. Prevalence of the gene trzN and biogeographic patterns among atrazine-degrading bacteria isolated from 13 Colombian agricultural soils. FEMS Microbiol Ecol 2010; 73:611-23. [PMID: 20597985 DOI: 10.1111/j.1574-6941.2010.00905.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The following study evaluated the diversity and biogeography of 83 new atrazine-degrading bacteria and the composition of their atrazine degradation genes. These strains were isolated from 13 agricultural soils and grouped according to rep-PCR genomic fingerprinting into 11 major clusters, which showed biogeographic patterns. Three clusters (54 strains) belonged to the genus Arthrobacter, seven clusters (28 strains) were similar to the genus Nocardioides and only one strain was a gram-negative from the genus Ancylobacter. PCR assays for the detection of the genes atzA, B, C, D, E, F and trzN conducted with each of the 83 strains revealed that 82 strains (all gram positive) possessed trzN, 74 of them possessed the combination of trzN, atzB and atzC, while only the gram-negative strain had atzA. A similar PCR assay for the two analogous genes, atzA and trzN, responsible for the first step of atrazine degradation, was performed with DNA extracted directly from the enrichment cultures and microcosms spiked with atrazine. In these assays, the gene trzN was detected in each culture, while atzA was detected in only six out of 13 soils. These results raise an interesting hypothesis on the evolutionary ecology of the two atrazine chlorohydrolase genes (i.e. atzA and trzN) and about the biogeography of atrazine-degrading bacteria.
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Affiliation(s)
- Ziv Arbeli
- Faculty of Agronomy, National University of Colombia, Bogotá, Colombia.
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Jason Krutz L, Shaner DL, Weaver MA, Webb RM, Zablotowicz RM, Reddy KN, Huang Y, Thomson SJ. Agronomic and environmental implications of enhanced s-triazine degradation. PEST MANAGEMENT SCIENCE 2010; 66:461-481. [PMID: 20127867 DOI: 10.1002/ps.1909] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Novel catabolic pathways enabling rapid detoxification of s-triazine herbicides have been elucidated and detected at a growing number of locations. The genes responsible for s-triazine mineralization, i.e. atzABCDEF and trzNDF, occur in at least four bacterial phyla and are implicated in the development of enhanced degradation in agricultural soils from all continents except Antarctica. Enhanced degradation occurs in at least nine crops and six crop rotation systems that rely on s-triazine herbicides for weed control, and, with the exception of acidic soil conditions and s-triazine application frequency, adaptation of the microbial population is independent of soil physiochemical properties and cultural management practices. From an agronomic perspective, residual weed control could be reduced tenfold in s-triazine-adapted relative to non-adapted soils. From an environmental standpoint, the off-site loss of total s-triazine residues could be overestimated 13-fold in adapted soils if altered persistence estimates and metabolic pathways are not reflected in fate and transport models. Empirical models requiring soil pH and s-triazine use history as input parameters predict atrazine persistence more accurately than historical estimates, thereby allowing practitioners to adjust weed control strategies and model input values when warranted.
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Affiliation(s)
- L Jason Krutz
- United States Department of Agriculture, Agriculture Research Service, Crop Production Systems Research Unit, Stoneville, MS 38776, USA
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Udiković Kolić N, Martin-Laurent F, Devers M, Petrić I, Begonja Kolar A, Hrsak D. Genetic potential, diversity and activity of an atrazine-degrading community enriched from a herbicide factory effluent. J Appl Microbiol 2010; 105:1334-43. [PMID: 19146484 DOI: 10.1111/j.1365-2672.2008.03890.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
AIMS To characterize an atrazine-degrading bacterial community enriched from the wastewater of a herbicide factory. METHODS AND RESULTS The community mineralized 81.4 +/- 1.9% of [(14)C-ring]atrazine and 31.0 +/- 1.8% of [(14)C-ethyl]atrazine within 6 days of batch cultivation in mineral salts medium containing atrazine as the sole nitrogen source. Degradation activity of the community towards different chloro- and methylthio-substituted s-triazine compounds was also demonstrated. Restriction analysis of amplified 16S rDNA revealed high diversity of bacterial populations forming the community, with Pseudomonas species dominating in the clone library. Atrazine-degrading genetic potential of the community determined by PCR revealed the presence of trzN, atzB, atzC and trzD genes. The trzN, atzB and atzC genes were shown to be located on a plasmid of 322 kb. Quantitative PCR showed that relative abundances of atzB, atzC and trzD genes were approx. 100-fold lower than 16S rDNA. CONCLUSIONS The enriched community represents a complex bacterial association expressing substantial atrazine-mineralizing activity and a broad specificity towards a range of s-triazine compounds. SIGNIFICANCE AND IMPACT OF THE STUDY Our study is beginning to yield insights into the richness, genetic potential and density of functional atrazine-mineralizing community that could be a potential bioaugmentation agent for improving biotransformation processes in wastewaters bearing different s-triazine compounds.
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Affiliation(s)
- N Udiković Kolić
- Rudjer Bosković Institute, Center for Marine and Environmental Research, Zagreb, Croatia.
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Mineralization of s-triazine herbicides by a newly isolated Nocardioides species strain DN36. Appl Microbiol Biotechnol 2010; 86:1585-92. [DOI: 10.1007/s00253-010-2460-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Revised: 01/03/2010] [Accepted: 01/18/2010] [Indexed: 10/19/2022]
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Chang JH, Shim YY, Cha SK, Chee KM. Probiotic characteristics of lactic acid bacteria isolated from kimchi. J Appl Microbiol 2009; 109:220-30. [PMID: 20102423 DOI: 10.1111/j.1365-2672.2009.04648.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS The present work was aimed at identifying strains of lactic acid bacteria (LAB) from kimchi, with properties suitable for use as starter cultures in yogurt fermentation. METHODS AND RESULTS A total of 2344 LAB strains were obtained from two different sources, one group consisted of commercial LAB strains from kimchi, and the second group consisted of those strains isolated from various types of kimchi. The LAB strains from both groups were screened for resistance to biological barriers (acid and bile salts), and the four most promising strains were selected. Further analysis revealed that KFRI342 of the four selected strains displayed the greatest ability to reduce the growth of the cancer cells, SNU-C4. The in vivo efficacy of strains in quinone reductase induction assay was evaluated, and the extent of DNA strand breakage in individual cells was investigated using the comet assay. Strain KFRI342 was identified as Lactobacillus acidophilus by 16S rRNA sequence analysis, showed protection against tumour initiation and imparted immunostimulation as well as protection against DNA damage. CONCLUSIONS Strain KFRI342, which showed probiotic characteristics reducing cancer cell growth, could be a suitable starter culture for yogurt fermentation because of its strong acid production and high acid tolerance. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report to describe a bacterium, isolated from kimchi, Lact. acidophilus KFRI342 which has the probiotic characteristics and the acid tolerance needed for its use as a starter culture in yogurt fermentation.
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Affiliation(s)
- J-H Chang
- School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
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Satsuma K. Complete biodegradation of atrazine by a microbial community isolated from a naturally derived river ecosystem (microcosm). CHEMOSPHERE 2009; 77:590-596. [PMID: 19596136 DOI: 10.1016/j.chemosphere.2009.06.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 06/14/2009] [Accepted: 06/15/2009] [Indexed: 05/28/2023]
Abstract
A microbial community, designated as AN4, capable of mineralizing the herbicide atrazine was isolated from a model river ecosystem (microcosm). The profile of degradation of atrazine by the AN4 community seemed to well reflect what occurred in the microcosm: rapid degradation of atrazine and transient accumulation of cyanuric acid, followed by relatively slow mineralization. The community comprised multiple phylogenetically distinct microbial strains, and the microbes were suspended and probably aggregated in the water phase of the microcosm. Denaturing gradient gel electrophoresis (DGGE) revealed that multiple bacterial strains exist in the AN4 community, and we successfully isolated two strains, which belonged to the genera Nocardioides and Pedomicrobium. Nocardioides sp. strain AN4-4 degraded atrazine to cyanuric acid and harbored the trzN and atzC genes encoding the s-triazine-degrading enzymes. This strain also degraded other chloro-substituted s-triazines like simazine and propazine, but it showed little degradability for simetryn (a methylthio-substituted s-triazine). Additionally, strain AN4-4 could grow on basal salt agar containing ethylamine or isopropylamine as the only carbon and nitrogen sources. Another strain, Pedomicrobium sp. strain AN4-9 could mineralize cyanuric acid alone. Therefore, we found that the coexistence of these two community members functionally serves to completely biodegrade atrazine.
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Affiliation(s)
- Koji Satsuma
- Chemistry Division, The Institute of Environmental Toxicology, 4321 Uchimoriya-Machi, Joso, Ibaraki 303-0043, Japan.
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Yang C, Li Y, Zhang K, Wang X, Ma C, Tang H, Xu P. Atrazine degradation by a simple consortium of Klebsiella sp. A1 and Comamonas sp. A2 in nitrogen enriched medium. Biodegradation 2009; 21:97-105. [DOI: 10.1007/s10532-009-9284-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2009] [Accepted: 07/01/2009] [Indexed: 11/30/2022]
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Siripattanakul S, Wirojanagud W, McEvoy J, Limpiyakorn T, Khan E. Atrazine degradation by stable mixed cultures enriched from agricultural soil and their characterization. J Appl Microbiol 2009; 106:986-92. [PMID: 19191954 DOI: 10.1111/j.1365-2672.2008.04075.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS The aim of this work was to enrich stable mixed cultures from atrazine-contaminated soil. The cultures were examined for their atrazine biodegradation efficiencies in comparison with J14a, a known atrazine-degrading strain of Agrobacterium radiobacter. The cultures were also characterized to identify community structure and bacterial species present. METHODS AND RESULTS The cultures were enriched and then stabilized in bacterial media. The stable mixed cultures and J14a were tested in a medium containing 100 microg l(-1) of atrazine. For all cultures, atrazine was removed 33-51% within 7 days and the cell optical density increased from 0.05 to between 0.50 and 0.70. Four isolates designated ND1, ND2, ND3 and ND4 were purified from the mixed cultures and identified based on sequence analysis of the 16 S rRNA gene as Alcaligenes faecalis, Klebsiella ornithinolytica, Bacillus megaterium and Agrobacterium tumefaciens, respectively. An atrazine-degrading gene, atzA, was present in ND2 and ND4. CONCLUSIONS The stable mixed cultures obtained could degrade atrazine. Klebsiella ornithinolytica ND2 and Ag. tumefaciens ND4 are atrazine degraders. SIGNIFICANCE AND IMPACT OF THE STUDY The novel stable mixed cultures could be used for bioremediating crop fields contaminated with atrazine. This is the first report of the atzA gene in Kl. ornithinolytica.
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Affiliation(s)
- S Siripattanakul
- National Center of Excellence for Environmental and Hazardous Waste Management, Chulalongkorn University, Bangkok, Thailand
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50
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Iwasaki A, Takagi K, Yoshioka Y, Fujii K, Kojima Y, Harada N. Isolation and characterization of a novel simazine-degrading beta-proteobacterium and detection of genes encoding s-triazine-degrading enzymes. PEST MANAGEMENT SCIENCE 2007; 63:261-8. [PMID: 17304635 DOI: 10.1002/ps.1334] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A moderately persistent herbicide, simazine, has been used globally and detected as a contaminant in soil and water. The authors have isolated a simazine-degrading bacterium from a simazine-degrading bacterial consortium that was enriched using charcoal as a microhabitat. The isolate, strain CDB21, was gram-negative, rod-shaped (0.5-0.6 microm x 1.0-1.2 microm) and motile by means of a single polar flagellum. Based on 16S rRNA sequence analysis, strain CDB21 was identified as a novel beta-proteobacterium exhibiting 100% sequence identity with the uncultured bacterium HOClCi25 (GenBank accession number AY328574). PCR using primers that were specific for the genes of the atrazine-degrading enzymes (atzABCDEF) of Pseudomonas sp. strain ADP showed that strain CDB21 also possessed the entire set of genes of these enzymes. Nucleotide sequences of the atzCDEF genes of strain CDB21 were 100% identical to those of Pseudomonas sp. strain ADP. Sequence identity of the atzA genes between these bacteria was 99.7%. The 398-nucleotide upstream fragment of the atzB gene of strain CDB21 was 100% identical to ORF30 of Pseudomonas sp. strain ADP, and the 1526-nucleotide downstream fragment showed 99.8% sequence similarity to the atzB gene of the pseudomonad.
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Affiliation(s)
- Akio Iwasaki
- Kowa Research Institute, Kowa Co., Ltd, 1-25-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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