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Liu ZS, Wang KH, Han Q, Jiang CY, Liu SJ, Li DF. Sphingobium sp. SJ10-10 encodes a not-yet-reported chromate reductase and the classical Rieske dioxygenases to simultaneously degrade PAH and reduce chromate. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134889. [PMID: 38878436 DOI: 10.1016/j.jhazmat.2024.134889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Both polycyclic aromatic hydrocarbons (PAHs) and heavy metals persist in the environment and are toxic to organisms. Their co-occurrence makes any of them difficult to remove during bioremediation and poses challenges to environmental management and public health. Microorganisms capable of effectively degrading PAHs and detoxifying heavy metals concurrently are required to improve the bioremediation process. In this study, we isolated a new strain, Sphingobium sp. SJ10-10, from an abandoned coking plant and demonstrated its capability to simultaneously degrade 92.6 % of 75 mg/L phenanthrene and reduce 90 % of 3.5 mg/L hexavalent chromium [Cr(VI)] within 1.5 days. Strain SJ10-10 encodes Rieske non-heme iron ring-hydroxylating oxygenases (RHOs) to initiate PAH degradation. Additionally, a not-yet-reported protein referred to as Sphingobium chromate reductase (SchR), with low sequence identity to known chromate reductases, was identified to reduce Cr(VI). SchR is distributed across different genera and can be classified into two classes: one from Sphingobium members and the other from non-Sphingobium species. The widespread presence of SchR in those RHO-containing Sphingobium members suggests that they are excellent candidates for bioremediation. In summary, our study demonstrates the simultaneous removal of PAHs and Cr(VI) by strain SJ10-10 and provides valuable insights into microbial strategies for managing complex pollutant mixtures.
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Affiliation(s)
- Ze-Shen Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke-Huan Wang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qun Han
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - De-Feng Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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2
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Su X, Liu M, Dai H, Dou J, Lu Z, Xu J, He Y. Novel insight into the aging process of microplastics: An in-situ study in coastal wetlands. WATER RESEARCH 2024; 248:120871. [PMID: 37979566 DOI: 10.1016/j.watres.2023.120871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/08/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023]
Abstract
Coastal wetlands, the critical interface between the terrestrial and marine environments, provide a dynamic and unique environment for the aging of microplastics (MPs). Nevertheless, both abiotic and biotic processes that contribute to the aging of MPs in coastal wetlands have been largely neglected. In this study, the aging of MPs was continuously characterized in Hangzhou Bay, a representative coastal wetland in Zhejiang, China. Three-month exposure of polymers in sediment-water interface induced the aging phenomenon with embrittlement and exfoliation, as evidenced by simultaneous observed alternations in crystallinity and functional groups. A first-order kinetic model was fitted to describe the rate and degree of aging quantitatively. As evidenced by the carbonyl index, the residence time of all the examined MPs exhibited significant variance, ranging from 335 to 661 days. These variations might be caused by the selective attachment of plastic-degrading microorganisms (such as Moraxella sp. and Rhodococcus sp.). A positive correlation between the carbonyl index, the number of OTUs in the MP-associated biofilm, and irradiation was observed (p < 0.001), suggesting that the aging process may be co-regulated by natural sunlight and wetland microbial colonization. This study sheds new light on the long-term environmental fate of MPs and their associated ecological risks.
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Affiliation(s)
- Xin Su
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meng Liu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hengyi Dai
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jibo Dou
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhijiang Lu
- Department of Environmental Science and Geology, Wayne State University, Detroit, MI 48201, United States
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan He
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou 310058, China.
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3
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Nemoto Y, Ozawa K, Mori JF, Kanaly RA. Nondesulfurizing benzothiophene biotransformation to hetero and homodimeric ortho-substituted diaryl disulfides by the model PAH-degrading Sphingobium barthaii. Biodegradation 2023; 34:215-233. [PMID: 36808269 DOI: 10.1007/s10532-023-10014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/06/2023] [Indexed: 02/21/2023]
Abstract
Understanding the biotransformation mechanisms of toxic sulfur-containing polycyclic aromatic hydrocarbon (PASH) pollutants such as benzothiophene (BT) is useful for predicting their environmental fates. In the natural environment, nondesulfurizing hydrocarbon-degrading bacteria are major active contributors to PASH biodegradation at petroleum-contaminated sites; however, BT biotransformation pathways by this group of bacteria are less explored when compared to desulfurizing organisms. When a model nondesulfurizing polycyclic aromatic hydrocarbon-degrading soil bacterium, Sphingobium barthaii KK22, was investigated for its ability to cometabolically biotransform BT by quantitative and qualitative methods, BT was depleted from culture media but was biotransformed into mostly high molar mass (HMM) hetero and homodimeric ortho-substituted diaryl disulfides (diaryl disulfanes). HMM diaryl disulfides have not been reported as biotransformation products of BT. Chemical structures were proposed for the diaryl disulfides by comprehensive mass spectrometry analyses of the chromatographically separated products and were supported by the identification of transient upstream BT biotransformation products, which included benzenethiols. Thiophenic acid products were also identified, and pathways that described BT biotransformation and novel HMM diaryl disulfide formation were constructed. This work shows that nondesulfurizing hydrocarbon-degrading organisms produce HMM diaryl disulfides from low molar mass polyaromatic sulfur heterocycles, and this may be taken into consideration when predicting the environmental fates of BT pollutants.
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Affiliation(s)
- Yuki Nemoto
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Kohei Ozawa
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Jiro F Mori
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Robert A Kanaly
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan.
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4
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Zhou M, Liu Z, Wang J, Zhao Y, Hu B. Sphingomonas Relies on Chemotaxis to Degrade Polycyclic Aromatic Hydrocarbons and Maintain Dominance in Coking Sites. Microorganisms 2022; 10:microorganisms10061109. [PMID: 35744627 PMCID: PMC9229013 DOI: 10.3390/microorganisms10061109] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/17/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants widely present in industrial sites. Microbial degradation is an effective method of removing PAHs. The identification of microorganisms that have important ecological functions at the site is of great significance for PAH removal. We collected soil samples at three depths in the range of 0–100 cm at 70-day intervals at the coking site and explored the degradation of PAHs. We combined molecular ecology networking, metagenomics, and genome assembly to search for microorganisms that persist, dominate, and affect the microbial community construction in the degradation process and analyzed their adaptation strategies. The results showed that 15.78 mg/kg of PAHs naturally decayed, and 13.33 mg/kg of PAHs migrated from 30–100 cm to 0–30 cm in the soil. Sphingomonas, which occupied a niche advantage, was both the core and keystone microorganism, and its spatial distribution pattern and temporal change dynamics were consistent with those of PAHs. We assembled the genome of Sphingomonas sp., revealing its multiple potential for degrading PAHs and other pollutants. Additionally, flagellar assembly and bacterial chemotaxis genes ranked high in the assembled genome of Sphingomonas sp., which might help it obtain a competitive advantage in the soil. The findings underscored the strategy of Sphingomonas to maintain dominance, enriched the understanding of PAH-degrading microorganisms in site soil, and provided references for the remediation of PAHs.
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Affiliation(s)
- Meng Zhou
- Department of Environmental Engineering, College of Environmental & Resources Sciences, Zhejiang University, Hangzhou 310058, China; (M.Z.); (Z.L.); (J.W.); (Y.Z.)
| | - Zishu Liu
- Department of Environmental Engineering, College of Environmental & Resources Sciences, Zhejiang University, Hangzhou 310058, China; (M.Z.); (Z.L.); (J.W.); (Y.Z.)
| | - Jiaqi Wang
- Department of Environmental Engineering, College of Environmental & Resources Sciences, Zhejiang University, Hangzhou 310058, China; (M.Z.); (Z.L.); (J.W.); (Y.Z.)
| | - Yuxiang Zhao
- Department of Environmental Engineering, College of Environmental & Resources Sciences, Zhejiang University, Hangzhou 310058, China; (M.Z.); (Z.L.); (J.W.); (Y.Z.)
| | - Baolan Hu
- Department of Environmental Engineering, College of Environmental & Resources Sciences, Zhejiang University, Hangzhou 310058, China; (M.Z.); (Z.L.); (J.W.); (Y.Z.)
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-0571-8898-2340
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5
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Behl T, Rachamalla M, Najda A, Sehgal A, Singh S, Sharma N, Bhatia S, Al-Harrasi A, Chigurupati S, Vargas-De-La-Cruz C, Hobani YH, Mohan S, Goyal A, Katyal T, Solarska E, Bungau S. Applications of Adductomics in Chemically Induced Adverse Outcomes and Major Emphasis on DNA Adductomics: A Pathbreaking Tool in Biomedical Research. Int J Mol Sci 2021; 22:10141. [PMID: 34576304 PMCID: PMC8467560 DOI: 10.3390/ijms221810141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/04/2021] [Accepted: 09/13/2021] [Indexed: 01/06/2023] Open
Abstract
Adductomics novel and emerging discipline in the toxicological research emphasizes on adducts formed by reactive chemical agents with biological molecules in living organisms. Development in analytical methods propelled the application and utility of adductomics in interdisciplinary sciences. This review endeavors to add a new dimension where comprehensive insights into diverse applications of adductomics in addressing some of society's pressing challenges are provided. Also focuses on diverse applications of adductomics include: forecasting risk of chronic diseases triggered by reactive agents and predicting carcinogenesis induced by tobacco smoking; assessing chemical agents' toxicity and supplementing genotoxicity studies; designing personalized medication and precision treatment in cancer chemotherapy; appraising environmental quality or extent of pollution using biological systems; crafting tools and techniques for diagnosis of diseases and detecting food contaminants; furnishing exposure profile of the individual to electrophiles; and assisting regulatory agencies in risk assessment of reactive chemical agents. Characterizing adducts that are present in extremely low concentrations is an exigent task and more over absence of dedicated database to identify adducts is further exacerbating the problem of adduct diagnosis. In addition, there is scope of improvement in sample preparation methods and data processing software and algorithms for accurate assessment of adducts.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; (T.B.); (A.S.); (S.S.); (N.S.)
| | - Mahesh Rachamalla
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada;
| | - Agnieszka Najda
- Department of Vegetable Crops and Medicinal Plants, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; (T.B.); (A.S.); (S.S.); (N.S.)
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; (T.B.); (A.S.); (S.S.); (N.S.)
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; (T.B.); (A.S.); (S.S.); (N.S.)
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa 33, Oman; (S.B.); (A.A.-H.)
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa 33, Oman; (S.B.); (A.A.-H.)
| | - Sridevi Chigurupati
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Celia Vargas-De-La-Cruz
- Faculty of Pharmacy and Biochemistry, Academic Department of Pharmacology, Bromatology and Toxicology, Centro Latinoamericano de Enseñanza e Investigación en Bacteriología Alimentaria, Universidad Nacional Mayor de San Marcos, Lima 15001, Peru;
- E-Health Research Center, Universidad de Ciencias y Humanidades, Lima 15001, Peru
| | - Yahya Hasan Hobani
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Jazan 114, Saudi Arabia;
| | - Syam Mohan
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan 114, Saudi Arabia;
| | - Amit Goyal
- GHG Khalsa College of Pharmacy, Gurusar Sadhar, Ludhiana 141104, India;
| | - Taruna Katyal
- RBMCH Division, ICMR Head Quarters, Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India;
| | - Ewa Solarska
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, 8 Skromna Street, 20-704 Lublin, Poland;
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania;
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6
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Nelson TF, Reddy CM, Ward CP. Product Formulation Controls the Impact of Biofouling on Consumer Plastic Photochemical Fate in the Ocean. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8898-8907. [PMID: 34132543 DOI: 10.1021/acs.est.1c02079] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The photodegradation rates of floating marine plastics govern their environmental lifetimes, but the controls on this process remain poorly understood. Photodegradation of these materials has so far been studied under ideal conditions in the absence of environmental factors such as biofouling, which may slow photochemical transformation rates through light screening. To investigate this interaction, we incubated different plastics in continuous flow seawater mesocosms to follow (i) the extent of biofilm growth on the samples and (ii) decreases in light transmittance through the samples over time. We used consumer products with high relevance (e.g., shopping bags, water bottles, and packaging materials) and with different formulations, referring to primary polymers (polyethylene (PE) and polyethylene terephthalate (PET)) and inorganic additives (titanium dioxide (TiO2)). The behavior of consumer-relevant formulations was compared to those of pure PE and PET films, revealing that the relative effects of UV- and, to a lesser extent, visible-light screening differ based on the formulation of the product. Pure PE showed greater relative UV-transmittance decreases (Δ = -34% through the entire sample, accounting for biofilm on both sides of the plastic film) than PET (Δ = -20%) and PE products with TiO2 (Δ = < -10%). Our results demonstrate that even with biofouling, photodegradation remains a highly relevant process for the fate of marine plastics. However, we expect photodegradation rates of plastics in the ocean to be slower than those measured in laboratory studies, due to light screening by biofilms, and the specific formulation of plastic products is a key determinant of the extent of this effect.
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Affiliation(s)
- Taylor F Nelson
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Christopher M Reddy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Collin P Ward
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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7
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Song D, Chen X, Xu M, Hai R, Zhou A, Tian R, Van Nostrand JD, Kempher ML, Guo J, Sun G, Zhou J. Adaptive Evolution of Sphingobium hydrophobicum C1 T in Electronic Waste Contaminated River Sediment. Front Microbiol 2019; 10:2263. [PMID: 31632374 PMCID: PMC6783567 DOI: 10.3389/fmicb.2019.02263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/17/2019] [Indexed: 11/13/2022] Open
Abstract
Electronic waste (e-waste) has caused a severe worldwide pollution problem. Despite increasing isolation of degradative microorganisms from e-waste contaminated environments, the mechanisms underlying their adaptive evolution in such habitats remain unclear. Sphingomonads generally have xenobiotic-degrading ability and may play important roles in bioremediation. Sphingobium hydrophobicum C1T, characterized with superior cell surface hydrophobicity, was recently isolated from e-waste contaminated river sediment. To dissect the mechanisms driving its adaptive evolution, we evaluated its stress resistance, sequenced its genome and performed comparative genomic analysis with 19 other Sphingobium strains. Strain C1T can feed on several kinds of e-waste-derived xenobiotics, exhibits a great resistance to heavy metals and possesses a high colonization ability. It harbors abundant genes involved in environmental adaptation, some of which are intrinsic prior to experiencing e-waste contamination. The extensive genomic variations between strain C1T and other Sphingobium strains, numerous C1T-unique genes, massive mobile elements and frequent genome rearrangements reflect a high genome plasticity. Positive selection, gene duplication, and especially horizontal gene transfer drive the adaptive evolution of strain C1T. Moreover, presence of type IV secretion systems may allow strain C1T to be a source of beneficial genes for surrounding microorganisms. This study provides new insights into the adaptive evolution of sphingomonads, and potentially guides bioremediation strategies.
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Affiliation(s)
- Da Song
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xingjuan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rong Hai
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, CA, United States
| | - Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Renmao Tian
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Megan L Kempher
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jun Guo
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Guoping Sun
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
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8
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Lee DW, Lee H, Lee AH, Kwon BO, Khim JS, Yim UH, Kim BS, Kim JJ. Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast, Korea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 234:503-512. [PMID: 29216488 DOI: 10.1016/j.envpol.2017.11.097] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 05/15/2023]
Abstract
The tidal flats near Sinduri beach in Taean, Korea, have been severely contaminated by heavy crude oils due to the Korea's worst oil spill accident, say the Hebei Spirit Oil Spill, in 2007. Crude oil compounds, including polycyclic aromatic hydrocarbons (PAHs), pose significant environmental damages due to their wide distribution, persistence, high toxicity, mutagenicity, and carcinogenicity. Microbial community of Sinduri beach sediments samples was analyzed by metagenomic data with 16S rRNA gene amplicons. Three phyla (Proteobacteria, Firmicutes, and Bacteroidetes) accounted for approximately ≥93.0% of the total phyla based on metagenomic analysis. Proteobacteria was the dominant phylum in Sinduri beach sediments. Cultivable bacteria were isolated from PAH-enriched cultures, and bacterial diversity was investigated through performing culture characterization followed by molecular biology methods. Sixty-seven isolates were obtained, comprising representatives of Actinobacteria, Firmicutes, α- and γ-Proteobacteria, and Bacteroidetes. PAH catabolism genes, such as naphthalene dioxygenase (NDO) and aromatic ring hydroxylating dioxygenase (ARHDO), were used as genetic markers to assess biodegradation of PAHs in the cultivable bacteria. The ability to degrade PAHs was demonstrated by monitoring the removal of PAHs using a gas chromatography mass spectrometer. Overall, various PAH-degrading bacteria were widely present in Sinduri beach sediments and generally reflected the restored microbial community. Among them, Cobetia marina, Rhodococcus soli, and Pseudoalteromonas agarivorans were found to be significant in degradation of PAHs. This large collection of PAH-degrading strains represents a valuable resource for studies investigating mechanisms of PAH degradation and bioremediation in oil contaminated coastal environment, elsewhere.
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Affiliation(s)
- Dong Wan Lee
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea; BK21 Plus Eco-Leader Education Center, Korea University, Seoul, 02841, Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Aslan Hwanhwi Lee
- Department of Civil and Geological Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK, S7N 5A9, Canada
| | - Bong-Oh Kwon
- School of Earth and Environmental Science & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Science & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Un Hyuk Yim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje, Republic of Korea
| | - Beom Seok Kim
- Division of Biotechnology, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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9
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Role and mechanism of cell-surface hydrophobicity in the adaptation of Sphingobium hydrophobicum to electronic-waste contaminated sediment. Appl Microbiol Biotechnol 2018; 102:2803-2815. [DOI: 10.1007/s00253-017-8734-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/29/2017] [Accepted: 12/12/2017] [Indexed: 01/16/2023]
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10
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Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium. mSystems 2017; 2:mSystems00020-17. [PMID: 28567447 PMCID: PMC5443232 DOI: 10.1128/msystems.00020-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/17/2017] [Indexed: 11/24/2022] Open
Abstract
This study highlights the significant role of the genetic repertoire of a microorganism in the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits for Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium. Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups—rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed β-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats—freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism’s genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.
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Sphingobium hydrophobicum sp. nov., a hydrophobic bacterium isolated from electronic-waste-contaminated sediment. Int J Syst Evol Microbiol 2016; 66:3912-3916. [DOI: 10.1099/ijsem.0.001287] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kanaly RA, Micheletto R, Matsuda T, Utsuno Y, Ozeki Y, Hamamura N. Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22. Microbiologyopen 2015; 4:841-56. [PMID: 26305056 PMCID: PMC4618615 DOI: 10.1002/mbo3.283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022] Open
Abstract
Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2'-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H](+) > [M + H - 116](+) transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work.
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Affiliation(s)
- Robert A Kanaly
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, Kanagawa, Yokohama, 236-0027, Japan
| | - Ruggero Micheletto
- Department of Nanosystem Science, Graduate School of Nanobiosciences, Yokohama City University, Kanagawa, Yokohama, 236-0027, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan
| | - Youko Utsuno
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, Kanagawa, Yokohama, 236-0027, Japan
| | - Yasuhiro Ozeki
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, Kanagawa, Yokohama, 236-0027, Japan
| | - Natsuko Hamamura
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan.,Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, 812-8581, Japan
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Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand. ISME JOURNAL 2014; 9:150-65. [PMID: 24936762 PMCID: PMC4274413 DOI: 10.1038/ismej.2014.101] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 05/07/2014] [Accepted: 05/12/2014] [Indexed: 11/08/2022]
Abstract
The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (that is, bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of genome-wide gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated non-sterile sand, compared with regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing dibenzodioxins and dibenzofurans. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well as during growth and stationary phase in sand. Cells during transition show stationary phase characteristics, evidence for stress and for nutrient scavenging, and adjust their primary metabolism if they were not precultured on the same contaminant as found in the soil. Cells growing and surviving in sand degrade dibenzofuran but display a very different transcriptome signature as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous 'soil-specific' expressed genes. Studies focusing on inoculation efficacy should test behaviour under conditions as closely as possible mimicking the intended microbiome conditions.
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Michelou VK, Caporaso JG, Knight R, Palumbi SR. The Ecology of Microbial Communities Associated with Macrocystis pyrifera. PLoS One 2013; 8:e67480. [PMID: 23840715 PMCID: PMC3686729 DOI: 10.1371/journal.pone.0067480] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/19/2013] [Indexed: 11/18/2022] Open
Abstract
Kelp forests are characterized by high biodiversity and productivity, and the cycling of kelp-produced carbon is a vital process in this ecosystem. Although bacteria are assumed to play a major role in kelp forest carbon cycling, knowledge of the composition and diversity of these bacterial communities is lacking. Bacterial communities on the surface of Macrocystis pyrifera and adjacent seawater were sampled at the Hopkins Marine Station in Monterey Bay, CA, and further studied using 454-tag pyrosequencing of 16S RNA genes. Our results suggest that M. pyrifera-dominated kelp forests harbor distinct microbial communities that vary temporally. The distribution of sequence tags assigned to Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the surface of the kelp and the surrounding water. Several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed considerable temporal variation, often with similar trends in the seawater and the surface of the kelp. Bacterial community structure and membership correlated with the kelp surface serving as host, and varied over time. Several kelp-specific taxa were highly similar to other bacteria known to either prevent the colonization of eukaryotic larvae or exhibit antibacterial activities. Some of these kelp-specific bacterial associations might play an important role for M. pyrifera. This study provides the first assessment of the diversity and phylogenetic profile of the bacterial communities associated with M. pyrifera.
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Affiliation(s)
- Vanessa K. Michelou
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California, United States of America
| | - J. Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
- Argonne National Laboratory, Institute for Genomics and Systems Biology, Argonne, Illinois, United States of America
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America
- Howard Hughes Medical Institute, Boulder, Colorado, United States of America
| | - Stephen R. Palumbi
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California, United States of America
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Handl S, German AJ, Holden SL, Dowd SE, Steiner JM, Heilmann RM, Grant RW, Swanson KS, Suchodolski JS. Faecal microbiota in lean and obese dogs. FEMS Microbiol Ecol 2013; 84:332-43. [PMID: 23301868 DOI: 10.1111/1574-6941.12067] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/07/2012] [Accepted: 12/12/2012] [Indexed: 12/25/2022] Open
Abstract
Previous work has shown obesity to be associated with changes in intestinal microbiota. While obesity is common in dogs, limited information is available about the role of the intestinal microbiota. The aim of this study was to investigate whether alterations in the intestinal microbiota may be associated with canine obesity. Using 16S rRNA gene pyrosequencing and quantitative real-time PCR, we evaluated the composition of the faecal microbiota in 22 lean and 21 obese pet dogs, as well as in five research dogs fed ad libitum and four research dogs serving as lean controls. Firmicutes, Fusobacteria and Actinobacteria were the predominant bacterial phyla. The phylum Actinobacteria and the genus Roseburia were significantly more abundant in the obese pet dogs. The order Clostridiales significantly increased under ad libitum feeding in the research dogs. Canine intestinal microbiota is highly diverse and shows considerable interindividual variation. In the pet dogs, influence on the intestinal microbiota besides body condition, like age, breed, diet or lifestyle, might have masked the effect of obesity. The study population of research dogs was small, and further work is required before the role of the intestinal microbiota in canine obesity is clarified.
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Affiliation(s)
- Stefanie Handl
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria.
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Lobelle D, Cunliffe M. Early microbial biofilm formation on marine plastic debris. MARINE POLLUTION BULLETIN 2011; 62:197-200. [PMID: 21093883 DOI: 10.1016/j.marpolbul.2010.10.013] [Citation(s) in RCA: 460] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 10/15/2010] [Accepted: 10/27/2010] [Indexed: 05/17/2023]
Abstract
An important aspect of the global problem of plastic debris pollution is plastic buoyancy. There is some evidence that buoyancy is influenced by attached biofilms but as yet this is poorly understood. We submerged polyethylene plastic in seawater and sampled weekly for 3 weeks in order to study early stage processes. Microbial biofilms developed rapidly on the plastic and coincided with significant changes in the physicochemical properties of the plastic. Submerged plastic became less hydrophobic and more neutrally buoyant during the experiment. Bacteria readily colonised the plastic but there was no indication that plastic-degrading microorganisms were present. This study contributes to improved understanding of the fate of plastic debris in the marine environment.
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Affiliation(s)
- Delphine Lobelle
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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Molecular assessment of microbiota structure and dynamics along mixed olive oil and winery wastewaters biotreatment. Biodegradation 2010; 22:773-95. [DOI: 10.1007/s10532-010-9434-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 10/26/2010] [Indexed: 10/18/2022]
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Microtiter susceptibility testing of microbes growing on peg lids: a miniaturized biofilm model for high-throughput screening. Nat Protoc 2010; 5:1236-54. [PMID: 20595953 DOI: 10.1038/nprot.2010.71] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Batch culture of biofilms on peg lids is a versatile method that can be used for microtiter determinations of biofilm antimicrobial susceptibility. In this paper, we describe a core protocol and a set of parameters (surface composition, the rate of rocking or orbital motion, temperature, cultivation time, inoculum size, atmospheric gases and nutritional medium) that can be adjusted to grow single- or multispecies biofilms on peg surfaces. Mature biofilms formed on peg lids can then be fitted into microtiter plates containing test agents. After a suitable exposure time, biofilm cells are disrupted into a recovery medium using sonication. Microbicidal endpoints can be determined qualitatively using optical density measurements or quantitatively using viable cell counting. Once equipment is calibrated and growth conditions are at an optimum, the procedure requires approximately 5 h of work over 4-6 d. This efficient method allows antimicrobial agents and exposure conditions to be tested against biofilms on a high-throughput scale.
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Kanaly RA, Harayama S. Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria. Microb Biotechnol 2010; 3:136-64. [PMID: 21255317 PMCID: PMC3836582 DOI: 10.1111/j.1751-7915.2009.00130.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/22/2009] [Accepted: 05/26/2009] [Indexed: 11/26/2022] Open
Abstract
Interest in understanding prokaryotic biotransformation of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) has continued to grow and the scientific literature shows that studies in this field are originating from research groups from many different locations throughout the world. In the last 10 years, research in regard to HMW PAH biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities. This has occurred in addition to the continuation of in-depth comprehensive characterizations of previously isolated organisms, such as Mycobacterium vanbaalenii PYR-1. New metabolites derived from prokaryotic biodegradation of four- and five-ring PAHs have been characterized, our knowledge of the enzymes involved in these transformations has been advanced and HMW PAH biodegradation pathways have been further developed, expanded upon and refined. At the same time, investigation of prokaryotic consortia has furthered our understanding of the capabilities of microorganisms functioning as communities during HMW PAH biodegradation.
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Affiliation(s)
- Robert A Kanaly
- Department of Genome Systems, Faculty of Bionanoscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Kanagawa-ken, Yokohama 236-0027, Japan.
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Coppotelli BM, Ibarrolaza A, Dias RL, Del Panno MT, Berthe-Corti L, Morelli IS. Study of the degradation activity and the strategies to promote the bioavailability of phenanthrene by Sphingomonas paucimobilis strain 20006FA. MICROBIAL ECOLOGY 2010; 59:266-76. [PMID: 19609598 DOI: 10.1007/s00248-009-9563-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 06/26/2009] [Indexed: 05/16/2023]
Abstract
The present study describes the phenanthrene-degrading activity of Sphingomonas paucimobilis 20006FA and its ability to promote the bioavailability of phenanthrene. S. paucimobilis 20006FA was isolated from a phenanthrene-contaminated soil microcosm. The strain was able to grow in liquid mineral medium saturated with phenanthrene as the sole carbon source, showing high phenanthrene elimination (52.9% of the supplied phenanthrene within 20 days). The accumulation of 1-hydroxy-2-naphthoic acid and salicylic acid as major phenanthrene metabolites and the capacity of the strain to grow with sodium salicylate as the sole source of carbon and energy indicated that the S. paucimobilis 20006FA possesses a complete phenanthrene degradation pathway. However, under the studied conditions, the strain was able to mineralize only the 10% of the consumed phenanthrene. Investigations on the cell ability to promote bioavailability of phenanthrene showed that the S. paucimobilis strain 20006FA exhibited low cell hydrophobicity (0.13), a pronounced chemotaxis toward phenanthrene, and it was able to reduce the surface tension of mineral liquid medium supplemented with phenanthrene as sole carbon source. Scanning electron micrographs revealed that: (1) in suspension cultures, cells formed flocks and showed small vesicles on the cell surface and (2) cells were also able to adhere to phenanthrene crystals and to produce biofilms. Clearly, the strain seems to exhibit two different mechanisms to enhance phenanthrene bioavailability: biosurfactant production and adhesion to the phenanthrene crystals.
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Affiliation(s)
- Bibiana M Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI), UNLP, CCT-La Plata, CONICET, La Plata 1900, Argentina
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Zhang GY, Ling JY, Sun HB, Luo J, Fan YY, Cui ZJ. Isolation and characterization of a newly isolated polycyclic aromatic hydrocarbons-degrading Janibacter anophelis strain JY11. JOURNAL OF HAZARDOUS MATERIALS 2009; 172:580-586. [PMID: 19660861 DOI: 10.1016/j.jhazmat.2009.07.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 07/10/2009] [Accepted: 07/10/2009] [Indexed: 05/28/2023]
Abstract
The PAHs-degradation bacterium strain JY11 was newly isolated from the polluted soil in Jinan Oil Refinery Factory, Shandong Province of China. The isolate was identified as Janibacter anophelis with respect to its 16S rDNA sequence, DNA-DNA relatedness and fatty acid profiles, as well as various physiological characteristics. The strain was Gram-positive, non-motile, non-spore-forming, short rods in young culture, 0.8-1.0 microm in diameter and 1.3-1.6 microm long, and coccoid cells in the stationary phase of growth that are 1.0-1.2 microm in diameter and 1.3-1.5 microm long, occurred in pairs and sometimes in chains or in group, aerobic, oxidase-week positive, catalase-positive. J. anophelis strain JY11 can utilize naphthalene, phenanthrene, anthracene, pyrene, xylene, methanol, ethanol and salicylic acid as sole carbon source. The strain could remove 98.5% of phenanthrene, 82.1% of anthracene, and 97.7% of pyrene with an initial concentration of 500 ppm in five days without adding co-metabolism substrates and surfactants.
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Affiliation(s)
- Guo-Ying Zhang
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
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Molecular characteristics of xenobiotic-degrading sphingomonads. Appl Microbiol Biotechnol 2008; 81:793-811. [PMID: 19002456 DOI: 10.1007/s00253-008-1752-3] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/06/2008] [Accepted: 10/15/2008] [Indexed: 10/21/2022]
Abstract
The genus Sphingomonas (sensu latu) belongs to the alpha-Proteobacteria and comprises strictly aerobic chemoheterotrophic bacteria that are widespread in various aquatic and terrestrial environments. The members of this genus are often isolated and studied because of their ability to degrade recalcitrant natural and anthropogenic compounds, such as (substituted) biphenyl(s) and naphthalene(s), fluorene, (substituted) phenanthrene(s), pyrene, (chlorinated) diphenylether(s), (chlorinated) furan(s), (chlorinated) dibenzo-p-dioxin(s), carbazole, estradiol, polyethylene glycols, chlorinated phenols, nonylphenols, and different herbicides and pesticides. The metabolic versatility of these organisms suggests that they have evolved mechanisms to adapt quicker and/or more efficiently to the degradation of novel compounds in the environment than members of other bacterial genera. Comparative analyses demonstrate that sphingomonads generally use similar degradative pathways as other groups of microorganisms but deviate from competing microorganisms by the existence of multiple hydroxylating oxygenases and the conservation of specific gene clusters. Furthermore, there is increasing evidence for the existence of plasmids that only can be disseminated among sphingomonads and which undergo after conjugative transfer pronounced rearrangements.
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Cunliffe M, Kawasaki A, Fellows E, Kertesz MA. Effect of inoculum pretreatment on survival, activity and catabolic gene expression of Sphingobium yanoikuyae B1 in an aged polycyclic aromatic hydrocarbon-contaminated soil. FEMS Microbiol Ecol 2006; 58:364-72. [PMID: 17117981 DOI: 10.1111/j.1574-6941.2006.00167.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The survival and effectiveness of a bioaugmentation strain in its target environment depend not only on physicochemical parameters in the soil but also on the physiological state of the inoculated organism. This study examined the effect of variations in inoculum pretreatment on the survival, metabolic activity (measured as rRNA content) and polycyclic aromatic hydrocarbon (PAH)-catabolic gene expression of Sphingobium yanoikuyae B1 in an aged PAH-contaminated soil. RNA denaturing gradient gel electrophoresis analysis showed stable colonization of PAH-contaminated soil by S. yanoikuyae B1 after four pretreatments (growth in complex or minimal medium, starvation, or acclimation to phenanthrene). By contrast, extractable CFUs decreased with time for all four treatments, and significantly faster for Luria Bertani-grown inocula, suggesting that these cells adhered strongly to soil particles while remaining metabolically active. Pretreatment of the inoculum had a dramatic effect on the expression of genes specific to the PAH-degradation pathway. The highest levels of bphC and xylE expression were seen for inocula that had been precultivated on complex medium, and degradation of PAHs was significantly enhanced in soils treated with these inocula. The results suggest that using complex media instead of minimal media for cultivating bioaugmentation inocula may improve the subsequent efficiency of contaminant biodegradation in the soil.
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Affiliation(s)
- Michael Cunliffe
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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