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Zhang L, Geng C, Chen X, Chen L, Deng T, Xu M. Niabella digestorum sp. nov., a High Cell-Surface Hydrophobic Bacterium Isolated from Waste Digestion System. Curr Microbiol 2024; 81:348. [PMID: 39251411 DOI: 10.1007/s00284-024-03873-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/24/2024] [Indexed: 09/11/2024]
Abstract
A high cell-surface hydrophobic bacterium, strain A18T, was isolated from a waste digestion system in Chaozhou, China. Cells of strain A18T were Gram-stain-positive, aerobic, non-spore-forming, non-motile, and rod-shaped. Phylogenetic analyses based on the 16S rRNA gene showed that strain A18T shared less than 94.2% sequence similarity to all validated species in the family Chitinophagaceae, and formed a distinct lineage close to genera Niabella and Terrimonas in the neighbor-joining tree, indicating that strain A18T is a novel species. Genome-based phylogenetic analyses revealed that strain A18T is affiliated to the genus Niabella. The cellular components, including iso-C15:0 and iso-C15:1 G as the major fatty acids, menaquinone-7 as the respiratory quinone and a DNA G + C content of 40.54% supported strain A18T as a member of the genus Niabella. However, the physiological and biochemical properties, such as enzyme activities, carbon source utilization and C18:0 3-OH as another major fatty acids, distinguished strain A18T from its close related species. Therefore, the name Niabella digestorum sp. nov. is proposed for this novel species. The type strain is A18T (= GDMCC 1.3242 T = KCTC 92386 T).
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Affiliation(s)
- Ling Zhang
- College of Life Sciences, South Agriculral University, Guangzhou, 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Chuansheng Geng
- College of Life Sciences, South Agriculral University, Guangzhou, 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China
| | - Letian Chen
- College of Life Sciences, South Agriculral University, Guangzhou, 510642, Guangdong, China
| | - Tongchu Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
- Guangdong Provincial Key Laboratory of Environmental Protection Microbiology and Regional Ecological Security, Guangzhou, 510070, Guangdong, China.
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Song D, Chen X, Yao H, Kong G, Xu M, Guo J, Sun G. The variations of native plasmids greatly affect the cell surface hydrophobicity of sphingomonads. mSystems 2023; 8:e0086223. [PMID: 37909742 PMCID: PMC10734547 DOI: 10.1128/msystems.00862-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Microbial cell surface hydrophobicity (CSH) reflects nonspecific adhesion ability and affects various physiological processes, such as biofilm formation and pollutant biodegradation. Understanding the regulation mechanisms of CSH will contribute to illuminating microbial adaptation strategies and provide guidance for controlling CSH artificially to benefit humans. Sphingomonads, a common bacterial group with great xenobiotic-degrading ability, generally show higher CSH than typical Gram-negative bacteria, which plays a positive role in organic pollutant capture and cell colonization. This study verified that the variations of two native plasmids involved in synthesizing outer membrane proteins and polysaccharides greatly affected the CSH of sphingomonads. It is feasible to control their CSH by changing the plasmid copy number and sequences. Additionally, considering that plasmids are likely to evolve faster than chromosomes, the CSH of sphingomonads may evolve quickly to respond to environmental changes. Our results provide valuable insights into the CSH regulation and evolution of sphingomonads.
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Affiliation(s)
- Da Song
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Hui Yao
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Guannan Kong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Environmental Protection Key Laboratory for Microbiology and Regional Ecological Safety, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
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Kim YR, Sang MK. Effects of di-(2-ethylhexyl) phthalate on growth, metabolism, and virulence of the plant pathogenic bacterium Acidovorax citrulli. Front Cell Infect Microbiol 2023; 13:1228713. [PMID: 37692166 PMCID: PMC10485622 DOI: 10.3389/fcimb.2023.1228713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Acidovorax citrulli is a seed-borne bacterial pathogen that causes bacterial fruit blotch in cucurbits and severely affects the production of cucumbers and watermelons globally. In this study, we investigated the effects of di-(2-ethylhexyl) phthalate (DEHP) on the growth, metabolism, and virulence of A. citrulli. Bacterial population was not affected by DEHP exposure; moreover, significant changes were not observed in lipid peroxidation, membrane permeability, and nucleic acid leakage. However, palmitoleic acid content was increased in the cell membrane of DEHP-exposed A. citrulli. Further, DEHP exposure increased the activity of TCA cycle-related enzymes, including α-ketoglutarate dehydrogenase and succinyl-CoA synthetase, along with increase in the content of glutamate, succinate, fumarate, and malate in TCA cycle. Additionally, total 270 genes were differentially expressed by the treatment, of which 28 genes were upregulated and 242 genes, including those related to translation, flagellum-dependent cell motility, and flagellum assembly, were downregulated. Regarding virulence traits, swimming activity was decreased in DEHP-exposed A. citrulli; however, biofilm formation was not affected in in vitro assay. Moreover, relative expression of pathogenicity genes, including hrpX and hrpG, were decreased in DEHP-exposed A. citrulli compared to that of unexposed A. citrulli. Therefore, these results suggest that DEHP accumulation in soil could potentially influence the metabolism and virulence traits of A. citrulli.
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Affiliation(s)
| | - Mee Kyung Sang
- Division of Agricultural Microbiology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
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Liu F, Zhou J, Hu M, Chen Y, Han J, Pan X, You J, Xu M, Yang T, Shao M, Zhang X, Rao Z. Efficient biosynthesis of (R)-mandelic acid from styrene oxide by an adaptive evolutionary Gluconobacter oxydans STA. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:8. [PMID: 36639820 PMCID: PMC9838050 DOI: 10.1186/s13068-023-02258-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/01/2023] [Indexed: 01/15/2023]
Abstract
BACKGROUND (R)-mandelic acid (R-MA) is a highly valuable hydroxyl acid in the pharmaceutical industry. However, biosynthesis of optically pure R-MA remains significant challenges, including the lack of suitable catalysts and high toxicity to host strains. Adaptive laboratory evolution (ALE) was a promising and powerful strategy to obtain specially evolved strains. RESULTS Herein, we report a new cell factory of the Gluconobacter oxydans to biocatalytic styrene oxide into R-MA by utilizing the G. oxydans endogenous efficiently incomplete oxidization and the epoxide hydrolase (SpEH) heterologous expressed in G. oxydans. With a new screened strong endogenous promoter P12780, the production of R-MA was improved to 10.26 g/L compared to 7.36 g/L of using Plac. As R-MA showed great inhibition for the reaction and toxicity to cell growth, adaptive laboratory evolution (ALE) strategy was introduced to improve the cellular R-MA tolerance. The adapted strain that can tolerate 6 g/L R-MA was isolated (named G. oxydans STA), while the wild-type strain cannot grow under this stress. The conversion rate was increased from 0.366 g/L/h of wild type to 0.703 g/L/h by the recombinant STA, and the final R-MA titer reached 14.06 g/L. Whole-genome sequencing revealed multiple gene-mutations in STA, in combination with transcriptome analysis under R-MA stress condition, we identified five critical genes that were associated with R-MA tolerance, among which AcrA overexpression could further improve R-MA titer to 15.70 g/L, the highest titer reported from bulk styrene oxide substrate. CONCLUSIONS The microbial engineering with systematic combination of static regulation, ALE, and transcriptome analysis strategy provides valuable solutions for high-efficient chemical biosynthesis, and our evolved G. oxydans would be better to serve as a chassis cell for hydroxyl acid production.
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Affiliation(s)
- Fei Liu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Junping Zhou
- School of Biotechnology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Mengkai Hu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yan Chen
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jin Han
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Minglong Shao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Liang J, Xu J, Zhao W, Wang J, Chen K, Li Y, Tian Y. Benzo[a]pyrene might be transported by a TonB-dependent transporter in Novosphingobium pentaromativorans US6-1. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124037. [PMID: 33059256 DOI: 10.1016/j.jhazmat.2020.124037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Sphingomonads are well known for their ability to efficiently degrade polycyclic aromatic hydrocarbons (PAHs), but little is known about the mechanism of PAH uptake and transport across the cell membrane. RNA sequencing analysis of a sphingomonad, Novosphingobium pentaromativorans US6-1 showed that 38 TonB-dependent transporter (TBDT) genes were significantly upregulated under 5-ring PAH-benzo[a]pyrene (BaP) stress. In order to reveal whether TBDTs are involved in uptake and transport BaP in US6-1, the key TBDT genes were deleted to generate mutants. The results showed that the growth status of these mutants was not different from that of the wild-type strains, but the PAH degradation ability decreased, especially for the mutant strain Δtbdt-11, which did not encode the tbdt-11 gene. Meanwhile, the cell surface hydrophobicity (CSH) of Δtbdt-11 was found to be significantly lower than that of the wild-type strain under BaP stress. Furthermore, the transcriptional activity of genes encoding PAH degradative enzymes was found to be greatly reduced in Δtbdt-11. Confocal microscopy observations showed that US6-1 could transport BaP across the outer membrane, but this transport capacity was significantly reduced in Δtbdt-11 and wild-type US6-1 treated with PMF uncoupler, further confirming that the tbdt-11 gene was associated with PAH active transport.
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Affiliation(s)
- Jiaqing Liang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiantao Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Weijun Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiaofeng Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Kai Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yuqian Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
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Parhamfar M, Abtahi H, Godini K, Saeedi R, Sartaj M, Villaseñor J, Coulon F, Kumar V, Soltanighias T, Ghaznavi-Rad E, Koolivand A. Biodegradation of heavy oily sludge by a two-step inoculation composting process using synergistic effect of indigenous isolated bacteria. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.12.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abtahi H, Parhamfar M, Saeedi R, Villaseñor J, Sartaj M, Kumar V, Coulon F, Parhamfar M, Didehdar M, Koolivand A. Effect of competition between petroleum-degrading bacteria and indigenous compost microorganisms on the efficiency of petroleum sludge bioremediation: Field application of mineral-based culture in the composting process. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 258:110013. [PMID: 31929055 DOI: 10.1016/j.jenvman.2019.110013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/08/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
The effect of competition between isolated petroleum-degrading bacteria (PDB) and indigenous compost microorganisms (ICM) on the efficiency of composting process in bioremediation of petroleum waste sludge (PWS) was investigated. After isolating two native PDB (Acinetobacter radioresistens strain KA5 and Enterobacter hormaechei strain KA6) from PWS, their ability for growth and crude oil degradation was examined in the mineral-based culture (MBC). Then, the PDB isolate were inoculated into the composting experiments and operated for 12 weeks. The results showed that the PDB degraded 21.65-68.73% of crude oil (1-5%) in the MBC after 7 days. The PDB removed 84.30% of total petroleum hydrocarbon (TPHs) in the composting bioreactor containing the initial TPH level of 20 g kg-1. Removal of petroleum hydrocarbons (PHCs) in the composting experiments proceeded according to the first-order kinetics. The computed values of degradation rate constants and half-lives showed a better performance of the PDB than ICM for TPHs removal. This finding suggests that simultaneous application of the PDB and ICM in the composting reactors resulted in a decline in the effectiveness of the PDB which is due to competition between them. The study also verified that the capability of PDB in degrading PHCs can be successfully scaled-up from MBC to composting process.
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Affiliation(s)
- Hamid Abtahi
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | - Milad Parhamfar
- Faculty of Science, Department of Chemistry, Duissburg-Essen University, Essen, Germany
| | - Reza Saeedi
- Workplace Health Promotion Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Health, Safety and Environment (HSE), School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - José Villaseñor
- Department of Chemical Engineering, Institute of Chemical&Environmental Technologies, University of Castilla-La Mancha, Campus Universitario S/n, 13071, Ciudad Real, Spain
| | - Majid Sartaj
- University of Ottawa, Department of Civil Engineering, 161 Louis Pasteur, Ottawa, Ontario, K1N 6N5, Canada
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Maryam Parhamfar
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | - Mojtaba Didehdar
- Department of Medical Parasitology and Mycology, Arak University of Medical Sciences, Arak, Iran
| | - Ali Koolivand
- Department of Environmental Health Engineering, Faculty of Health, Arak University of Medical Sciences, Arak, Iran.
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Aziz G, Fakhar H, Rahman SU, Tariq M, Zaidi A. An assessment of the aggregation and probiotic characteristics of Lactobacillus species isolated from native (desi) chicken gut. J APPL POULTRY RES 2019. [DOI: 10.3382/japr/pfz042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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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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Koolivand A, Abtahi H, Parhamfar M, Didehdar M, Saeedi R, Fahimirad S. Biodegradation of high concentrations of petroleum compounds by using indigenous bacteria isolated from petroleum hydrocarbons-rich sludge: Effective scale-up from liquid medium to composting process. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 248:109228. [PMID: 31306924 DOI: 10.1016/j.jenvman.2019.06.129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/25/2019] [Accepted: 06/30/2019] [Indexed: 06/10/2023]
Abstract
The scale-up of petroleum hydrocarbons-rich sludge (PHRS) bioremediation from liquid medium to a composting method bioaugmentated with two indigenous bacteria, capable of degrading high levels of crude oil, was surveyed. After isolating the strains (Sphingomonas olei strain KA1 and Acinetobacter radioresistens strain KA2) and determining their biomass production, emulsification index (E24), bacterial adhesion to hydrocarbon (BATH), and crude oil degradation in liquid medium, they were inoculated into the composting experiments. In liquid medium, the removal rate of crude oil were 67.25, 70.86, 61.77, 42.13, and 27.92%, respectively for the initial oil levels of 1, 2, 3, 4, and 5% after 7 days. Degradation of 10, 20, 30, 40 and 50 g kg-1 concentrations of total petroleum hydrocarbons (TPH) were also calculated to be 91.24, 87.23, 84.69, 74.08, and 60.14%, respectively after a composting duration of 12 weeks. The values of the rate constants (k) and half-lives (t1/2) of petroleum hydrocarbons degradation were 0.083-0.212 day-1 and 3.27-8.35 days for the first-order and 0.003-0.089 g kg-1day-1 and 1.12-6.67 days for the second-order model, respectively. This study verified the suitability of the isolated strains for PHRS bioremediation. Successful scale-up of PHRS bioremediation from a liquid medium to a composting process for degrading high amounts of TPH was also confirmed.
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Affiliation(s)
- Ali Koolivand
- Department of Environmental Health Engineering, Faculty of Health, Arak University of Medical Sciences, P.O. Box, 3818146851, Arak, Iran.
| | - Hamid Abtahi
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | - Maryam Parhamfar
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | - Mojtaba Didehdar
- Department of Medical Parasitology and Mycology, Arak University of Medical Sciences, Arak, Iran
| | - Reza Saeedi
- Department of Health, Safety and Environment (HSE), School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Workplace Health Promotion Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shohreh Fahimirad
- Agriculture and Natural Resources Biotechnology Department, University of Tehran, Karaj, 31587-11167, Iran
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11
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Wang Z, Zhu X, Su Y, Xu W, Liu H, Liu Z, Chen W, Wang J. Dimethyl phthalate damaged the cell membrane of Escherichia coli K12. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 180:208-214. [PMID: 31096126 DOI: 10.1016/j.ecoenv.2019.05.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/25/2019] [Accepted: 05/02/2019] [Indexed: 05/22/2023]
Abstract
Dimethyl phthalate (DMP), a phthalate ester (PAE), is a ubiquitous and organic pollutant. In this study, the toxicity of DMP to Escherichia coli K12 and its underlying mechanism were investigated. The results showed that DMP inhibited the growth of E. coli K12 and induced cell inactivation and/or death. DMP caused serious damage to the cell membrane of E. coli K12, and the damage increased with higher DMP concentrations. DMP exposure disrupted cell membranes, as evidenced by dose-dependent variations of cell structures, surface properties, and membrane compositions. Increases in the malondialdehyde (MDA) content indicated an increase in oxidative stress induced by DMP in E. coli K12. The activity of succinic dehydrogenase (SDH) was changed by DMP, which could affect energy metabolism in the membrane of E. coli K12. The expression levels of OmpA and OmpX were increased, and the expression levels of OmpF and OmpW were decreased, in E. coli K12 exposed to DMP. The toxicities of DMP to E. coli K12 could be ascribed to membrane disruption and oxidative stress-induced cell inactivation and/or death. The outcomes will shed new light on the assessment of the ecological effects of DMP.
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Affiliation(s)
- Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China
| | - Xiaohui Zhu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China
| | - Yunpeng Su
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China
| | - Weihui Xu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China.
| | - Hong Liu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China
| | - Zeping Liu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China
| | - Wenjing Chen
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China
| | - Junhe Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, Heilongjiang, 161006, China
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Bacterial Biodegradation of 4-Monohalogenated Diphenyl Ethers in One-Substrate and Co-Metabolic Systems. Catalysts 2018. [DOI: 10.3390/catal8100472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The use of diphenyl ether (DE) and its 4-monohalogenated derivatives (4-HDE) as flame retardants, solvents, and substrates in biocide production significantly increases the risk of ecosystem contamination. Their removal is important from the point of view of environmental protection. The aim of this study was to evaluate the degradation processes of DE and 4-HDE by enzymes of the environmental bacterial strains under one-substrate and co-metabolic conditions. The study is focused on the biodegradation of DE and 4-HDE, the enzymatic activity of microbial strains, and the cell surface properties after contact with compounds. The results show that the highest biodegradation (96%) was observed for 4-chlorodiphenyl ether in co-metabolic culture with P. fluorescens B01. Moreover, the activity of 1,2-dioxygenase during degradation of 4-monohalogenated diphenyl ethers was higher than that of 2,3-dioxygenase for each strain tested. The presence of a co-substrate provoked changes in dioxygenase activity, resulting in the increased activity of 1,2-dioxygenase. Moreover, the addition of phenol as a co-substrate allowed for increased biodegradation of the diphenyl ethers and noticeable modification of the cell surface hydrophobicity during the process. All observations within the study performed have led to a deeper understanding of the contaminants’ biodegradation processes catalyzed by environmental bacteria.
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