1
|
Zhang F, Yu H, Ai L, Hao Y, Peng R. Tsrp1 Is a Novel Cyclic Diguanosine Monophosphate Effector that Plays a Role in the Organic-Solvent Tolerance of Rhodococcus ruber. J Microbiol Biotechnol 2025; 35:e2410039. [PMID: 40147940 PMCID: PMC11985408 DOI: 10.4014/jmb.2410.10039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 01/19/2025] [Accepted: 01/24/2025] [Indexed: 03/29/2025]
Abstract
Cyclic diguanosine monophosphate is a ubiquitous second messenger that regulates diverse cellular processes. Rhodococcus ruber SD3 has potential for use in removing environmental pollutants such as phenol and toluene. In this study, Tsrp1 was found to be a novel cyclic diguanosine monophosphate effector in this strain. The interaction between Tsrp1 and c-di-GMP was verified by surface plasmon resonance, and the dissociation constant was 64 ± 6.84 μM. Moreover, in comparison with the wild-type strain, the recombinant R. ruber SD3 strain, which exhibited elevated levels tsrp1 gene expression, demonstrated enhanced growth in the presence of toluene and phenol. Both recombinant R. ruber SD3 and the wild-type strain completely degraded toluene (0.3 g/l, 0.6 g/l and 0.9 g/l) and phenol (0.6 g/l, 0.8 g/l and 1.0 g/l) in 72 h. Furthermore, differential expression of key genes encoding transcription factors was identified based on the transcriptomic comparison between the two strains. This study is the first to describe a novel cyclic diguanosine monophosphate effector and its role in the characteristics of R. ruber SD3, which will shed new light on the mechanisms underlying the organic solvent tolerance of R. ruber SD3.
Collapse
Affiliation(s)
- Fan Zhang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Han Yu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Lei Ai
- College of Life Science, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Yixin Hao
- College of Life Science, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Ren Peng
- College of Life Science, Jiangxi Normal University, Nanchang 330022, P.R. China
| |
Collapse
|
2
|
Hoque MN, Hossain A, Faisal GM, Bukharid MZ, Hossain MA, Sultana M. Draft genome sequence of an arsenotrophic Achromobacter aegrifaciens strain isolated from soil in Bangladesh. Microbiol Resour Announc 2024; 13:e0013724. [PMID: 39315834 PMCID: PMC11556063 DOI: 10.1128/mra.00137-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
We report the draft genome of an arsenotrophic Achromobacter aegrifaciens BAS32 isolated from arsenic (As)-contaminated soil in Bangladesh. This genome contains several predicted gene clusters for As-conversion, namely, As resistance (arsHCsO), arsenite-oxidizing (aioBA), and arsenate-reducing (arsRCDAB) gene clusters along with antibiotic resistance genes (ARGs).
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Anamica Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics Laboratory, Department of Gynaecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Momtaz Zamila Bukharid
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Research Fellow, One Health Laboratory, icddr,b, Dhaka, Bangladesh
| | - M. Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Jashore University of Science and Technology, Jashore, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| |
Collapse
|
3
|
Hou S, Chen Z, Luo X, Zhang M, Yang P. Hydrogel immobilized bacteria@MOFs composite towards Bisphenol A degradation and the interconnection mechanism elucidation. ENVIRONMENTAL RESEARCH 2024; 251:118718. [PMID: 38490623 DOI: 10.1016/j.envres.2024.118718] [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: 12/14/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
Bisphenol A (BPA) degradation efficiency by bacteria or by metal-organic-frameworks (MOFs) catalyzed persulfate (PMS) oxidation have been studied intensively. However, their synergistic effect on BPA degradation was less reported. In this study, we combined previously synthesized CNT-hemin/Mn-MOF with an BPA degrading bacteria SQ-2 to form a composite (SQ-2@MOFs). CNT-hemin/Mn-MOF in the composite catalyzed little PMS to promote the degradation efficiency of SQ-2 on BPA. Results indicated SQ-2@MOFs significantly accelerated BPA degradation rate than SQ-2 alone. Furthermore, SQ-2@MOFs composite was successfully immobilized in hydrogel to achieve better degradation performance. Immobilized SQ-2@MOFs could almost completely degrade 1-20 mg/L BPA within 24 h and completely degrade 5 mg/L BPA at pH 4-8. Besides, degradation byproducts also reduced by immobilized SQ-2@MOFs, which promoted the cleaner biodegradation of BPA. Metabolomics and multiple chemical characterization results revealed the interconnection mechanism between CNT-hemin/Mn-MOFs, SQ-2 and hydrogel. CNT-hemin/Mn-MOF helped SQ-2 degrade BPA into more biodegradable products, promoted electron transfer, and augmented BPA degradation ability of SQ-2 itself. SQ-2 enabled the surface electronegativity of SQ-2@MOFs more suitable for BPA contact. Meanwhile, SQ-2 avoided the loss of Fe and Mn of CNT-hemin/Mn-MOF. Hydrogel augmented the above synergistic effect. This study provided new perspective for the development of biodegradation materials through interdisciplinary integration.
Collapse
Affiliation(s)
- Siyu Hou
- Chengdu Medical College, Chengdu, 610500, China; College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | | | | | - Ming Zhang
- China Railway Water Group CO. LTD, Xi'an, 710000, China
| | - Ping Yang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China.
| |
Collapse
|
4
|
Pakar NP, Rehman FU, Mehmood S, Ali S, Zainab N, Munis MFH, Chaudhary HJ. Microbial detoxification of chlorpyrifos, profenofos, monocrotophos, and dimethoate by a multifaceted rhizospheric Bacillus cereus strain PM38 and its potential for the growth promotion in cotton. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:39714-39734. [PMID: 38831144 DOI: 10.1007/s11356-024-33804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
Bacillus genera, especially among rhizobacteria, are known for their ability to promote plant growth and their effectiveness in alleviating several stress conditions. This study aimed to utilize indigenous Bacillus cereus PM38 to degrade four organophosphate pesticides (OPs) such as chlorpyrifos (CP), profenofos (PF), monocrotophos (MCP), and dimethoate (DMT) to mitigate the adverse effects of these pesticides on cotton crop growth. Strain PM38 exhibited distinct characteristics that set it apart from other Bacillus species. These include the production of extracellular enzymes, hydrogen cyanide, exopolysaccharides, Indol-3-acetic acid (166.8 μg/mL), siderophores (47.3 μg/mL), 1-aminocyclopropane-1-carboxylate deaminase activity (32.4 μg/mL), and phosphorus solubilization (162.9 μg/mL), all observed at higher concentrations. This strain has also shown tolerance to salinity (1200 mM), drought (20% PEG-6000), and copper and cadmium (1200 mg/L). The amplification of multi-stress-responsive genes, such as acdS, ituC, czcD, nifH, sfp, and pqqE, further confirmed the plant growth regulation and abiotic stress tolerance capability in strain PM38. Following the high-performance liquid chromatography (HPLC) analysis, the results showed striking compatibility with the first kinetic model. Strain PM38 efficiently degraded CP (98.4%), PF (99.7%), MCP (100%), and DMT (95.5%) at a concentration of 300 ppm over 48 h at 35 °C under optimum pH conditions, showing high coefficients of determination (R2) of 0.974, 0.967, 0.992, and 0.972, respectively. The Fourier transform infrared spectroscopy (FTIR) analysis and the presence of opd, mpd, and opdA genes in the strain PM38 further supported the potential to degrade OPs. In addition, inoculating cotton seedlings with PM38 improved root length under stressful conditions. Inoculation of strain PM38 reduces stress by minimizing proline, thiobarbituric acid-reactive compounds, and electrolyte leakage. The strain PM38 has the potential to be a good multi-stress-tolerant option for a biological pest control agent capable of improving global food security and managing contaminated sites.
Collapse
Affiliation(s)
- Najeeba Parre Pakar
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Fazal Ur Rehman
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, Hobart, TAS, Australia
| | - Shehzad Mehmood
- Department of Biotechnology, COMSATS University Islamabad, Vehari Campus, Vehari, 61100, Pakistan
| | - Sarfaraz Ali
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Nida Zainab
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | | | | |
Collapse
|
5
|
Yang L, Liu Y, Li C, Li P, Zhang A, Liu Z, Wang Z, Wei C, Yang Z, Li Z. Optimizing carbon sources regulation in the biochemical treatment systems for coal chemical wastewater: Aromatic compounds biodegradation and microbial response strategies. WATER RESEARCH 2024; 256:121627. [PMID: 38642539 DOI: 10.1016/j.watres.2024.121627] [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: 01/23/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
The complex composition of coal chemical wastewater (CCW), marked by numerous highly toxic aromatic compounds, induces the destabilization of the biochemical treatment system, leading to suboptimal treatment efficacy. In this study, a biochemical treatment system was established to efficiently degrade aromatic compounds by quantitatively regulating the dosage of co-metabolized substrates (specifically, the chemical oxygen demand (COD) Glucose: COD Sodium acetate = 3:1, 1:3, and 1:1). The findings demonstrated that the system achieved optimal performance under the condition that the ratio of COD Glucose to COD Sodium acetate was 3:1. When the co-metabolized substrate was added to the system at an optimal ratio, examination of pollutant removal and cumulative effects revealed that the removal efficiencies for COD and total organic carbon (TOC) reached 94.61 % and 86.40 %, respectively. The removal rates of benzene series, nitrogen heterocyclic compounds, polycyclic aromatic hydrocarbons, and phenols were 100 %, 100 %, 63.58 %, and 94.12 %, respectively. Research on the physiological response of microbial cells showed that, under optimal ratio regulation, co-metabolic substrates led to a substantial rise in microbial extracellular polymeric substances (EPS) secretion, particularly extracellular proteins. When the system reached the end of its operation, the contents of loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) for proteins in the optimal group were 7.12 mg/g-SS and 152.28 mg/g-SS, respectively. Meanwhile, the ratio of α-Helix / (β-Sheet + Random coil) and the proportion of intermolecular interaction forces were also increased in the optimal group. At system completion, the ratio of α-Helix / (β-Sheet + Random coil) reached 0.717 (LB-EPS) and 0.618 (TB-EPS), respectively. Additionally, the proportion of intermolecular interaction forces reached 74.83 % (LB-EPS) and 55.03 % (TB-EPS). An in-depth analysis of the metabolic regulation of microorganisms indicated that the introduction of optimal ratios of co-metabolic substrates contributed to a noteworthy upregulation in the expression of Catechol 2,3-dioxygenase (C23O) and Dehydrogenase (DHA). The expression levels of C23O and DHA were measured at 0.029 U/mg Pro·g MLSS and 75.25 mg TF·(g MLSS·h)-1 (peak value), respectively. Correspondingly, enrichment of aromatic compound-degrading bacteria, including Thauera, Saccharimonadales, and Candidatus_Competibacter, occurred, along with the upregulation of associated functional genes such as Catechol 1,2-dioxygenase, Catechol 2,3-dioxygenase, Protocatechuate 3,4-dioxygenase, and Protocatechuate 4,5-dioxygenase. Considering the intricate system of multiple coexisting aromatic compounds in real CCW, this study not only obtained an optimal ratio for carbon source addition but also enhanced the efficient utilization of carbon sources and improved the capability of the system to effectively degrade aromatic compounds. Additionally, this paper established a theoretical foundation for metabolic regulation and harmless treatment within the biochemical treatment of intricate systems, exemplified by real CCW.
Collapse
Affiliation(s)
- Lu Yang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China
| | - Yongjun Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Chen Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China
| | - Pengfei Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China
| | - Aining Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhe Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhu Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China
| | - Chunxiao Wei
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China
| | - Zhuangzhuang Yang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China
| | - Zhihua Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| |
Collapse
|
6
|
Nzabanita D, Shen H, Grist S, Lewis PJ, Hampton JO, Firestone SM, Hufschmid J, Nugegoda D. Exposure to Persistent Organic Pollutants in Australian Waterbirds. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:736-747. [PMID: 38085117 DOI: 10.1002/etc.5804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 08/30/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
There is growing worldwide recognition of the threat posed by persistent organic pollutants (POPs) to wildlife populations. We aimed to measure exposure levels to POPs in a Southern Hemisphere aquatic waterbird species, the nomadic gray teal (Anas gracilis), which is found across Australia. We collected wings from 39 ducks harvested by recreational hunters at two sites (one coastal, one inland) in Victoria, southeastern Australia, in 2021. We examined three groups of POPs: nine congeners of polychlorinated biphenyls (PCBs), 13 organochlorine pesticides (OCPs), and 12 polycyclic aromatic hydrocarbons (PAHs). The PCBs, OCPs, and PAHs were detected at quantifiable levels in 13%, 72%, and 100% of birds, respectively. Of the congeners we tested for in PCBs, OCPs, and PAHs, 33%, 38%, and 100% were detected at quantifiable levels, respectively. The highest levels of exposure to POPs that we found were to the PAH benzo[b]fluoranthene, occurring at a concentration range of 1.78 to 161.05 ng/g wet weight. There were some trends detected relating to differences between geographical sites, with higher levels of several PAHs at the coastal versus inland site. There were several strong, positive associations among PAHs found. We discuss potential sources for the POPs detected, including industrial and agricultural sources, and the likely role of large-scale forest fires in PAH levels. Our results confirm that while Australian waterbirds are exposed to a variety of POPs, exposure levels are currently relatively low. Additional future investigations are required to further characterize POPs within Australian waterbird species. Environ Toxicol Chem 2024;43:736-747. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Collapse
Affiliation(s)
- Damien Nzabanita
- School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria, Australia
| | - Hao Shen
- School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria, Australia
| | - Stephen Grist
- School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria, Australia
| | - Phoebe J Lewis
- Applied Sciences Division, Environment Protection Authority Victoria, Macleod, Victoria, Australia
| | - Jordan O Hampton
- Faculty of Science, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Simon M Firestone
- Faculty of Science, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
| | - Jasmin Hufschmid
- Faculty of Science, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
| | - Dayanthi Nugegoda
- School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria, Australia
| |
Collapse
|
7
|
Ma J, Zhuang Y, Wang Y, Zhu N, Wang T, Xiao H, Chen J. Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:93345-93362. [PMID: 37548784 DOI: 10.1007/s11356-023-28894-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.
Collapse
Affiliation(s)
- Jinglin Ma
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Yan Zhuang
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ning Zhu
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Ting Wang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Hongbin Xiao
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730030, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China.
| |
Collapse
|
8
|
Jin J, Shi Y, Zhang B, Wan D, Zhang Q, Li Y. Biotransformation of benzo[ a]pyrene by Pannonibacter sp. JPA3 and the degradation mechanism through the initially oxidized benzo[ a]pyrene-4,5-dihydrodiol to downstream metabolites. RSC Adv 2023; 13:18878-18887. [PMID: 37350855 PMCID: PMC10282733 DOI: 10.1039/d3ra01453c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
Owing to its adverse effects on the environment and human health, benzo[a]pyrene (BaP) has attracted considerable attention and has been used as a model compound in ecotoxicology. In this study, Pannonibacter sp. JPA3 as a BaP-degrading strain was isolated from the production water of an oil well. The strain could remove 80% of BaP at an initial concentration of 100 mg L-1 after 35 d culture. The BaP-4,5-dihydrodiol, BaP-4,5-epoxide, 5-hydroxychrysene, and 2-hydroxy-1-naphthoic acid metabolites were identified in the biodegradation process. Simultaneously, the gene sequence coding for dioxygenase in the strain was amplified and a dioxygenase model was built by homology modeling. Combined with the identification of the metabolites, the interaction mechanism of BaP with dioxygenase was investigated using molecular docking. It was assumed that BaP was initially oxidized at the C4-C5 positions in the active cavity of dioxygenase. Moreover, a hypothesis for the progressive degradation mechanism of BaP by this strain was proposed via the identification of the downstream metabolites. In conclusion, our study provided an efficient BaP degrader and a comprehensive reference for the study of the degradation mechanism in terms of the degrading metabolites and theoretical research at the molecular level.
Collapse
Affiliation(s)
- Jingnan Jin
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| | - Yahui Shi
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| | - Baozhong Zhang
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| | - Dongjin Wan
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| | - Qingye Zhang
- College of Informatics, Huazhong Agricultural University Wuhan 430070 China
| | - Ying Li
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| |
Collapse
|
9
|
Paker NP, Mehmood S, Javed MT, Damalas CA, Rehman FU, Chaudhary HJ, Munir MZ, Malik M. Elucidating molecular characterization of chlorpyrifos and profenofos degrading distinct bacterial strains for enhancing seed germination potential of Gossypium arboreum L. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:48120-48137. [PMID: 36752920 DOI: 10.1007/s11356-023-25343-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Chlorpyrifos (CP) and profenofos (PF) are organophosphate pesticides (OPs) widely used in agriculture and are noxious to both fauna and flora. The presented work was designed to attenuate the toxicity of both pesticides in the growth parameters of a cotton crop by applying plant growth-promoting rhizobacteria (PGPR), namely Pseudomonas aeruginosa PM36 and Bacillus sp. PM37. The multifarious biological activities of both strains include plant growth-promoting traits, including phosphate solubilization; indole-3-acetic acid (IAA), siderophore, and HCN production; nitrogen fixation; and enzymatic activity such as cellulase, protease, amylase, and catalase. Furthermore, the molecular profiling of multi-stress-responsive genes, including acdS, ituC, czcD, nifH, and sfp, also confirmed the plant growth regulation and abiotic stress tolerance potential of PM36 and PM37. Both strains (PM36 and PM37) revealed 92% and 89% of CP degradation at 50 ppm and 87% and 81% at 150 ppm within 7 days. Simultaneously 94% and 98% PF degradation was observed at 50 ppm and 90% and 92% at 150 ppm within 7 days at 35 °C and pH 7. Biodegradation was analyzed using HPLC and FTIR. The strains exhibited first-order reaction kinetics, indicating their reliance on CP and PF as energy and carbon sources. The presence of opd, mpd, and opdA genes in both strains also supported the CP and PF degradation potential of both strains. Inoculation of strains under normal and OP stress conditions resulted in a significant increase in seed germination, plant biomass, and chlorophyll contents of the cotton seedling. Our findings indicate that the strains PM36 and PM37 have abilities as biodegraders and plant growth promoters, with potential applications in crop sciences and bioremediation studies. These strains could serve as an environmentally friendly, sustainable, and socially acceptable solution to manage OP-contaminated sites.
Collapse
Affiliation(s)
- Najeeba Paree Paker
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Shehzad Mehmood
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, Vehari, 61100, Pakistan
| | | | - Christos A Damalas
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Fazal Ur Rehman
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| | - Muhammad Zeshan Munir
- Schools of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Rd, Shenzhen, 518055, China
| | - Mahrukh Malik
- Drug Control and Traditional Medicines Division, National Institute of Health, Islamabad, Pakistan
| |
Collapse
|
10
|
Liu X, Liu Y, Li S, Zhang A, Liu Z, Li Z. Metabolic fates and response strategies of microorganisms to aromatic compounds with different structures. BIORESOURCE TECHNOLOGY 2022; 366:128210. [PMID: 36323372 DOI: 10.1016/j.biortech.2022.128210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
In this study, the metabolic fates and response strategies of microorganisms to aromatic compounds with different structures (phenol, naphthalene, phenanthrene, and pyrene) were comparatively studied. The results indicated that the phenol (90.9%), naphthalene (68.4%), phenanthrene (69.5%), and pyrene (67.1%) could be mineralized, and the biotoxicity also has been drastically reduced. The degradation characteristics and toxic effects were closely related to their chemical structure. The microorganisms showed different response strategies to aromatic compounds with different structures. Phenol had a simple structure and low toxicity, the microbial community structure was simple, and the rapid expression of key enzymes enabled it to be rapidly degraded. For the hydrophobic and complex naphthalene, phenanthrene, and pyrene, the more complex the structure, the higher the microbial diversity, the EPS showed different response for the purpose of improving their bioavailability, and the activity of key enzymes was positively correlated with their structural complexity.
Collapse
Affiliation(s)
- Xingshe Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China
| | - Yongjun Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Shuang Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China
| | - Aining Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhe Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Zhihua Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Yan Ta Road. No.13, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| |
Collapse
|
11
|
BPA biodegradation driven by isolated strain SQ-2 and its metabolism mechanism elucidation. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Luo C, Hu X, Bao M, Sun X, Li F, Li Y, Liu W, Yang Y. Efficient biodegradation of phenanthrene using Pseudomonas stutzeri LSH-PAH1 with the addition of sophorolipids: Alleviation of biotoxicity and cometabolism studies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 301:119011. [PMID: 35182655 DOI: 10.1016/j.envpol.2022.119011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Phenanthrene (PHE) is widely distributed, and it can cause genotoxicity in humans by interacting with enzymes in the body. A current challenge for PHE bioremediation is the inhibitory effect of biotoxic intermediates on bacterial growth. Notably, the aerobic biotransformation processes for PHE in the presence of sophorolipids have been poorly studied. Here, a PHE-degrading strain was isolated from sediments and identified as Pseudomonas stutzeri and named LSH-PAH1. It was observed that 1-naphthol (a biotoxic substance that can inhibit strain growth) was produced during the PHE metabolism process of LSH-PAH1. The biodegradation ratio increased from 21.4% to 91.7% within 48 h after the addition of sophorolipids. Unexpectedly, this addition accelerated the metabolic process for 1-naphthol rather than causing its accumulation. The cometabolism of 1-naphthol and sophorolipids alleviated the biotoxic effects for the strain, which was verified by gene expression analysis. We identified a new PHE-degrading strain and provided a mechanism for PHE biodegradation using LSH-PAH1 with the addition of sophorolipids, which provides a reference for practical applications of the bioremediation of PHE and study of the cometabolism of biotoxic intermediates.
Collapse
Affiliation(s)
- Chengyi Luo
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Xin Hu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Mutai Bao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China.
| | - Xiaojun Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Fengshu Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Yiming Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, And Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, 266100, PR China
| | - Wenxiu Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, PR China
| | - Yan Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, PR China
| |
Collapse
|
13
|
Changmei L, Gengrui W, Haizhen W, Yuxiao W, Shuang Z, Chaohai W. Kinetics and molecular mechanism of enhanced fluoranthene biodegradation by co-substrate phenol in co-culture of Stenotrophomonas sp. N5 and Advenella sp. B9. ENVIRONMENTAL RESEARCH 2022; 205:112413. [PMID: 34861230 DOI: 10.1016/j.envres.2021.112413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and phenol are persistent pollutants that coexist in coking wastewater (CWW). Fluoranthene (Flu) is the predominant PAH species in the CWW treatment system. Our work emphasized on distinguishing the effects of phenol on Flu biodegradation by co-culture of Stenotrophomonas sp. N5 and Advenella sp. B9 and illustrated the molecular mechanisms. Results showed Flu biodegradation by co-culture was enhanced by phenol. According to the first-order degradation kinetic analysis of Flu, phenol significantly increased the biodegradation rate constant and shortened the half-life of Flu. Transcriptome analysis pointed out the up-regulation of DNA repair activity and 3717 significantly differentially expressed genes (DEGs), were triggered by 800 mg/L phenol. GO enrichment analysis suggested these DEGs are mainly concentrated in biochemical processes such as metal ion binding and alpha-amino acid biosynthesis, which are closely associated with Flu biodegradation, indicating that phenol promotes DNA repair activity and reduces Flu genotoxicity. qRT-PCR was performed to detect the gene expression of aromatic ring-opening dioxygenase. Combined with transcriptome analysis, the qRT-PCR results suggested phenol did not induce the expression of related PAHs-degrading enzymes. RNA extraction and microbial growth curves of COC and COC + Ph provided further evidence that phenol serves as co-substrate which increases biomass and the concentration of degrading enzymes, therefore promoting the Flu degradation.
Collapse
Affiliation(s)
- Li Changmei
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Wei Gengrui
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Wu Haizhen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
| | - Wang Yuxiao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Zhu Shuang
- Cener for Bioresources & Drug Discovery and School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Wei Chaohai
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| |
Collapse
|
14
|
Liu J, Zhang AN, Liu YJ, Liu Z, Liu Y, Wu XJ. Analysis of the mechanism for enhanced pyrene biodegradation based on the interactions between iron-ions and Rhodococcus ruber strain L9. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112789. [PMID: 34560613 DOI: 10.1016/j.ecoenv.2021.112789] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
A slow degradation rate and low transformation efficiency are the main problems in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). This study selected pyrene as the target PAH to investigate the effect of ferrous ion and ferric ion on pyrene degradation. The driving effect and mechanism, including the interaction between pyrene and iron ions and the bacterial physiological response during the biodegradation process by Rhodococcus ruber strain L9, were investigated. The results showed that iron ions did not enhance bacterial growth but improved bacteria's pyrene removal capacity, contributing to the total efficiency of pyrene biodegradation. The process started with an initial formation of "cation-π" between Fe (III) and pyrene, which subsequently drove the pyrene removal process and accelerated the bacterial metabolic process. Moreover, a significant increase in the protein concentration, catechol dioxygenase (C12O and C23O) activities, and intracellular protein regulation in crude enzyme solution indicate a positive response of the bacteria during the iron ion-enhanced pyrene degradation process.
Collapse
Affiliation(s)
- Jing Liu
- School of Civil Engineering, Yulin University, Yulin 719000, China; Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Ai-Ning Zhang
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Yong-Jun Liu
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China.
| | - Zhe Liu
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Yu Liu
- School of Petroleum and Environment Engineering, Yanan University, Yanan 716000, China
| | - Xi-Jun Wu
- School of Civil Engineering, Yulin University, Yulin 719000, China
| |
Collapse
|
15
|
Espinosa-Ortiz EJ, Rene ER, Gerlach R. Potential use of fungal-bacterial co-cultures for the removal of organic pollutants. Crit Rev Biotechnol 2021; 42:361-383. [PMID: 34325585 DOI: 10.1080/07388551.2021.1940831] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.
Collapse
Affiliation(s)
- Erika J Espinosa-Ortiz
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Eldon R Rene
- Department of Water Supply, Sanitary and Environmental Engineering, IHE Delft Institute for Water Education, 2601DA Delft, The Netherlands
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| |
Collapse
|
16
|
Laothamteep N, Kawano H, Vejarano F, Suzuki-Minakuchi C, Shintani M, Nojiri H, Pinyakong O. Effects of environmental factors and coexisting substrates on PAH degradation and transcriptomic responses of the defined bacterial consortium OPK. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116769. [PMID: 33676341 DOI: 10.1016/j.envpol.2021.116769] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 05/12/2023]
Abstract
The present study showed that syntrophic associations in a defined bacterial consortium, named OPK, containing Mycolicibacterium strains PO1 and PO2, Novosphingobium pentaromativorans PY1 and Bacillus subtilis FW1, led to effective pyrene degradation over a wide range of pH values, temperatures and salinities, as well as in the presence of a second polycyclic aromatic hydrocarbon (PAH). Anthracene, phenanthrene or fluorene facilitated complete pyrene degradation within 9 days, while fluoranthene delayed pyrene degradation. Interestingly, fluoranthene degradation was enhanced in the presence of pyrene. Transcriptome analysis confirmed that Mycolicibacterium strains were the key PAH-degraders during the cometabolism of pyrene and fluoranthene. Notably, the transcription of genes encoding pyrene-degrading enzymes were shown to be important for enhanced fluoranthene degradation. NidAB was the major initial oxygenase involved in the degradation of pyrene and fluoranthene mixture. Other functional genes encoding ribosomal proteins, an iron transporter, ABC transporters and stress response proteins were induced in strains PO1 and PO2. Furthermore, an intermediate pyrene-degrading Novosphingobium strain contributed to protocatechuate degradation. The results demonstrated that synergistic interactions among the bacterial members (PO1, PO2 and PY1) of the consortium OPK promoted the simultaneous degradation of two high molecular weight (HMW) PAHs.
Collapse
Affiliation(s)
- Natthariga Laothamteep
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Microbial Technology for Marine Pollution Treatment Research Unit, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hibiki Kawano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Felipe Vejarano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka, 432-8561, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Onruthai Pinyakong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Microbial Technology for Marine Pollution Treatment Research Unit, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand.
| |
Collapse
|
17
|
Shi Y, Ye Z, Hu P, Wei D, Gao Q, Zhao Z, Xiao J, Liao M, Cao H. Removal of prothioconazole using screened microorganisms and identification of biodegradation products via UPLC-QqTOF-MS. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 206:111203. [PMID: 32866888 DOI: 10.1016/j.ecoenv.2020.111203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Degradation of the prothioconazole by three strains of microorganisms isolated from activated sludge obtained from a pesticide factory was assessed, and an ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QqTOF-MS) method for the determination of prothioconazole and its metabolites was established. The optimal conditions for the degradation of prothioconazole were determined by single factor optimization experiments. A degradation rate of 93.32% is achieved when the prothioconazole is co-cultured with the strain W313 at a cultivation time of 60 h, a cultivation temperature of 30 °C, a pH of 6.33, a prothioconazole concentration of 50 mg L-1, a microorganism volume of 10%, and a dextrose volume of 4%. The three effective microorganism strains were identified by morphological and molecular biology to be Candida tropicalis, Enterobacter cloacae, and Pseudomonas aeruginosa. UPLC-QqTOF-MS analysis allowed the identification of 62 different prothioconazole degradation products produced by the strain cultures, with prothioconazole-desthio, prothioconazole-dechloropropyl, and oxidizing prothioconazole being the main products. In addition, degradation products from different strains and conditions were compared. The results of scatter plot (S-Plot) analysis indicated that C9H7NO, C10H17N7, and C12H13ClN2O were only detected in the products incubated with Enterobacter cloacae. Thus, this study demonstrates that Enterobacter cloacae and Pseudomonas aeruginosa possesses high potential for bioremediation of prothioconazole-contaminated environments.
Collapse
Affiliation(s)
- Yanhong Shi
- School of Resource and Environment, Anhui Agricultural University, Hefei, 230036, PR China; Provincial Key Laboratory for Agri-Food Safety, Hefei, 230036, Hefei, 230036, PR China
| | - Zhuang Ye
- School of Resource and Environment, Anhui Agricultural University, Hefei, 230036, PR China
| | - Peng Hu
- School of Resource and Environment, Anhui Agricultural University, Hefei, 230036, PR China
| | - Dong Wei
- School of Resource and Environment, Anhui Agricultural University, Hefei, 230036, PR China
| | - Quan Gao
- School of Plant Protection, Anhui Agricultural University, Hefei, 230036, PR China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Anhui Agricultural University, Hefei, 230036, PR China
| | - Zhenyu Zhao
- School of Plant Protection, Anhui Agricultural University, Hefei, 230036, PR China
| | - Jinjing Xiao
- School of Plant Protection, Anhui Agricultural University, Hefei, 230036, PR China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Anhui Agricultural University, Hefei, 230036, PR China
| | - Min Liao
- School of Plant Protection, Anhui Agricultural University, Hefei, 230036, PR China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Anhui Agricultural University, Hefei, 230036, PR China
| | - Haiqun Cao
- School of Plant Protection, Anhui Agricultural University, Hefei, 230036, PR China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Anhui Agricultural University, Hefei, 230036, PR China.
| |
Collapse
|
18
|
Meng Q, Han Y, Zhu H, Yang W, Bello A, Deng L, Jiang X, Wu X, Sheng S, Xu Y, Xu X. Differences in distribution of functional microorganism at DNA and cDNA levels in cow manure composting. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 191:110161. [PMID: 31954219 DOI: 10.1016/j.ecoenv.2019.110161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Denitrification and nitrification processes are the two prominent pathways of nitrogen (N) transformation in composting matrix. This study explored the dynamics of denitrifying and nitrifying bacteria at different composting stages of cow manure and corn straw using functional gene sequencing at DNA and cDNA levels. Corresponding agreement among OTUs, NMDS, mental test and network analyses revealed that functional bacteria community compositions and responses to physicochemical factors were different at DNA and cDNA levels. Specifically, some OTUs were detected at the DNA level but were not observed at cDNA level, differences were also found in the distribution patterns of nitrifying and denitrifying bacteria communities at both levels. Furthermore, co-occurrence network analysis indicated that Pseudomonas, Paracoccus and Nitrosomonas were identified as the keystone OTUs at the DNA level, while Paracoccus, Agrobacterium and Nitrosospira were keystone OTUs at the cDNA level. Mantel test revealed that TN, C/N and moisture content significantly influenced both the denitrifying bacteria and ammonia-oxidizing bacteria (AOB) communities at the DNA level. NO3--N, NH4+-N, TN, C/N, and moisture content only registered significant correlation with the nosZ-type denitrifiers and ammonia-oxidizing bacteria (AOB) communities at the cDNA level. Structural equation model (SEM) showed that TN, NH4+-N, and pH were direct and significantly influenced the gene abundance of denitrifying bacteria. Howbeit, TN, NH4+-N, and NO3--N had significant direct effects on amoA gene abundance.
Collapse
Affiliation(s)
- Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Han
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Haifeng Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaotong Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Siyuan Sheng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yingying Xu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161006, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
19
|
Sun L, Han X, Li J, Zhao Z, Liu Y, Xi Q, Guo X, Gun S. Microbial Community and Its Association With Physicochemical Factors During Compost Bedding for Dairy Cows. Front Microbiol 2020; 11:254. [PMID: 32153538 PMCID: PMC7047772 DOI: 10.3389/fmicb.2020.00254] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 02/03/2020] [Indexed: 11/27/2022] Open
Abstract
Overproduction of livestock manure can cause significant environmental challenges. Compost bedding (CB) is considered an effective approach for recycling the agricultural byproducts and improving the welfare of dairy cattle. During the CB preparing, the composition of microbial communities is usually altered; however, the patterns and drivers of CB microbial communities remains to be investigated. The current study aimed to explore the dynamics of bacterial and fungal communities during the various padded stages, using high throughput sequencing technology and qPCR. The relationships across physicochemical parameters, microbial community composition, and abundance were also evaluated. Sequencing results revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes of bacteria, and Ascomycota of fungi as the major phyla found in CB. qPCR results showed a significant increase in the number of bacterial genome copies from 1.20 × 107 to 3.35 × 107 copies/gram of dry soil, while the number of fungal genome copies significantly increased from 8.43 × 104 to 7.02 × 106 copies/gram of dry soil. Linear discriminant analysis effect size (LEfSe) showed that Actinobacteria was the primary indicator in raw materials while the phylum Bacteroidetes was in the other padded stages. Dothideomycetes was significantly enriched in the initial stage of fungi, whereas Sordariomycetes, including a pathogen Scedosporium prolificans, was the major indicator in CB after 9 days of padding. Mantel test showed that pH significantly influenced bacterial community composition while temperature and total organic carbon (TOC) had a significant effect on fungal community structure. Redundancy analysis indicated that TOC, temperature, and water content had a significant effect on bacterial abundance while total nitrogen, water content, and pH significantly affected fungal abundance. Our finding contributed to the understanding of microbial community succession in CB across different padded stages, and suggests CB management by changing the bedding material every 7 days.
Collapse
Affiliation(s)
- Likun Sun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,Gansu Provincial Engineering Research Center for Animal Waste Utilization, Gansu Agricultural University, Lanzhou, China
| | - Xiangmin Han
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Jianshu Li
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Zhidong Zhao
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Yuzhen Liu
- Grassland Science College of Gansu Agricultural University, Lanzhou, China
| | - Qiming Xi
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Xinyu Guo
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Shuangbao Gun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
20
|
Paria K, Chakraborty SK. Eco-potential of Aspergillus penicillioides (F12): bioremediation and antibacterial activity. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-1545-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
21
|
Anyasi RO, Atagana HI, Sutherland R. Identification and characterization of PAH-degrading endophytes isolated from plants growing around a sludge dam. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 21:672-682. [PMID: 30942084 DOI: 10.1080/15226514.2018.1556585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This study involved the isolation of bacteria endophytes with PAH-degrading ability from plants growing around a sludge dam. A total of 19 distinct isolates that were morphologically identified were isolated from 4 species of plant with a follow-up confirmatory identification using the molecular technique. Polymerase chain reaction (PCR) of the 16S rRNA gene with specific primers (16S-27F PCR and 16S-1491R PCR) was carried out. The sequence of the PCR products was carried out, compared with similar nucleotides available in GenBank. Results of the phylogenetic analysis of the isolates indicated their belonging to 4 different clades including Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes. These were related to the genera Bacillus, Pseudomonas, Terribacillus, Virgibacillus, Stenotrophomonas, Paenibacillus, Brevibacterium, Geobacillus, Acinetobacter. From the result, Pseudomonas demonstrated a high incidence in the plants sampled. The in-vitro degradation study and the presence of dioxygenase genes indicated that these lists of endophytes are able to use the list of PAHs tested as their source of food and energy leading to their breakdown. This means that the bacterial endophytes contributed to the remediation of petroleum hydrocarbons in planta, a situation that may have been phytotoxic to plant alone. Therefore, these bacteria endophytes could be potential organisms for enhanced phytoremediation of PAHs.
Collapse
Affiliation(s)
- Raymond O Anyasi
- a Department of Environmental Sciences, Institute for Science and Technology Education , University of South Africa , Pretoria , South Africa
| | - Harrison I Atagana
- a Department of Environmental Sciences, Institute for Science and Technology Education , University of South Africa , Pretoria , South Africa
| | - Rene Sutherland
- b Plant Protection Unit , Agricultural Research Council , Pretoria , South Africa
| |
Collapse
|
22
|
Meng Q, Yang W, Men M, Bello A, Xu X, Xu B, Deng L, Jiang X, Sheng S, Wu X, Han Y, Zhu H. Microbial Community Succession and Response to Environmental Variables During Cow Manure and Corn Straw Composting. Front Microbiol 2019; 10:529. [PMID: 30936861 PMCID: PMC6431636 DOI: 10.3389/fmicb.2019.00529] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/01/2019] [Indexed: 11/13/2022] Open
Abstract
In composting system, the composition of microbial communities is determined by the constant change in the physicochemical parameters. This study explored the dynamics of bacterial and fungal communities during cow manure and corn straw composting using high throughput sequencing technology. The relationships between physicochemical parameters and microbial community composition and abundance were also evaluated. The sequencing results revealed the major phyla included Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Actinobacteria, Ascomycota, and Basidiomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Actinomycetales and Sordariomycetes were the indicators of bacteria and fungi in the maturation phase, respectively. Mantel test showed that NO3 --N, NH4 +-N, TN, C/N, temperature and moisture content significantly influenced bacterial community composition while only TN and moisture content had a significant effect on fungal community structure. Structural equation model (SEM) indicated that TN, NH4 +-N, NO3 --N and pH had a significant effect on fungal abundance while TN and temperature significantly affected bacterial abundance. Our finding increases the understanding of microbial community succession in cow manure and corn straw composting under natural conditions.
Collapse
Affiliation(s)
| | | | | | | | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Fluoranthene Biodegradation by Serratia sp. AC-11 Immobilized into Chitosan Beads. Appl Biochem Biotechnol 2019; 188:1168-1184. [DOI: 10.1007/s12010-019-02980-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 02/20/2019] [Indexed: 01/14/2023]
|
24
|
Zhao HM, Hu RW, Du H, Xin XP, Li YW, Li H, Cai QY, Mo CH, Liu JS, Zhou DM, Wong MH, He ZL. Functional genomic analysis of phthalate acid ester (PAE) catabolism genes in the versatile PAE-mineralising bacterium Rhodococcus sp. 2G. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:646-652. [PMID: 29870940 DOI: 10.1016/j.scitotenv.2018.05.337] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/26/2018] [Accepted: 05/27/2018] [Indexed: 06/08/2023]
Abstract
Microbial degradation is considered the most promising method for removing phthalate acid esters (PAEs) from polluted environments; however, a comprehensive genomic understanding of the entire PAE catabolic process is still lacking. In this study, the repertoire of PAE catabolism genes in the metabolically versatile bacterium Rhodococcus sp. 2G was examined using genomic, metabolic, and bioinformatic analyses. A total of 4930 coding genes were identified from the 5.6 Mb genome of the 2G strain, including 337 esterase/hydrolase genes and 48 transferase and decarboxylase genes that were involved in hydrolysing PAEs into phthalate acid (PA) and decarboxylating PA into benzoic acid (BA). One gene cluster (xyl) responsible for transforming BA into catechol and two catechol-catabolism gene clusters controlling the ortho (cat) and meta (xyl &mhp) cleavage pathways were also identified. The proposed PAE catabolism pathway and some key degradation genes were validated by intermediate-utilising tests and real-time quantitative polymerase chain reaction. Our results provide novel insight into the mechanisms of PAE biodegradation at the molecular level and useful information on gene resources for future studies.
Collapse
Affiliation(s)
- Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL 34945, USA
| | - Rui-Wen Hu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huan Du
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiao-Ping Xin
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL 34945, USA
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Jie-Sheng Liu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Dong-Mei Zhou
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ming-Hung Wong
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhen-Li He
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL 34945, USA
| |
Collapse
|
25
|
Gola D, Malik A, Namburath M, Ahammad SZ. Removal of industrial dyes and heavy metals by Beauveria bassiana: FTIR, SEM, TEM and AFM investigations with Pb(II). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:20486-20496. [PMID: 28965177 DOI: 10.1007/s11356-017-0246-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
Presence of industrial dyes and heavy metal as a contaminant in environment poses a great risk to human health. In order to develop a potential technology for remediation of dyes (Reactive remazol red, Yellow 3RS, Indanthrene blue and Vat novatic grey) and heavy metal [Cu(II), Ni(II), Cd(II), Zn(II), Cr(VI) and Pb(II)] contamination, present study was performed with entomopathogenic fungi, Beauveria bassiana (MTCC no. 4580). High dye removal (88-97%) was observed during the growth of B. bassiana while removal percentage for heavy metals ranged from 58 to 75%. Further, detailed investigations were performed with Pb(II) in terms of growth kinetics, effect of process parameters and mechanism of removal. Growth rate decreased from 0.118 h-1 (control) to 0.031 h-1, showing 28% reduction in biomass at 30 mg L-1 Pb(II) with 58.4% metal removal. Maximum Pb(II) removal was observed at 30 °C, neutral pH and 30 mg L-1 initial metal concentration. FTIR analysis indicated the changes induced by Pb(II) in functional groups on biomass surface. Further, microscopic analysis (SEM and atomic force microscopy (AFM)) was performed to understand the changes in cell surface morphology of the fungal cell. SEM micrograph showed a clear deformation of fungal hyphae, whereas AFM studies proved the increase in surface roughness (RSM) in comparison to control cell. Homogenous bioaccumulation of Pb(II) inside the fungal cell was clearly depicted by TEM-high-angle annular dark field coupled with EDX. Present study provides an insight into the mechanism of Pb(II) bioremediation and strengthens the significance of using entomopathogenic fungus such as B. bassiana for metal and dye removal.
Collapse
Affiliation(s)
- Deepak Gola
- Applied Microbiology Laboratory, Centre for Rural Development and Technology, New Delhi, India
| | - Anushree Malik
- Applied Microbiology Laboratory, Centre for Rural Development and Technology, New Delhi, India.
| | - Maneesh Namburath
- Applied Microbiology Laboratory, Centre for Rural Development and Technology, New Delhi, India
| | - Shaikh Ziauddin Ahammad
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Hauz Khas, Delhi, India
| |
Collapse
|
26
|
Al-Hawash AB, Zhang X, Ma F. Removal and biodegradation of different petroleum hydrocarbons using the filamentous fungus Aspergillus sp. RFC-1. Microbiologyopen 2018; 8:e00619. [PMID: 29577679 PMCID: PMC6341139 DOI: 10.1002/mbo3.619] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 11/22/2022] Open
Abstract
Petroleum pollution inevitably occurs at any stage of oil production and exerts a negative impact on the environment. Some microorganisms can degrade petroleum hydrocarbons (PHs). Polluted sludge of Rumaila oil field was use to isolate the highly efficient hydrocarbon‐degrading fungal strain. Aspergillus sp. RFC‐1 was obtained and its degradation ability for petroleum hydrocarbons was evaluated through surface adsorption, cell uptake, hydrophobicity, surface tension, biosurfactant production, and emulsification activity. In addition, the degradation mechanism was investigated. The results indicated the strain RFC‐1 showed high removal activity for PHs, including biodegradation, adsorption, and emulsifiability. On the day 7 of incubation, the removal efficiencies of crude oil, naphthalene (NAP), phenanthrene (PHE), and pyrene (PYR) reached 60.3%, 97.4%, 84.9%, and 90.7%, respectively. Biodegradation efficiencies of crude oil, NAP, PHE, and PYR were 51.8%, 84.6%, 50.3%, and 55.1%, respectively. Surface adsorption and cell absorption by live mycelial pellets followed a decreasing order: PYR ≥ PHE > NAP > crude oil. Adsorption by heat‐killed mycelial pellets increased within 40 and 10 min for crude oil and PAHs, respectively, and remained constant thereafter. Effects of cell surface hydrophobicity, surface tension, and emulsification index were discussed. Intra‐ and extracellular enzymes of strain RFC‐1 played important roles in PHs degradation. The strain RFC‐1 is a prospective strain for removing PHs from aqueous environments.
Collapse
Affiliation(s)
- Adnan B Al-Hawash
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Ministry of Education, Directorate of Education, Basra, Iraq
| | - Xiaoyu Zhang
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Fuying Ma
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
27
|
Jauhari N, Mishra S, Kumari B, Singh SN, Chauhan PS, Upreti DK. Bacteria Induced Degradation of Anthracene Mediated by Catabolic Enzymes. Polycycl Aromat Compd 2018. [DOI: 10.1080/10406638.2017.1420667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nitanshi Jauhari
- Plant Ecology and Environmental Science Division, Plant microbe interaction, Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - Shweta Mishra
- Plant Ecology and Environmental Science Division, Plant microbe interaction, Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - Babita Kumari
- Plant Ecology and Environmental Science Division, Plant microbe interaction, Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - S. N. Singh
- Plant Ecology and Environmental Science Division, Plant microbe interaction, Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - Puneet S. Chauhan
- Plant microbe interaction, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| | - D. K. Upreti
- Herbarium division, CSIR‐National Botanical Research Institute, Lucknow, U.P., India
| |
Collapse
|
28
|
Complete genome sequence of a versatile hydrocarbon degrader, Pseudomonas aeruginosa DN1 isolated from petroleum-contaminated soil. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
29
|
Singh P, Tiwary BN. Optimization of conditions for polycyclic aromatic hydrocarbons (PAHs) degradation by Pseudomonas stutzeri P2 isolated from Chirimiri coal mines. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.02.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
30
|
Jin J, Yao J, Zhang Q, Liu J. Biodegradation of pyrene by pseudomonas sp. JPN2 and its initial degrading mechanism study by combining the catabolic nahAc gene and structure-based analyses. CHEMOSPHERE 2016; 164:379-386. [PMID: 27596825 DOI: 10.1016/j.chemosphere.2016.08.113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 05/02/2023]
Abstract
In this study, a pyrene-degrading bacterial strain Pseudomonas sp. JPN2 was isolated from crude oil in Dagang Oilfield, China. The degrading percent of the strain JPN2 to pyrene was increased with the extension of culture time and achieved a maximum of 82.88% after 25 d culture. Meanwhile, four metabolites 4,5-dihydroxy-4,5-dihydropyrene, 4-phenanthrol, 1-hydroxy-2-naphthoic acid and phthalate were detected in the culture solution by GC-MS analysis. In addition, DNA fragments of nahAc gene, encoding α subunit of naphthalene dioxygenase, were amplified by PCR program and sequenced. As a result, it was presumed that the initial cleavage of the aromatic rings on pyrene was occurred at C4 and C5 positions and formed the intermediate 4,5-dihydroxy-4,5-dihydropyrene. This issue had been verified by the interaction analysis between pyrene and the active site of naphthalene dioxygenase in the strain JPN2 by molecular docking. Meanwhile, the differences of the amino acid residues in the active sites of template and target enzymes may be a factor leading to the different biological activity between the strain JPN2 and the other bacteria from the genus Pseudomonas. Additionally, the microcalorimetry analysis displayed that the strain JPN2 had high tolerance for pyrene, and the effect could be negligible under the experimental concentration (100 mg L-1). Consequently, the strain JPN2 was considered as an excellent candidate for the further bioremediation study of pyrene and the other aromatic contaminants.
Collapse
Affiliation(s)
- Jingnan Jin
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jun Yao
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; State Key Laboratory of Biogeology and Environmental Geology of Chinese Ministry of Education, and Sino-Hungarian Joint Laboratory of Environmental Science and Health, China University of Geoscience, Wuhan 430074, China.
| | - Qingye Zhang
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianli Liu
- School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| |
Collapse
|
31
|
Obi LU, Atagana HI, Adeleke RA. Isolation and characterisation of crude oil sludge degrading bacteria. SPRINGERPLUS 2016; 5:1946. [PMID: 27933233 PMCID: PMC5102992 DOI: 10.1186/s40064-016-3617-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022]
Abstract
Background The use of microorganisms in remediating environmental contaminants such as crude oil sludge has become a promising technique owing to its economy and the fact it is environmentally friendly. Polycyclic aromatic hydrocarbons (PAHs), as the major components of oil sludge, are hydrophobic and recalcitrant. An important way of enhancing the rate of PAH desorption is to compost crude oil sludge by incorporating commercial surfactants, thereby making them available for microbial degradation. In this study, crude oil sludge was composted for 16 weeks during which surfactants were added in the form of a solution. Results Molecular characterisation of the 16S rRNA genes indicated that the isolates obtained on a mineral salts medium belonged to different genera, including Stenotrophmonas, Pseudomonas, Bordetella, Brucella, Bacillus, Achromobacter, Ochrobactrum, Advenella, Mycobacterium, Mesorhizobium, Klebsiella, Pusillimonas and Raoultella. The percentage degradation rates of these isolates were estimated by measuring the absorbance of the 2,6-dichlorophenol indophenol medium. Pseudomonas emerged as the top degrader with an estimated percentage degradation rate of 73.7% after 7 days of incubation at 28 °C. In addition, the presence of the catabolic gene, catechol-2,3-dioxygenase was detected in the bacteria isolates as well as in evolutionary classifications based on phylogeny. Conclusions The bacteria isolated in this study are potential agents for the bioremediation of crude oil sludge.
Collapse
Affiliation(s)
- Linda U Obi
- Department of Environmental Sciences, University of South Africa, Johannesburg, South Africa ; Microbiology and Environmental Biotechnology Research Group, Agricultural Research Council - Institute for Soil, Climate and Water, Pretoria, South Africa
| | - Harrison I Atagana
- Institute for Science and Technology Education, University of South Africa, Pretoria, South Africa
| | - Rasheed A Adeleke
- Department of Environmental Sciences, University of South Africa, Johannesburg, South Africa ; Microbiology and Environmental Biotechnology Research Group, Agricultural Research Council - Institute for Soil, Climate and Water, Pretoria, South Africa ; Unit for Environment Science and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| |
Collapse
|
32
|
Gola D, Dey P, Bhattacharya A, Mishra A, Malik A, Namburath M, Ahammad SZ. Multiple heavy metal removal using an entomopathogenic fungi Beauveria bassiana. BIORESOURCE TECHNOLOGY 2016; 218:388-396. [PMID: 27387415 DOI: 10.1016/j.biortech.2016.06.096] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
Towards the development of a potential remediation technology for multiple heavy metals [Zn(II), Cu(II), Cd(II), Cr(VI) and Ni(II)] from contaminated water, present study examined the growth kinetics and heavy metal removal ability of Beauveria bassiana in individual and multi metals. The specific growth rate of B. bassiana varied from 0.025h(-1) to 0.039h(-1) in presence of individual/multi heavy metals. FTIR analysis indicated the involvement of different surface functional groups in biosorption of different metals, while cellular changes in fungus was reflected by various microscopic (SEM, AFM and TEM) analysis. TEM studies proved removal of heavy metals via sorption and accumulation processes, whereas AFM studies revealed increase in cell surface roughness in fungal cells exposed to heavy metals. Present study delivers first report on the mechanism of bioremediation of heavy metals when present individually as well as multi metal mixture by entomopathogenic fungi.
Collapse
Affiliation(s)
- Deepak Gola
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Hauz Khas, Delhi, India
| | - Priyadarshini Dey
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Hauz Khas, Delhi, India
| | - Arghya Bhattacharya
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Hauz Khas, Delhi, India
| | - Abhishek Mishra
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Hauz Khas, Delhi, India
| | - Anushree Malik
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Hauz Khas, Delhi, India.
| | - Maneesh Namburath
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology, Hauz Khas, Delhi, India
| | - Shaikh Ziauddin Ahammad
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Hauz Khas, Delhi, India
| |
Collapse
|
33
|
Singh P, Tiwary BN. Isolation and characterization of glycolipid biosurfactant produced by a Pseudomonas otitidis strain isolated from Chirimiri coal mines, India. BIORESOUR BIOPROCESS 2016. [DOI: 10.1186/s40643-016-0119-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
34
|
Xu X, Chen X, Su P, Fang F, Hu B. Biodegradation potential of polycyclic aromatic hydrocarbons by bacteria strains enriched from Yangtze River sediments. ENVIRONMENTAL TECHNOLOGY 2015; 37:513-520. [PMID: 26227671 DOI: 10.1080/09593330.2015.1074289] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Microbial degradation is an effective method for the removal of polycyclic aromatic hydrocarbons (PAHs) compounds from polluted sediments. Surface sediments collected from Yangtze River in the downtown area of Chongqing were found to contain PAH concentrations to various different degrees. Two bacteria strains (termed PJ1 and PJ2) isolated from the sediment samples could use phenanthrene (Phe) and fluoranthene (Flu) as carbon sources for growth thereby degrading these two PAH compounds. Using 16S rDNA gene sequencing, the isolates were identified as Sphingomonas sp. and Klebsiella sp., respectively. Biodegradation assays showed that the PJ1 presented an efficient degradation capability compared to PJ2 in cultures with the initial Phe and Flu concentrations ranging from 20 to 200 mg/L. The highest rates of Phe and Flu biodegradation by PJ1 reached 74.32% and 58.18% after incubation for 15 and 30 days, respectively. This is the first report on the biodegradation potential of the bacterial from surface sediments of an industrial area upstream of the Gorge Reservoir.
Collapse
Affiliation(s)
- Xiaoyi Xu
- a Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education , Chongqing University , Chongqing , People's Republic of China
- b National Center for International Research of Low-carbon and Green Buildings , Chongqing University , Chongqing , People's Republic of China
- c College of Urban Construction and Environmental Engineering , Chongqing University , 174#, Shazheng Street, Shapingba District, Chongqing 400045 , People's Republic of China
| | - Xi Chen
- a Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education , Chongqing University , Chongqing , People's Republic of China
- b National Center for International Research of Low-carbon and Green Buildings , Chongqing University , Chongqing , People's Republic of China
| | - Pan Su
- a Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education , Chongqing University , Chongqing , People's Republic of China
- b National Center for International Research of Low-carbon and Green Buildings , Chongqing University , Chongqing , People's Republic of China
| | - Fang Fang
- a Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education , Chongqing University , Chongqing , People's Republic of China
- b National Center for International Research of Low-carbon and Green Buildings , Chongqing University , Chongqing , People's Republic of China
| | - Bibo Hu
- a Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education , Chongqing University , Chongqing , People's Republic of China
- b National Center for International Research of Low-carbon and Green Buildings , Chongqing University , Chongqing , People's Republic of China
| |
Collapse
|
35
|
Khemili-Talbi S, Kebbouche-Gana S, Akmoussi-Toumi S, Angar Y, Gana ML. Isolation of an extremely halophilic arhaeon Natrialba sp. C21 able to degrade aromatic compounds and to produce stable biosurfactant at high salinity. Extremophiles 2015; 19:1109-20. [PMID: 26334644 DOI: 10.1007/s00792-015-0783-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/20/2015] [Indexed: 12/30/2022]
Abstract
Natrialba sp. strain C21 was isolated from oil contaminated saline water in Ain Salah (Algeria) and has exhibited a good potential for degrading phenol (3% v/v), naphthalene (3% v/v), and pyrene (3% v/v) at high salinity with high growth, enzymatic activity and biosurfactant production. Successful metabolism of aromatic hydrocarbon compounds of the strain Natrialba sp. C21 appears to require the ortho-cleavage pathway. Indeed, assays of the key enzymes involved in the ring cleavage of catechol 1, 2-dioxygenase indicated that degradation of the phenol, naphthalene and pyrene by strain Natrialba sp. C21 was via the ortho-cleavage pathway. Cells grown on aromatic hydrocarbons displayed greater ortho-activities mainly towards catechol, while the meta-activity was very low. Besides, biosurfactants derived from the strain C21 were capable of effectively emulsifying both aromatic and aliphatic hydrocarbons and seem to be particularly promising since they have particular adaptations like the increased stability at high temperature and salinity conditions. This study clearly demonstrates for the first time that strain belonging to the genera Natrialba is able to grow at 25% (w/v) NaCl, utilizing phenol, naphthalene, and pyrene as the sole carbon sources. The results suggest that the isolated halophilic archaeon could be a good candidate for the remediation process in extreme environments polluted by aromatic hydrocarbons. Moreover, the produced biosurfactant offers a multitude of interesting potential applications in various fields of biotechnology.
Collapse
Affiliation(s)
- Souad Khemili-Talbi
- Laboratoire Conservation et Valorisation des Ressources Biologiques (VALCOR), Faculté des Sciences, Université M'Hamed Bougara de Boumerdes, Avenue de l'Indépendance, 35000, Boumerdès, Algeria.
| | - Salima Kebbouche-Gana
- Laboratoire Conservation et Valorisation des Ressources Biologiques (VALCOR), Faculté des Sciences, Université M'Hamed Bougara de Boumerdes, Avenue de l'Indépendance, 35000, Boumerdès, Algeria.
| | - Siham Akmoussi-Toumi
- Laboratoire Conservation et Valorisation des Ressources Biologiques (VALCOR), Faculté des Sciences, Université M'Hamed Bougara de Boumerdes, Avenue de l'Indépendance, 35000, Boumerdès, Algeria
| | - Yassmina Angar
- Faculté des Sciences, Université M'Hamed Bougara de Boumerdes, Avenue de l'Indépendance, 35000, Boumerdès, Algeria
| | - Mohamed Lamine Gana
- Centre de Recherche et de Développement, SONATRACH, 35000, Boumerdès, Algeria
| |
Collapse
|