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Yessentayeva K, Reinhard A, Berzhanova R, Mukasheva T, Urich T, Mikolasch A. Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support. Appl Microbiol Biotechnol 2024; 108:189. [PMID: 38305872 PMCID: PMC10837267 DOI: 10.1007/s00253-024-13010-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.
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Affiliation(s)
- Kuralay Yessentayeva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Anne Reinhard
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Ramza Berzhanova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Togzhan Mukasheva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Tim Urich
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Annett Mikolasch
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany.
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Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
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Lyu L, Li J, Chen Y, Mai Z, Wang L, Li Q, Zhang S. Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea. Front Microbiol 2022; 13:920067. [PMID: 36338091 PMCID: PMC9626528 DOI: 10.3389/fmicb.2022.920067] [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: 04/14/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.
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Affiliation(s)
- Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Lina Lyu,
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Si Zhang,
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Complete Genome Sequence of Micrococcus luteus Strain CW.Ay, Isolated from Indoor Air in a Hong Kong School. Microbiol Resour Announc 2022; 11:e0119421. [PMID: 35175116 PMCID: PMC8852316 DOI: 10.1128/mra.01194-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Micrococcus luteus strain CW.Ay was isolated from indoor air in Hong Kong. The complete genome (2,543,764 bp; GC content, 72.93%) was established by hybrid assembly and comprised a linear plasmid and a single chromosome featuring many genes to account for its broad distribution in very diverse habitats.
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Ma M, Gao W, Li Q, Han B, Zhu A, Yang H, Zheng L. Biodiversity and oil degradation capacity of oil-degrading bacteria isolated from deep-sea hydrothermal sediments of the South Mid-Atlantic Ridge. MARINE POLLUTION BULLETIN 2021; 171:112770. [PMID: 34492563 DOI: 10.1016/j.marpolbul.2021.112770] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Studies have reported that various hydrocarbons and hydrocarbon-degrading bacteria are found in global deep-sea hydrothermal regions. However, little is known about degradation characteristics of culturable hydrocarbon-degrading bacteria from these regions. We speculate that these bacteria can be used as resources for the bioremediation of oil pollution. In this study, six oil-degrading consortia were obtained from the hydrothermal region of the Southern Mid-Atlantic Ridge through room-temperature enrichment experiments. The dominant oil-degrading bacteria belonged to Nitratireductor, Pseudonocardia, Brevundimonas and Acinetobacter. More varieties of hydrocarbon-degrading bacteria were obtained from sediments (preserved at 4 °C) near hydrothermal vents. Most strains had the ability to degrade high molecular weight petroleum components. In addition, Pseudonocardia was shown to exhibit a high degradation ability for phytane and pristine for the first time. This study may provide new insights into the community structure and biodiversity of culturable oil-degrading bacteria in deep-sea hydrothermal regions.
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Affiliation(s)
- Meng Ma
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Wei Gao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China.
| | - Qian Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Bin Han
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Aimei Zhu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Huanghao Yang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Li Zheng
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China.
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Soares PRS, Birolli WG, Ferreira IM, Porto ALM. Biodegradation pathway of the organophosphate pesticides chlorpyrifos, methyl parathion and profenofos by the marine-derived fungus Aspergillus sydowii CBMAI 935 and its potential for methylation reactions of phenolic compounds. MARINE POLLUTION BULLETIN 2021; 166:112185. [PMID: 33640600 DOI: 10.1016/j.marpolbul.2021.112185] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/28/2020] [Accepted: 02/12/2021] [Indexed: 05/21/2023]
Abstract
The indiscriminate use of organophosphate pesticides causes serious environmental and human health problems. This study aims the biodegradation of chlorpyrifos, methyl parathion and profenofos with the proposal of new biodegradation pathways employing marine-derived fungi as biocatalysts. Firstly, a growth screening was carried out with seven fungi strains and Aspergillus sydowii CBMAI 935 was selected. For chlorpyrifos, 32% biodegradation was observed and the metabolites tetraethyl dithiodiphosphate, 3,5,6-trichloropyridin-2-ol, 2,3,5-trichloro-6-methoxypyridine, and 3,5,6-trichloro-1-methylpyridin-2(1H)-one were identified. Whereas 80% methyl parathion was biodegraded with the identification of isoparathion, methyl paraoxon, trimethyl phosphate, O,O,O-trimethyl phosphorothioate, O,O,S-trimethyl phosphorothioate, 1-methoxy-4-nitrobenzene, and 4-nitrophenol. For profenofos, 52% biodegradation was determined and the identified metabolites were 4-bromo-2-chlorophenol, 4-bromo-2-chloro-1-methoxybenzene and O,O-diethyl S-propylphosphorothioate. Moreover, A. sydowii CBMAI 935 methylated different phenolic substrates (phenol, 2-chlorophenol, 6-chloropyridin-3-ol, and pentachlorophenol). Therefore, the knowledge about the fate of these compounds in the sea was expanded, and the marine-derived fungus A. sydowii CBMAI 935 showed potential for biotransformation reactions.
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Affiliation(s)
- Paulo Roberto S Soares
- São Carlos Institute of Chemistry, University of São Paulo, Av. João Dagnone, 1100, Ed. Química Ambiental, J. Santa Angelina, 13563-120 São Carlos, SP, Brazil
| | - Willian G Birolli
- São Carlos Institute of Chemistry, University of São Paulo, Av. João Dagnone, 1100, Ed. Química Ambiental, J. Santa Angelina, 13563-120 São Carlos, SP, Brazil; Chemistry Department, Center for Exact Sciences and Technology, Federal University of São Carlos, Via Washington Luiz, km 235, 13565-905 São Carlos, SP, Brazil
| | - Irlon M Ferreira
- Federal University of Amapá, Campus Ground Zero of Ecuador, Rod. Juscelino Kubitschek Km 02, Bairro Zerão, 68902-280 Macapá, AP, Brazil
| | - André Luiz M Porto
- São Carlos Institute of Chemistry, University of São Paulo, Av. João Dagnone, 1100, Ed. Química Ambiental, J. Santa Angelina, 13563-120 São Carlos, SP, Brazil.
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Oyewusi HA, Wahab RA, Huyop F. Dehalogenase-producing halophiles and their potential role in bioremediation. MARINE POLLUTION BULLETIN 2020; 160:111603. [PMID: 32919122 DOI: 10.1016/j.marpolbul.2020.111603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
This review aims to briefly describe the potential role of dehalogenase-producing halophilic bacteria in decontamination of organohalide pollutants. Hypersaline habitats pose challenges to life because of low water activity (water content) and is considered as the largest and ultimate sink for pollutants due to naturally and anthropogenic activities in which a substantial amount of ecological contaminants are organohalides. Several such environments appear to host and support substantial diversity of extremely halophilic and halotolerant bacteria as well as halophilic archaea. Biodegradation of several toxic inorganic and organic compounds in both aerobic and anaerobic conditions are carried out by halophilic microbes. Therefore, remediation of polluted marine/hypersaline environments are the main scorching issues in the field of biotechnology. Although many microbial species are reported as effective pollutants degrader, but little has been isolated from marine/hypersaline environments. Therefore, more novel microbial species with dehalogenase-producing ability are still desired.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, PMB, 5351, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia.
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