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Mupamhadzi TL, Machona O, Chidzwondo F, Mangoyi R. Molecular Detection and Phylogenetic Analysis of the alkB Gene in Klebsiella oxytoca Strains Isolated from the Gut of Tenebrio molitor. ScientificWorldJournal 2024; 2024:3350591. [PMID: 38756480 PMCID: PMC11098606 DOI: 10.1155/2024/3350591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/17/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The challenge in polystyrene disposal has caused researchers to look for urgent innovative and ecofriendly solutions for plastic degradation. Some insects have been reported to use polystyrene as their sole carbon source, and this has been linked to the presence of microbes in their guts that aid in plastic digestion. Thus, this study focuses on the molecular detection and phylogenetic analysis of the alkane-1-monooxygenase (alkB) gene in Klebsiella oxytoca strains isolated from the gut of Tenebrio molitor. The alkB gene encodes for alkane-1-monooxygenase, an enzyme involved in the oxidation of inactivated alkanes. This gene can be used as a marker to assess bacteria's ability to biodegrade polystyrene. Three bacterial strains were isolated from the guts of T. molitor mealworms and were confirmed using polymerase chain reaction (PCR) of the 16S ribosomal RNA gene. The primers used in the amplification of the 16S ribosomal RNA region were designed using NCBI, a bioinformatics tool. To detect the presence of the alkB gene in the isolated bacterial strains, a set of primers used in the amplification of this gene was manually designed from the conserved regions of the alkB nucleotide sequences of eleven bacterial species from GenBank. TCOFFE online tool was used to align the alkB sequences of the bacteria, while Jalview and ConSurf were used to view the alignment. The amplified alkB gene was then sequenced using the Sanger sequencing technique, blasted on NCBI to look for similar sequences, and a phylogenetic tree was constructed. Based on the 16S ribosomal RNA gene sequences, the isolated bacterial strains were confirmed to be Klebsiella oxytoca NBRC 102593, Klebsiella oxytoca JCM 1665, and Klebsiella oxytoca ATCC 13182. The alkB gene sequence identical to fourteen alkB gene sequences derived from Actinobacteria whole genome was detected in Klebsiella oxytoca for the first time to the best of our knowledge. The novel nucleotide sequence was published in the NCBI database under accession number OP959069. This gene sequence was found to be for the enzyme alkane-1-monooxygenase and may be one of the enzymes responsible for polystyrene degradation by the putative Klebsiella oxytoca ATCC 13182 in T. molitor.
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Affiliation(s)
| | - Oleen Machona
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - Farisai Chidzwondo
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - Rumbidzai Mangoyi
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
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Giovanella P, Taketani RG, Gil-Solsona R, Saldanha LL, Naranjo SBE, Sancho JV, Portolés T, Andreote FD, Rodríguez-Mozaz S, Barceló D, Sette LD. A comprehensive study on diesel oil bioremediation under microcosm conditions using a combined microbiological, enzymatic, mass spectrometry, and metabarcoding approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:101250-101266. [PMID: 37648922 DOI: 10.1007/s11356-023-29474-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Abstract
This study aims at the application of a marine fungal consortium (Aspergillus sclerotiorum CRM 348 and Cryptococcus laurentii CRM 707) for the bioremediation of diesel oil-contaminated soil under microcosm conditions. The impact of biostimulation (BS) and/or bioaugmentation (BA) treatments on diesel-oil biodegradation, soil quality, and the structure of the microbial community were studied. The use of the fungal consortium together with nutrients (BA/BS) resulted in a TPH (Total Petroleum Hydrocarbon) degradation 42% higher than that obtained by natural attenuation (NA) within 120 days. For the same period, a 72 to 92% removal of short-chain alkanes (C12 to C19) was obtained by BA/BS, while only 3 to 65% removal was achieved by NA. BA/BS also showed high degradation efficiency of long-chain alkanes (C20 to C24) at 120 days, reaching 90 and 92% of degradation of icosane and heneicosane, respectively. In contrast, an increase in the levels of cyclosiloxanes (characterized as bacterial bioemulsifiers and biosurfactants) was observed in the soil treated by the consortium. Conversely, the NA presented a maximum of 37% of degradation of these alkane fractions. The 5-ringed PAH benzo(a)pyrene, was removed significantly better with the BA/BS treatment than with the NA (48 vs. 38 % of biodegradation, respectively). Metabarcoding analysis revealed that BA/BS caused a decrease in the soil microbial diversity with a concomitant increase in the abundance of specific microbial groups, including hydrocarbon-degrading (bacteria and fungi) and also an enhancement in soil microbial activity. Our results highlight the great potential of this consortium for soil treatment after diesel spills, as well as the relevance of the massive sequencing, enzymatic, microbiological and GC-HRMS analyses for a better understanding of diesel bioremediation.
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Affiliation(s)
- Patricia Giovanella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Rodrigo Gouvêa Taketani
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, SP, Brazil
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, United Kingdom
| | - Ruben Gil-Solsona
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research - Severo Ochoa Excellence Center (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain
| | - Luiz Leonardo Saldanha
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Samantha Beatríz Esparza Naranjo
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino Americana, Parque tecnológico Itaipu, Foz do Iguaçu, PR, Brazil
| | - Juan V Sancho
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón de la Plana, Spain
| | - Tania Portolés
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón de la Plana, Spain
| | - Fernando Dini Andreote
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, SP, Brazil
| | - Sara Rodríguez-Mozaz
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research - Severo Ochoa Excellence Center (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain
| | - Lara Durães Sette
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
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Groups of Geomicrobiological Indicators Are Spread across Gas-Hydrate and Non-Gas-Hydrate Areas in the Northern Part of the Sea of Japan. BIOLOGY 2022; 11:biology11121802. [PMID: 36552312 PMCID: PMC9774978 DOI: 10.3390/biology11121802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
The bioindication of oil and gas fields is a field of geomicrobiology that is mainly devoted to the detection of hydrocarbon-oxidizing microbial indicator species or functional genes in total DNA. However, it appears promising to use the physiological properties of microorganisms detection deposit type of hydrocarbons, in particular their ability to oxidize hydrocarbons under aerobic and anaerobic conditions. In this study, the most promising approach in this area was the method used for assessing the anaerobic degradation of hydrocarbons. When comparing molecular genetics and cultured methods of bioindication, it can be concluded that molecular biomarkers of functional genes for the anaerobic destruction of hydrocarbons (masD) make it possible to separate areas with traditional and gas-hydrate types of deposits. Using cultured methods, we found that representatives of the Nocardiaceae family of the phylum Actinomycetota were tied to the areas where gas hydrates were found. The ability of aerobic and facultative anaerobic hydrocarbon-oxidizing microorganisms to anaerobically utilize hydrocarbons was determined with cultured methods. For the first time, this ability was revealed for the genera Stenotrophomonas, Psychrobacter, Micrococcus and Peribacillus. The wide distribution of this ability that we found in strains isolated from both study regions suggests its prominent role in the destruction of hydrocarbons in marine sediments.
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Liu Y, Sun Y, Yu J, Xia X, Ding A, Zhang D. Impacts of groundwater level fluctuation on soil microbial community, alkane degradation efficiency and alkane-degrading gene diversity in the critical zone: Evidence from an accelerated water table fluctuation simulation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:83060-83070. [PMID: 35759097 DOI: 10.1007/s11356-022-21246-2] [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: 11/18/2021] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Petroleum hydrocarbons are hazardous to ecosystems and human health, commonly containing n-alkanes and polycyclic aromatic hydrocarbons. Previous researches have studied alkane degraders and degrading genes under aerobic or anaerobic conditions, but seldom discussed them in the intermittent saturation zone which is a connective area between the vadose zone and the groundwater aquifer with periodic alteration of oxygen and moisture. The present study investigated the difference in alkane degradation efficiency, bacterial community, and alkane degrading gene diversity in aerobic, anaerobic, and aerobic-anaerobic fluctuated treatments. All biotic treatments achieved over 90% of n-alkane removal after 120 days of incubation. The removal efficiencies of n-alkanes with a carbon chain length from 16 to 25 were much higher in anaerobic scenarios than those in aerobic scenarios, explained by different dominant microbes between aerobic and anaerobic conditions. The highest removal efficiency was found in fluctuation treatments, indicating an accelerated n-alkane biodegradation under aerobic-anaerobic alternation. In addition, the copy numbers of the 16S rRNA gene and two alkB genes (alkB-P and alkB-R) declined dramatically when switched from aerobic to anaerobic scenarios and oppositely from anaerobic to aerobic conditions. This suggested that water level fluctuation could notably change the presence of aerobic alkane degrading genes. Our results suggested that alkane degradation efficiency, soil microbial community, and alkane-degrading genes were all driven by water level fluctuation in the intermittent saturation zone, helping better understand the effects of seasonal water table fluctuation on the biodegradation of petroleum hydrocarbons in the subsurface environment.
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Affiliation(s)
- Yueqiao Liu
- Experiment and Practice Innovation Education Center, Beijing Normal University at Zhuhai, Zhuhai, 519087, China
| | - Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jingshan Yu
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xuefeng Xia
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, China.
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, China.
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Physiological changes in Rhodococcus ruber S103 immobilized on biobooms using low-cost media enhance stress tolerance and crude oil-degrading activity. Sci Rep 2022; 12:10474. [PMID: 35729341 PMCID: PMC9213463 DOI: 10.1038/s41598-022-14488-0] [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] [Received: 03/29/2022] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
For economic feasibility, sugarcane molasses (0.5%, w/v) containing K2HPO4 (0.26%, w/v) and mature coconut water, low value byproducts, were used in cultivation of Rhodococcus ruber S103 for inoculum production and immobilization, respectively. Physiological changes of S103 grown in low-cost media, including cell hydrophobicity, saturated/unsaturated ratio of cellular fatty acids and biofilm formation activity, enhanced stress tolerance and crude oil biodegradation in freshwater and even under high salinity (5%, w/v). Biobooms comprised of S103 immobilized on polyurethane foam (PUF) was achieved with high biomass content (1010 colony-forming units g-1 PUF) via a scale-up process in a 5-L modified fluidized-bed bioreactor within 3 days. In a 500-L mesocosm, natural freshwater was spiked with crude oil (72 g or 667 mg g-1 dry biobooms), and a simulated wave was applied. Biobooms could remove 100% of crude oil within only 3 days and simultaneously biodegraded 60% of the adsorbed oil after 7 days when compared to boom control with indigenous bacteria. In addition, biobooms had a long shelf-life (at least 100 days) with high biodegradation activity (85.2 ± 2.3%) after storage in 10% (w/v) skimmed milk at room temperature. This study demonstrates that the low-cost production of biobooms has potential for future commercial bioremediation.
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Degradation of long-chain n-alkanes by a novel thermal-tolerant Rhodococcus strain. Arch Microbiol 2022; 204:259. [PMID: 35419660 DOI: 10.1007/s00203-022-02872-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/02/2022]
Abstract
A novel bacterial strain, CH91, was isolated from a high-temperature oil reservoir. Morphological characterization, phylogenetic analyses of 16S rRNA gene sequence and genome relatedness indicated that the strain is a potential new species in the genus Rhodococcus. Strain CH91 could grow in the temperature range of 25-50 °C (optimally at 37 °C) and utilize a broad range of long-chain n-alkanes from hexadecane to hexatriacontane. The utilization of the n-alkanes mixture of strain CH91 revealed that the degradation rate was correlated to the length of the carbon chain. Two novel alkB genes encoding alkane 1-monooxygenase were found in the genome of this strain. The protein sequences of both alkane 1-monooxygenases showed a remarkable phylogenetic distance to other reported AlkB protein sequences. These results would help broaden our knowledge about alkane degradation by Rhodocuccus and its potential ecological role. The ability of the strain in the long-chain alkane degradation and thermal tolerance could also be further exploited for bioremediation of oil contaminations and microbial enhanced oil recovery.
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Naloka K, Polrit D, Muangchinda C, Thoetkiattikul H, Pinyakong O. Bioballs carrying a syntrophic Rhodococcus and Mycolicibacterium consortium for simultaneous sorption and biodegradation of fuel oil in contaminated freshwater. CHEMOSPHERE 2021; 282:130973. [PMID: 34091296 DOI: 10.1016/j.chemosphere.2021.130973] [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: 08/06/2020] [Revised: 04/14/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Nonpathogenic effective bacterial hydrocarbon degraders, Rhodococcus ruber S103, Mycolicibacterium parafortuitum J101 and Mycolicibacterium austroafricanum Y502, were isolated from mixed polycyclic aromatic hydrocarbon (PAH)-enriched river sediments. They possessed broad substrate specificities toward various PAHs and aliphatic compounds as sole carbon sources. These strains exhibited promising characteristics, including biosurfactant production, high cell hydrophobicity, biofilm formation and no antagonistic interactions, and contained genes encoding hydrocarbon-degrading enzymes. The mixed bacterial consortium combining S103, J101 and Y502, showed more effective syntrophic degradation of two types of refined petroleum products, diesel and fuel oils, than monocultures. The defined consortium immobilized on plastic balls achieved over 50% removal efficiency of high fuel oil concentration (3000 mg L-1) in a synthetic medium and contaminated freshwater. Furthermore, the immobilized cells simultaneously degraded more than 46% of total fuel oil adsorbed on plastic balls in both culture systems. SEM imaging confirmed that the immobilized consortium exhibited biofilm formation with the bacterial community covering most of the bioball surface, resulting in high bacterial survival against toxic contaminants. The results of this study showed the potential use of the cooperative interaction between Rhodococcus and Mycolicibacterium as immobilized bioballs for the bioremediation of fuel oil-contaminated environments. Additionally, this research has motivated further investigations into the development of bioremediation products for fuel oil degradation.
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Affiliation(s)
- Kallayanee Naloka
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Duangporn Polrit
- International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chanokporn Muangchinda
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Honglada Thoetkiattikul
- Technology Management Center, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Onruthai Pinyakong
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, 10330, Thailand.
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Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India. World J Microbiol Biotechnol 2021; 37:56. [PMID: 33619649 DOI: 10.1007/s11274-021-03018-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH4) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH4 utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, Ks of 1.92 ± 0.092 mg CH4 L-1. Besides the ability to utilize CH4, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
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Peltek SE, Bryanskaya AV, Uvarova YE, Rozanov AS, Ivanisenko TV, Ivanisenko VA, Lazareva EV, Saik OV, Efimov VM, Zhmodik SM, Taran OP, Slynko NM, Shekhovtsov SV, Parmon VN, Dobretsov NL, Kolchanov NA. Young «oil site» of the Uzon Caldera as a habitat for unique microbial life. BMC Microbiol 2020; 20:349. [PMID: 33228530 PMCID: PMC7685581 DOI: 10.1186/s12866-020-02012-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/15/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The Uzon Caldera is one of the places on our planet with unique geological, ecological, and microbiological characteristics. Uzon oil is the youngest on Earth. Uzon oil has unique composition, with low proportion of heavy fractions and relatively high content of saturated hydrocarbons. Microbial communities of the «oil site» have a diverse composition and live at high temperatures (up to 97 °C), significant oscillations of Eh and pH, and high content of sulfur, sulfides, arsenic, antimony, and mercury in water and rocks. RESULTS The study analyzed the composition, structure and unique genetics characteristics of the microbial communities of the oil site, analyzed the metabolic pathways in the communities. Metabolic pathways of hydrocarbon degradation by microorganisms have been found. The study found statistically significant relationships between geochemical parameters, taxonomic composition and the completeness of metabolic pathways. It was demonstrated that geochemical parameters determine the structure and metabolic potential of microbial communities. CONCLUSIONS There were statistically significant relationships between geochemical parameters, taxonomic composition, and the completeness of metabolic pathways. It was demonstrated that geochemical parameters define the structure and metabolic potential of microbial communities. Metabolic pathways of hydrocarbon oxidation was found to prevail in the studied communities, which corroborates the hypothesis on abiogenic synthesis of Uzon hydrothermal petroleum.
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Affiliation(s)
- Sergey E Peltek
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Alla V Bryanskaya
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090.
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090.
| | - Yuliya E Uvarova
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Aleksey S Rozanov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Timofey V Ivanisenko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia, 630090
| | - Vladimir A Ivanisenko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Elena V Lazareva
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Olga V Saik
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Vadim M Efimov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia, 630090
| | - Sergey M Zhmodik
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Oxana P Taran
- Institute of Chemistry and Chemical Technology SB RAS, FRC Krasnoyarsk Science Center SB RAS, Akademgorodok, 50/24, Krasnoyarsk, Russia, 660036
- Siberian Federal University, Svobodny ave. 79, Krasnoyarsk, Russia, 660041
- Boreskov Institute of Catalysis SB RAS, pr. Lavrentieva 5, Novosibirsk, Russia, 630090
| | - Nikolay M Slynko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Sergey V Shekhovtsov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Valentin N Parmon
- Boreskov Institute of Catalysis SB RAS, pr. Lavrentieva 5, Novosibirsk, Russia, 630090
| | - Nikolay L Dobretsov
- Trofimuk Institute of Petroleum Geology and Geophysics SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Nikolay A Kolchanov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
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Complete Genome Sequence of Rhodococcus erythropolis X5, a Psychrotrophic Hydrocarbon-Degrading Biosurfactant-Producing Bacterium. Microbiol Resour Announc 2019; 8:8/48/e01234-19. [PMID: 31776221 PMCID: PMC6883108 DOI: 10.1128/mra.01234-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus erythropolis X5 is a psychrotrophic (cold-adapted) hydrocarbon-degrading bacterium, as it showed effective n-alkane destruction at low positive temperatures. Here, the genome of strain X5 was completely sequenced; it consists of a 6,472,161-bp circular chromosome (62.25% GC content) and a 526,979-bp linear plasmid, pRhX5-526k (62.37% GC content). Rhodococcus erythropolis X5 is a psychrotrophic (cold-adapted) hydrocarbon-degrading bacterium, as it showed effective n-alkane destruction at low positive temperatures. Here, the genome of strain X5 was completely sequenced; it consists of a 6,472,161-bp circular chromosome (62.25% GC content) and a 526,979-bp linear plasmid, pRhX5-526k (62.37% GC content).
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Gibu N, Kasai D, Ikawa T, Akiyama E, Fukuda M. Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1. Microorganisms 2019; 7:microorganisms7110479. [PMID: 31652785 PMCID: PMC6921075 DOI: 10.3390/microorganisms7110479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022] Open
Abstract
Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway-a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in n-alkane degradation-was identified and the transcriptional regulation of these genes was characterized. Reverse transcription-PCR analyses revealed that these genes constituted an operon and were transcribed in the presence of n-alkane. Inactivation of alkB led to the absence of the ability to utilize n-undecane. The alkB mutation resulted in reduction of growth rates on C10 and C12 n-alkanes; however, growths on C13 to C19 n-alkanes were not affected by this mutation. These results suggested that alkB was essential for the utilization of C10 to C12 n-alkanes. Inactivation of alkU showed the constitutive expression of alkB. Purified AlkU is able to bind to the putative promoter region of alkB, suggesting that AlkU played a role in repression of the transcription of alk operon. The results of this study indicated that alkB was involved in the medium-chain n-alkanes degradation of strain RHA1 and the transcription of alk operon was negatively regulated by alkU-encoded regulator. This report is important to understand the n-alkane degradation pathway of R. jostii, including the transcriptional regulation of alk gene cluster.
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Affiliation(s)
- Namiko Gibu
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan.
| | - Takumi Ikawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Emiko Akiyama
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
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Zhang M, Zhao Y, Qin X, Jia W, Chai L, Huang M, Huang Y. Microplastics from mulching film is a distinct habitat for bacteria in farmland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:470-478. [PMID: 31254812 DOI: 10.1016/j.scitotenv.2019.06.108] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 05/07/2023]
Abstract
Microplastics, as an emerging pollutant of global importance, have been well documented in aquatic ecosystems. However, little is known about the effects of microplastics on agroecosystems, particularly for soil microbial communities. Herein, microplastics collected from cotton fields in Xinjiang, China, were analysed with a scanning electron microscope (SEM) and high-throughput sequencing to investigate the attached bacterial communities. Microplastic surfaces, especially pits and flakes, were colonized by various microorganisms, suggesting active hydrolysis of plastic debris. The bacterial communities colonizing microplastics were significantly different in structure from those in the surrounding soil, plant litter and macroplastics. In addition, statistical analysis of differentially abundant OTUs showed that microplastics serve as a "special microbial accumulator" in farmland soil, enriching some taxa that degrade polyethylene, such as Actinobacteria, Bacteroidetes and Proteobacteria. Co-occurrence network analysis revealed that the biotic interactions between microorganisms on microplastics are as complex as those in soil, and Acidobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes are considered keystone species in bacterial communities. Collectively, the findings imply that microplastics acted as a distinct habitat for bacteria in farmland soil, which increases our understanding of microplastic pollution.
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Affiliation(s)
- Mengjun Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yanran Zhao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Xiao Qin
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Weiqian Jia
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Liwei Chai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Muke Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing 100871, China.
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Yang R, Zhang G, Li S, Moazeni F, Li Y, Wu Y, Zhang W, Chen T, Liu G, Zhang B, Wu X. Degradation of crude oil by mixed cultures of bacteria isolated from the Qinghai-Tibet plateau and comparative analysis of metabolic mechanisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:1834-1847. [PMID: 30456621 DOI: 10.1007/s11356-018-3718-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
This study investigates the biodegradation of crude oil by a mixed culture of bacteria isolated from the Qinghai-Tibet plateau using gas chromatography-mass spectrometer (GC-MS) and the gravimetric method. The results showed that a mixed culture has a stronger ability to degrade hydrocarbon than pure cultures. Once both Nocardia soli Y48 and Rhodococcus erythropolis YF28-1 (8) were present in a culture, the culture demonstrated the highest crude oil removal efficiency of almost 100% after 10 days of incubation at 20 °C. Moreover, further analysis of the degradation mechanisms used by the above strains, which revealed utilization of different n-alkane substrates, indicated the diversity of evolution and variations in different strains, as well as the importance of multiple metabolic mechanisms for alkane degradation. Therefore, it is concluded that a mixed culture of Y48 and YF28-1 (8) strains can provide a more effective method for bioremediation of hydrocarbon-contaminated soil in permafrost regions.
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Affiliation(s)
- Ruiqi Yang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Shiweng Li
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Faegheh Moazeni
- School of Science Engineering and Technology, Penn State Harrisburg University, Middletown, PA, 17057, USA
| | - Yunshi Li
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yongna Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
| | - Binglin Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
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Zampolli J, Zeaiter Z, Di Canito A, Di Gennaro P. Genome analysis and -omics approaches provide new insights into the biodegradation potential of Rhodococcus. Appl Microbiol Biotechnol 2018; 103:1069-1080. [PMID: 30554387 DOI: 10.1007/s00253-018-9539-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/05/2023]
Abstract
The past few years observed a breakthrough of genome sequences of bacteria of Rhodococcus genus with significant biodegradation abilities. Invaluable knowledge from genome data and their functional analysis can be applied to develop and design strategies for attenuating damages caused by hydrocarbon contamination. With the advent of high-throughput -omic technologies, it is currently possible to utilize the functional properties of diverse catabolic genes, analyze an entire system at the level of molecule (DNA, RNA, protein, and metabolite), simultaneously predict and construct catabolic degradation pathways. In this review, the genes involved in the biodegradation of hydrocarbons and several emerging plasticizer compounds in Rhodococcus strains are described in detail (aliphatic, aromatics, PAH, phthalate, polyethylene, and polyisoprene). The metabolic biodegradation networks predicted from omics-derived data along with the catabolic enzymes exploited in diverse biotechnological and bioremediation applications are characterized.
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Affiliation(s)
- Jessica Zampolli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Zahraa Zeaiter
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Alessandra Di Canito
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
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15
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Li G, Gao P, Zhi B, Fu B, Gao G, Chen Z, Gao M, Wu M, Ma T. The relative abundance of alkane-degrading bacteria oscillated similarly to a sinusoidal curve in an artificial ecosystem model from oil-well products. Environ Microbiol 2018; 20:3772-3783. [DOI: 10.1111/1462-2920.14382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/19/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK USA
| | - Peike Gao
- College of Life Sciences; Qufu Normal University; Qufu People's Repubic of China
| | - Bo Zhi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Bing Fu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Ge Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Zhaohui Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Mengli Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Mengmeng Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
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16
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Stanislauskienė R, Kutanovas S, Kalinienė L, Bratchikov M, Meškys R. Tetramethylpyrazine-Inducible Promoter Region from Rhodococcus jostii TMP1. Molecules 2018; 23:molecules23071530. [PMID: 29941849 PMCID: PMC6099782 DOI: 10.3390/molecules23071530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 11/17/2022] Open
Abstract
An inducible promoter region, PTTMP (tetramethylpyrazine [TTMP]), has been identified upstream of the tpdABC operon, which contains the genes required for the initial degradation of 2,3,5,6-tetramethylpyrazine in Rhodococcus jostii TMP1 bacteria. In this work, the promoter region was fused with the gene for the enhanced green fluorescent protein (EGFP) to investigate the activity of PTTMP by measuring the fluorescence of bacteria. The highest promoter activity was observed when bacteria were grown in a nutrient broth (NB) medium supplemented with 5 mM 2,3,5,6-tetramethylpyrazine for 48 h. Using a primer extension reaction, two transcriptional start sites for tpdA were identified, and the putative −35 and −10 promoter motifs were determined. The minimal promoter along with two 15 bp long direct repeats and two 7 bp inverted sequences were identified. Also, the influence of the promoter elements on the activity of PTTMP were determined using site-directed mutagenesis. Furthermore, PTTMP was shown to be induced by pyrazine derivatives containing methyl groups in the 2- and 5-positions of the heterocyclic ring, in the presence of the LuxR family transcriptional activator TpdR.
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Affiliation(s)
- Rūta Stanislauskienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Simonas Kutanovas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Laura Kalinienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Maksim Bratchikov
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio 21, LT-03101 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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17
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Brzeszcz J, Kaszycki P. Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility. Biodegradation 2018; 29:359-407. [PMID: 29948519 DOI: 10.1007/s10532-018-9837-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.
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Affiliation(s)
- Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland.
| | - Paweł Kaszycki
- Unit of Biochemistry, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, al. 29 Listopada 54, 31-425, Kraków, Poland
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Park C, Park W. Survival and Energy Producing Strategies of Alkane Degraders Under Extreme Conditions and Their Biotechnological Potential. Front Microbiol 2018; 9:1081. [PMID: 29910779 PMCID: PMC5992423 DOI: 10.3389/fmicb.2018.01081] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/07/2018] [Indexed: 11/17/2022] Open
Abstract
Many petroleum-polluted areas are considered as extreme environments because of co-occurrence of low and high temperatures, high salt, and acidic and anaerobic conditions. Alkanes, which are major constituents of crude oils, can be degraded under extreme conditions, both aerobically and anaerobically by bacteria and archaea of different phyla. Alkane degraders possess exclusive metabolic pathways and survival strategies, which involve the use of protein and RNA chaperones, compatible solutes, biosurfactants, and exopolysaccharide production for self-protection during harsh environmental conditions such as oxidative and osmotic stress, and ionic nutrient-shortage. Recent findings suggest that the thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition, gene expression data suggest that extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions. Alkane degraders possess biotechnological potential for bioremediation because of their unusual characteristics. This review will provide genomic and molecular insights on alkane degraders under extreme conditions.
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation. Genomics 2018; 111:356-366. [PMID: 29474825 DOI: 10.1016/j.ygeno.2018.02.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 02/16/2018] [Indexed: 11/22/2022]
Abstract
A strain of Nocardia isolated from crude oil-contaminated soils in the Qinghai-Tibetan Plateau degrades nearly all components of crude oil. This strain was identified as Nocardia soli Y48, and its growth conditions were determined. Complete genome sequencing showed that N. soli Y48 has a 7.3 Mb genome and many genes responsible for hydrocarbon degradation, biosurfactant synthesis, emulsification and other hydrocarbon degradation-related metabolisms. Analysis of the clusters of orthologous groups (COGs) and genomic islands (GIs) revealed that Y48 has undergone significant gene transfer events to adapt to changing environmental conditions (crude oil contamination). The structural features of the genome might provide a competitive edge for the survival of N. soli Y48 in oil-polluted environments and reflect the adaptation of coexisting bacteria to distinct nutritional niches.
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Chiciudean I, Nie Y, Tănase AM, Stoica I, Wu XL. Complete genome sequence of Tsukamurella sp. MH1: A wide-chain length alkane-degrading actinomycete. J Biotechnol 2017; 268:1-5. [PMID: 29292131 DOI: 10.1016/j.jbiotec.2017.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023]
Abstract
Tsukamurella sp. strain MH1, capable to use a wide range of n-alkanes as the only carbon source, was isolated from petroleum-contaminated soil (Pitești, Romania) and its complete genome was sequenced. The 4,922,396 bp genome contains only one circular chromosome with a G + C content of 71.12%, much higher than the type strains of this genus (68.4%). Based on the 16S rRNA genes sequence similarity, strain MH1 was taxonomically identified as Tsukamurella carboxydivorans. Genome analyses revealed that strain MH1 is harboring only one gene encoding for the alkB-like hydroxylase, arranged in a complete alkane monooxygenase operon. This is the first complete genome of the specie T. carboxydivorans, which will provide insights into the potential of Tsukamurella sp. MH1 and related strains for bioremediation of petroleum hydrocarbons-contaminated sites and into the environmental role of these bacteria.
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Affiliation(s)
- Iulia Chiciudean
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China; Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest 060101, Romania.
| | - Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China.
| | - Ana-Maria Tănase
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest 060101, Romania.
| | - Ileana Stoica
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest 060101, Romania.
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China.
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21
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Gravouil K, Ferru-Clément R, Colas S, Helye R, Kadri L, Bourdeau L, Moumen B, Mercier A, Ferreira T. Transcriptomics and Lipidomics of the Environmental Strain Rhodococcus ruber Point out Consumption Pathways and Potential Metabolic Bottlenecks for Polyethylene Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5172-5181. [PMID: 28345896 DOI: 10.1021/acs.est.7b00846] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Polyethylene (PE), one of the most prominent synthetic polymers used worldwide, is very poorly biodegradable in the natural environment. Consequently, PE represents by itself more than half of all plastic wastes. PE biodegradation is achieved through the combination of abiotic and biotic processes. Several microorganisms have been shown to grow on the surface of PE materials, among which are the species of the Rhodococcus genus, suggesting a potent ability of these microorganisms to use, at least partly, PE as a potent carbon source. However, most of them, if not all, fail to induce a clear-cut degradation of PE samples, showing that bottlenecks to reach optimal biodegradation clearly exist. To identify the pathways involved in PE consumption, we used in the present study a combination of RNA-sequencing and lipidomic strategies. We show that short-term exposure to various forms of PE, displaying different molecular weight distributions and oxidation levels, lead to an increase in the expression of 158 genes in a Rhodococcus representative, R. ruber. Interestingly, one of the most up-regulated pathways is related to alkane degradation and β-oxidation of fatty acids. This approach also allowed us to identify metabolic limiting steps, which could be fruitfully targeted for optimized PE consumption by R. ruber.
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Affiliation(s)
- Kévin Gravouil
- Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France
| | - Romain Ferru-Clément
- Laboratory of Signalisation and Membrane Ionic Transports, National Center for Scientific Research STIM CNRS ERL 7368, University of Poitiers , Poitiers 86073, France
| | - Steven Colas
- Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France
| | - Reynald Helye
- Laboratory of Signalisation and Membrane Ionic Transports, National Center for Scientific Research STIM CNRS ERL 7368, University of Poitiers , Poitiers 86073, France
| | - Linette Kadri
- Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France
| | - Ludivine Bourdeau
- Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France
| | - Bouziane Moumen
- Team Ecology, Evolution, Symbiosis, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France
| | - Anne Mercier
- Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France
| | - Thierry Ferreira
- Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France
- Laboratory of Signalisation and Membrane Ionic Transports, National Center for Scientific Research STIM CNRS ERL 7368, University of Poitiers , Poitiers 86073, France
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22
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Wang X, Zhao X, Li H, Jia J, Liu Y, Ejenavi O, Ding A, Sun Y, Zhang D. Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation. Res Microbiol 2016; 167:731-744. [PMID: 27475037 DOI: 10.1016/j.resmic.2016.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 11/18/2022]
Abstract
Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.
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Affiliation(s)
- Xinzi Wang
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Xiaohui Zhao
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Hanbing Li
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Jianli Jia
- School of Chemical and Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, PR China
| | - Yueqiao Liu
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Odafe Ejenavi
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Dayi Zhang
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK.
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23
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Viggor S, Jõesaar M, Vedler E, Kiiker R, Pärnpuu L, Heinaru A. Occurrence of diverse alkane hydroxylase alkB genes in indigenous oil-degrading bacteria of Baltic Sea surface water. MARINE POLLUTION BULLETIN 2015; 101:507-516. [PMID: 26541986 DOI: 10.1016/j.marpolbul.2015.10.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/21/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
Formation of specific oil degrading bacterial communities in diesel fuel, crude oil, heptane and hexadecane supplemented microcosms of the Baltic Sea surface water samples was revealed. The 475 sequences from constructed alkane hydroxylase alkB gene clone libraries were grouped into 30 OPFs. The two largest groups were most similar to Pedobacter sp. (245 from 475) and Limnobacter sp. (112 from 475) alkB gene sequences. From 56 alkane-degrading bacterial strains 41 belonged to the Pseudomonas spp. and 8 to the Rhodococcus spp. having redundant alkB genes. Together 68 alkB gene sequences were identified. These genes grouped into 20 OPFs, half of them being specific only to the isolated strains. Altogether 543 diverse alkB genes were characterized in the brackish Baltic Sea water; some of them representing novel lineages having very low sequence identities with corresponding genes of the reference strains.
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Affiliation(s)
- Signe Viggor
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
| | - Merike Jõesaar
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Eve Vedler
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Riinu Kiiker
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Liis Pärnpuu
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Ain Heinaru
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
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24
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Táncsics A, Benedek T, Szoboszlay S, Veres PG, Farkas M, Máthé I, Márialigeti K, Kukolya J, Lányi S, Kriszt B. The detection and phylogenetic analysis of the alkane 1-monooxygenase gene of members of the genus Rhodococcus. Syst Appl Microbiol 2014; 38:1-7. [PMID: 25466921 DOI: 10.1016/j.syapm.2014.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 11/18/2022]
Abstract
Naturally occurring and anthropogenic petroleum hydrocarbons are potential carbon sources for many bacteria. The AlkB-related alkane hydroxylases, which are integral membrane non-heme iron enzymes, play a key role in the microbial degradation of many of these hydrocarbons. Several members of the genus Rhodococcus are well-known alkane degraders and are known to harbor multiple alkB genes encoding for different alkane 1-monooxygenases. In the present study, 48 Rhodococcus strains, representing 35 species of the genus, were investigated to find out whether there was a dominant type of alkB gene widespread among species of the genus that could be used as a phylogenetic marker. Phylogenetic analysis of rhodococcal alkB gene sequences indicated that a certain type of alkB gene was present in almost every member of the genus Rhodococcus. These alkB genes were common in a unique nucleotide sequence stretch absent from other types of rhodococcal alkB genes that encoded a conserved amino acid motif: WLG(I/V/L)D(G/D)GL. The sequence identity of the targeted alkB gene in Rhodococcus ranged from 78.5 to 99.2% and showed higher nucleotide sequence variation at the inter-species level compared to the 16S rRNA gene (93.9-99.8%). The results indicated that the alkB gene type investigated might be applicable for: (i) differentiating closely related Rhodococcus species, (ii) properly assigning environmental isolates to existing Rhodococcus species, and finally (iii) assessing whether a new Rhodococcus isolate represents a novel species of the genus.
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Affiliation(s)
- András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary.
| | - Tibor Benedek
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllő, Hungary
| | - Péter G Veres
- Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllő, Hungary
| | - Milán Farkas
- Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllő, Hungary
| | - István Máthé
- Bioengineering Department, Sapientia Hungarian University of Transylvania, Miercurea Ciuc, Romania
| | | | - József Kukolya
- Department of Applied and Environmental Microbiology, Research Institute of Agro-Environmental Sciences, National Agricultural Research and Innovation Centre, Budapest, Hungary
| | - Szabolcs Lányi
- Bioengineering Department, Sapientia Hungarian University of Transylvania, Miercurea Ciuc, Romania
| | - Balázs Kriszt
- Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllő, Hungary
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25
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Nie Y, Chi CQ, Fang H, Liang JL, Lu SL, Lai GL, Tang YQ, Wu XL. Diverse alkane hydroxylase genes in microorganisms and environments. Sci Rep 2014; 4:4968. [PMID: 24829093 PMCID: PMC4021335 DOI: 10.1038/srep04968] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/07/2014] [Indexed: 11/08/2022] Open
Abstract
AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.
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Affiliation(s)
- Yong Nie
- College of Engineering, Peking University, Beijing 100871, P. R. China
- Institute of Engineering (Baotou), College of Engineering, Peking University, Baotou 014030, China
| | - Chang-Qiao Chi
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Hui Fang
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Jie-Liang Liang
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - She-Lian Lu
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Guo-Li Lai
- College of Engineering, Peking University, Beijing 100871, P. R. China
- Institute of Engineering (Baotou), College of Engineering, Peking University, Baotou 014030, China
| | - Yue-Qin Tang
- College of Engineering, Peking University, Beijing 100871, P. R. China
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, P. R. China
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26
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Procópio L, de Cassia Pereira e Silva M, van Elsas JD, Seldin L. Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain. Braz J Microbiol 2013; 44:633-41. [PMID: 24294263 PMCID: PMC3833169 DOI: 10.1590/s1517-83822013000200044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/23/2012] [Indexed: 11/24/2022] Open
Abstract
The petroleum-derived degrading Dietzia cinnamea strain P4 recently had its genome sequenced and annotated. This allowed employing the data on genes that are involved in the degradation of n-alkanes. To examine the physiological behavior of strain P4 in the presence of n-alkanes, the strain was grown under varying conditions of pH and temperature. D. cinnamea P4 was able to grow at pH 7.0–9.0 and at temperatures ranging from 35 ºC to 45 ºC. Experiments of gene expression by real-time quantitative RT-PCR throughout the complete growth cycle clearly indicated the induction of the regulatory gene alkU (TetR family) during early growth. During the logarithmic phase, a large increase in transcriptional levels of a lipid transporter gene was noted. Also, the expression of a gene that encodes the protein fused rubredoxin-alkane monooxygenase was enhanced. Both genes are probably under the influence of the AlkU regulator.
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Affiliation(s)
- Luciano Procópio
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Ilha do Fundão, Rio de Janeiro, RJ, Brazil. ; Department of Microbial Ecology, University of Groningen, Kerklaan, Haren, The Netherlands
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27
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Schulz S, Giebler J, Chatzinotas A, Wick LY, Fetzer I, Welzl G, Harms H, Schloter M. Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments. THE ISME JOURNAL 2012; 6:1763-74. [PMID: 22402403 PMCID: PMC3498921 DOI: 10.1038/ismej.2012.17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 02/10/2012] [Accepted: 02/10/2012] [Indexed: 11/09/2022]
Abstract
Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.
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Affiliation(s)
- Stephan Schulz
- Chair of Soil Ecology, Technische Universität München, Neuherberg, Germany
- Research Unit for Environmental Genomics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Julia Giebler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Ingo Fetzer
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Gerhard Welzl
- Institute of Developmental Genetics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Michael Schloter
- Research Unit for Environmental Genomics, HelmholtzZentrum München, German Research Center for Environmental Health, Neuherberg, Germany
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28
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Meyer DD, Santestevan NA, Bücker F, Salamoni SP, Andreazza R, De Oliveira Camargo FA, Bento FM. Capability of a selected bacterial consortium for degrading diesel/biodiesel blends (B20): enzyme and biosurfactant production. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2012; 47:1776-1784. [PMID: 22755524 DOI: 10.1080/10934529.2012.689227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The search for alternative sources of energy, such as biodiesel, has been stimulated, since this biofuel is highly susceptible for biodegradation and has low toxicity, thus, reducing the impact in ecosystems. The objective of this study was to select a bacterial consortium with potential for degrading diesel/biodiesel blends (B20) obtained from areas contaminated with hydrocarbons/esters. In order to evaluate the biodegrability of the blend, six enzyme assays were conducted: alkane hydroxylase, Catechol 1,2-dioxygenase, Catechol 2,3-dioxygenase, Protocatechol 3,4-dioxygenase, ρ-NPA hydrolysis (esterase), and release of fatty acids through titration (lipase), with estimative of total protein and biosurfactant production (surface tension measurement and emulsifying index E(24)). The best results obtained allowed the selection of four bacteria isolates (Bacillus megaterium, Bacillus pumilus, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia) for compiling a consortium, which will be used for bioaugmentation strategies in soils contaminated with these fuels. This consortium exhibited high potential for biodegradation of biodiesel, and might be an efficient alternative for cleaning up these contaminated environments.
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Affiliation(s)
- Daniel Derrossi Meyer
- Department of Microbiology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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29
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Nie Y, Liang J, Fang H, Tang YQ, Wu XL. Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation. Appl Environ Microbiol 2011; 77:7279-88. [PMID: 21873474 PMCID: PMC3194844 DOI: 10.1128/aem.00203-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 08/19/2011] [Indexed: 11/20/2022] Open
Abstract
Two alkane hydroxylase-rubredoxin fusion gene homologs (alkW1 and alkW2) were cloned from a Dietzia strain, designated DQ12-45-1b, which can grow on crude oil and n-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1- and AlkG2-type Rds. Expression of the alkW1 gene in DQ12-45-1b was induced when cells were grown on C(8) to C(32) n-alkanes as sole carbon sources, but expression of the alkW2 gene was not detected. Functional heterologous expression in an alkB deletion mutant of Pseudomonas fluorescens KOB2Δ1 suggested the alkW1 could restore the growth of KOB2Δ1 on C(14) and C(16) n-alkanes and induce faster growth on C(18) to C(32) n-alkanes than alkW1ΔRd, the Rd domain deletion mutant gene of alkW1, which also caused faster growth than KOB2Δ1 itself. In addition, the artificial fusion of AlkB from the Gram-negative P. fluorescens CHA0 and the Rds from both Gram-negative P. fluorescens CHA0 and Gram-positive Dietzia sp. DQ12-45-1b significantly increased the degradation of C(32) alkane compared to that seen with AlkB itself. In conclusion, the alkW1 gene cloned from Dietzia species encoded an alkane hydroxylase which increased growth on and degradation of n-alkanes up to C(32) in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain n-alkanes (such as C(32)) in the Gram-negative bacterium.
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Affiliation(s)
- Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Jieliang Liang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Hui Fang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Yue-Qin Tang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
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30
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Song X, Xu Y, Li G, Zhang Y, Huang T, Hu Z. Isolation, characterization of Rhodococcus sp. P14 capable of degrading high-molecular-weight polycyclic aromatic hydrocarbons and aliphatic hydrocarbons. MARINE POLLUTION BULLETIN 2011; 62:2122-2128. [PMID: 21871639 DOI: 10.1016/j.marpolbul.2011.07.013] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 07/10/2011] [Accepted: 07/15/2011] [Indexed: 05/31/2023]
Abstract
Rhodococcus sp. P14 was isolated from crude oil-contaminated sediments. This strain was capable of utilizing three to five rings polycyclic aromatic hydrocarbons (PAHs) including phenanthrene (Phe), pyrene (Pyr), and benzo[a]pyrene (BaP) as a sole carbon and energy source. After cultivated with 50mg/L of each PAH, strain P14 removed 43% Phe, 34% Pyr and 30% BaP in 30 d. Four different hydroxyphenanthrene products derived from Phe by strain P14 (1,2,3,4-hydroxyphenanthrene) were detected using SPME-GC-MS. Strain P14 also was capable of degrading mineral oil with n-alkanes of C17 to C21 carbon chain length. Compared with glucose-grown cells, PAHs-grown cells had decreased contents of shorter-chain length fatty acids (≤ C16:0), increased contents of C18:0, Me-C19:0 and disappeared odd-number carbon chain fatty acids. The contents of unsaturated C19:1, Me-C19:0 increased and C18:0 decreased in mineral oil-grown cells. At the same time, the strain P14 tended to float when cultivated in mineral oil-supplemented liquid medium. The degradation capability of P14 to alkane and PAHs and its floating characteristics will be very helpful for future's application in oil-spill bioremediation.
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Affiliation(s)
- Xiaohui Song
- Department of Biology, Shantou University, Shantou 515063, PR China
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31
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Complete genome sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil. J Bacteriol 2011; 193:4538-9. [PMID: 21725023 DOI: 10.1128/jb.05388-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amycolicicoccus subflavus DQS3-9A1(T), isolated from crude oil-polluted soil in the Daqing Oilfield in China, is a type strain of a newly published novel species in the novel genus Amycolicicoccus. Here we report the complete genome of DQS3-9A1(T)and genes associated with oil-polluted environment.
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