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Gyasi SF, Sarfo MK, Kabo-Bah AT, Adu B, Appiah AS, Serfor-Armah Y. In vitro assessment of crude oil degradation by Acinetobacter junii and Alcanivorax xenomutans isolated from the coast of Ghana. Heliyon 2024; 10:e24994. [PMID: 38318038 PMCID: PMC10838785 DOI: 10.1016/j.heliyon.2024.e24994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
This study was aimed at using in vitro microcosm experiments to assess crude oil degradation efficiency of Acinetobacter junii and Alcanivorax xenomutans isolated along Ghana's coast. Uncontaminated seawater from selected locations along the coast was used to isolate bacterial species by employing enrichment culture procedures with crude oil as the only carbon source. The isolates were identified by means of the extended direct colony transfer method of the Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectroscopy (MALDI-TOF MS), as Acinetobacter junii, and Alcanivorax xenomutans. Remediation tests showed that Acinetobacter junii yielded degradation efficiencies of 27.59 %, 41.38 % and 57.47 %. Whereas efficiencies of 21.14 %, 32.18 % and 43.68 % were recorded by Alcanivorax xenomutans representing 15, 30 and 45 days respectively. Consortia of Acinetobacter junii, and Alcanivorax xenomutans also yielded 32.18 %, 48.28 % and 62.07 % for the selected days respectively. Phylogenetic characterization using ClustalW and BLAST of sequences generated from the Oxford Nanopore Sequencing technique, showed that the Ghanaian isolates clustered with Alcanivorax xenomutans and Acinetobacter junii species respectively. An analysis of the sequenced data for the 1394-bp portion of the 16S rRNA gene of the isolates revealed >99 % sequence identity with the isolates present on the GenBank database. The isolates of closest identity were Alcanivorax xenomutans and Acinetobacter junii with accession numbers, NR_133958.1 and KJ147060.1 respectively. Acinetobacter junii and Alcanivorax xenomutans isolated from Ghana's coast under pristine seawater conditions have therefore demonstrated their capacity to be used for the remediation of crude oil spills.
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Affiliation(s)
- Samuel Fosu Gyasi
- Department of Biological Science, University of Energy and Natural Resources. Sunyani, Ghana
- Centre for Research in Applied Biology, University of Energy and Natural Resources. Sunyani, Ghana
| | - Mark Kwasi Sarfo
- National Nuclear Research Institute, Ghana Atomic Energy Commission, Ghana
| | | | - Bright Adu
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
| | - Andrew Sarkodie Appiah
- Biotechnology Center, Biotechnology and Nuclear Agricultural Research Institute, Ghana Atomic Energy Commission, Ghana
| | - Yaw Serfor-Armah
- School of Nuclear and Allied Sciences, University of Ghana, Legon, Accra, Ghana
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2
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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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3
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Das S, Das N, Choure K, Pandey P. Biodegradation of asphaltene by lipopeptide-biosurfactant producing hydrocarbonoclastic, crude oil degrading Bacillus spp. BIORESOURCE TECHNOLOGY 2023; 382:129198. [PMID: 37201870 DOI: 10.1016/j.biortech.2023.129198] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 05/20/2023]
Abstract
Asphaltene is the most recalcitrant compound in crude oil. Bacteria were isolated from crude oil contaminated soil and their efficiency for hydrocarbon degradation was determined using GC-MS and isolates were screened for biosurfactant production using FT-IR. Two Bacillus spp. having hydrocarbonoclastic and lipo-peptide biosurfactant-producing abilities were experimented for their asphaltene removal potential through oil removal efficiency (ORE%) and asphaltene degradation efficiency (ADE%). B. thuringeinsis SSL1 and B. cereus SSL3 could degrade 76.4% and 67.4% of asphaltene (20gL-1), in vitro, respectively, which is much higher than previous reports. B. thuringiensis SSL1 is recommended for effective breakdown of asphaltene, total petroleum hydrocarbon, and polyaromatic hydrocarbon degradation, aided by its biosurfactants, which is useful for crude oil cleanup. Biosurfactants are important for enhancing the availability of hydrophobic hydrocarbons to bacteria, which is beneficial for efficient crude oil remediation. These findings could lead to more effective strategies for complete clean-up of crude oil pollution.
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Affiliation(s)
- Sandeep Das
- Soil and Environment Microbiology Laboratory, Department of Microbiology, Assam University, Silchar 788011, Assam, India
| | - Nandita Das
- Soil and Environment Microbiology Laboratory, Department of Microbiology, Assam University, Silchar 788011, Assam, India
| | - Kamlesh Choure
- Department of Biotechnology, AKS University, Satna 485001, Madhya Pradesh, India
| | - Piyush Pandey
- Soil and Environment Microbiology Laboratory, Department of Microbiology, Assam University, Silchar 788011, Assam, India.
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4
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Ravi A, Ravuri M, Krishnan R, Narenkumar J, Anu K, Alsalhi MS, Devanesan S, Kamala-Kannan S, Rajasekar A. Characterization of petroleum degrading bacteria and its optimization conditions on effective utilization of petroleum hydrocarbons. Microbiol Res 2022; 265:127184. [PMID: 36115172 DOI: 10.1016/j.micres.2022.127184] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/17/2022] [Accepted: 09/02/2022] [Indexed: 11/27/2022]
Abstract
Hydrocarbon contamination is continuing to be a serious environmental problem because of their toxicity. Hydrocarbon components have been known to be carcinogens and neurotoxic organic pollutants. The physical and chemical methods of petroleum removal have become ineffective and also are very costly. Therefore, bioremediation is considered the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization.The current study also concentrates on bioremediation of petroleum products by bacterium isolated from petroleum hydrocarbon contaminated soil. The current work shows that bacterial strains obtained from a petroleum hydrocarbon contaminated environment may degrade petroleum compounds. Two strains Bacillus licheniformis ARMP2 and Pseudomonas aeruginosa ARMP8 were identified as petroleum-degrading bacteria of the isolated bacterial colonies. The best growth conditions for the ARMP2 strain were determined to be pH 9, temperature 29 °C with sodium nitrate as its nitrogen source, whereas for the ARMP8 strain the optimal growth was found at pH 7, temperature 39 °C, and ammonium chloride as the nitrogen source. Both strains were shown to be effective at degrading petroleum chemicals confirmed by GCMS. Overall petroleum product degradation efficiency of the strains ARMP2 and ARMP8 was about 88 % and 73 % respectively in 48 h.The strains Bacillus licheniformis ARMP2 and Pseudomonas aeruginosa ARMP8 were shown to be effective at degrading petroleum compounds in the current study. Even greater results might be obtained if the organisms were utilised in consortia or the degradation time period was extended.
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Affiliation(s)
- Ashwini Ravi
- Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous), Chennai, Tamilnadu 600106, India.
| | - Mounesh Ravuri
- Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous), Chennai, Tamilnadu 600106, India
| | - Ramkishore Krishnan
- Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous), Chennai, Tamilnadu 600106, India
| | - Jayaraman Narenkumar
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, Selaiyur, Chennai, Tamil Nadu 600073, India
| | - Kasi Anu
- PG and Research Department of Zoology, Auxilium College for Women (Autonomous), Gandhinagar, Vellore, Tamilnadu 632007, India
| | - Mohamad S Alsalhi
- Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box, 2455, Riyadh, 11451, Saudi Arabia
| | - Sandhanasamy Devanesan
- Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box, 2455, Riyadh, 11451, Saudi Arabia.
| | - Seralathan Kamala-Kannan
- Division of Biotechnology Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Science, Jeonbuk National University, Iksan 54596, South Korea
| | - Aruliah Rajasekar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu 632115, India.
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5
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Gonzáles M, Pucci G. Aislamientos de bacterias post tratamiento con gasoil - agua y centrifugación de fondo de tanques petroleros. REVISTA PERUANA DE BIOLOGÍA 2022. [DOI: 10.15381/rpb.v29i2.21526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
En la industria petrolera se almacenan grandes cantidades de hidrocarburos en tanques en las diferentes etapas de extracción y procesamiento del crudo hasta su refinamiento. Esto genera un residuo denominado fondo de tanque, es una emulsión estable de sedimentos agua e hidrocarburos. Este trabajo tuvo como objeto estudiar las bacterias que están presentes en el sedimento después de la primera etapa de tratamiento con gasoil, agua, temperatura y posterior centrifugación. El sedimento, considerado por la legislación como residuo peligroso se le realizo un estudio bacteriológico, que consistió en recuento, aislamiento e identifican de bacterias. Se obtuvieron 34 cepas de las cuales 86.1% pertenecieron al género Bacillus. Las mismas presentaron capacidad para desarrollar en alguno de los siguientes hidrocarburos o mezclas de hidrocarburos gasoil, kerosene, hexadecano y ciclohexano.
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6
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Liu H, Prajapati V, Prajapati S, Bais H, Lu J. Comparative Genome Analysis of Bacillus amyloliquefaciens Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes. Front Genet 2021; 12:724217. [PMID: 34659348 PMCID: PMC8514880 DOI: 10.3389/fgene.2021.724217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
Bacillus amyloliquefaciens is a gram-positive, nonpathogenic, endospore-forming, member of a group of free-living soil bacteria with a variety of traits including plant growth promotion, production of antifungal and antibacterial metabolites, and production of industrially important enzymes. We have attempted to reconstruct the biogeographical structure according to functional traits and the evolutionary lineage of B. amyloliquefaciens using comparative genomics analysis. All the available 96 genomes of B. amyloliquefaciens strains were curated from the NCBI genome database, having a variety of important functionalities in all sectors keeping a high focus on agricultural aspects. In-depth analysis was carried out to deduce the orthologous gene groups and whole-genome similarity. Pan genome analysis revealed that shell genes, soft core genes, core genes, and cloud genes comprise 17.09, 5.48, 8.96, and 68.47%, respectively, which demonstrates that genomes are very different in the gene content. It also indicates that the strains may have flexible environmental adaptability or versatile functions. Phylogenetic analysis showed that B. amyloliquefaciens is divided into two clades, and clade 2 is further dived into two different clusters. This reflects the difference in the sequence similarity and diversification that happened in the B. amyloliquefaciens genome. The majority of plant-associated strains of B. amyloliquefaciens were grouped in clade 2 (73 strains), while food-associated strains were in clade 1 (23 strains). Genome mining has been adopted to deduce antimicrobial resistance and virulence genes and their prevalence among all strains. The genes tmrB and yuaB codes for tunicamycin resistance protein and hydrophobic coat forming protein only exist in clade 2, while clpP, which codes for serine proteases, is only in clade 1. Genome plasticity of all strains of B. amyloliquefaciens reflects their adaption to different niches.
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Affiliation(s)
- Hualin Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Vimalkumar Prajapati
- Division of Microbiology and Environmental, Biotechnology, Aspee Shakilam Biotechnology Institute, Navsari Agricultural University, Surat, India
| | - Shobha Prajapati
- SVP-A School of Sardar Vallabhbhai National Institute of Technology, Surat, India
| | - Harsh Bais
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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7
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Hou N, Wang Q, Sun Y, Li X, Song Q, Jiang X, Li B, Zhao X, Zang H, Li D, Li C. A novel biodemulsifier of Bacillus mojavensis XH1 - Oxalate decarboxylase with the potential for demulsification of oilfield emulsion. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124737. [PMID: 33321372 DOI: 10.1016/j.jhazmat.2020.124737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
In recent years, special attention has been devoted to biodemulsifiers as a new type of environment-friendly demulsifiers. A novel biodemulsifying oxalate decarboxylase (OxdC) secreted by Bacillus mojavensis XH1 is reported in the present study. A genome-wide comparison showed that strains with high demulsification efficiencies all possess alkane degradation genes. An analysis of the differentially expressed genes and proteins induced by different substrates showed that OxdC secreted by XH1 was an effective demulsifier. Moreover, the demulsification ability was verified by prokaryotic gene expression, knockout and complementation analyses. OxdC from XH1 exhibited a strong demulsification capacity and significantly outperformed the model protein Bacillus subtilis 168 OxdC (Yvrk), which shared a high amino acid similarity but showed limited demulsification ability. Based on a comparison of the structural characteristics, the hydrophobic amino acids on the surface of OxdC were identified as a key factor driving the favorable demulsification activity of XH1. The metabolic pathways of XH1 used liquid paraffin and glucose as substrates, illustrating that hydrocarbons are necessary for biodemulsifier secretion. The present study provides new insight into the application of OxdC as an additional genetic resource in biodemulsification.
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Affiliation(s)
- Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Qiaoruo Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Yang Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xianyue Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Qiuying Song
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xinxin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Baoxin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Dapeng Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
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8
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Ke CY, Lu GM, Wei YL, Sun WJ, Hui JF, Zheng XY, Zhang QZ, Zhang XL. Biodegradation of crude oil by Chelatococcus daeguensis HB-4 and its potential for microbial enhanced oil recovery (MEOR) in heavy oil reservoirs. BIORESOURCE TECHNOLOGY 2019; 287:121442. [PMID: 31085429 DOI: 10.1016/j.biortech.2019.121442] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 06/09/2023]
Abstract
Biodegradation of crude heavy oil was investigated with Chelatococcus daeguensis HB-4 that was isolated from the produced fluid of Baolige Oilfield in China. Batch growth characterization and crude oil degradation tests confirmed HB-4 to be facultative anaerobic and able to degrade heavy oil. The oil degradation was found to occur through degrading long hydrocarbons chains to shorter ones, resulting in oil viscosity reduction. By mixing crude oil with glucose, or using sole crude oil as carbon source, the content of light fractions (C8-C22) increased by 4.97% while heavy fractions (C23-C37) decreased by 7.98%. It was also found that bioemulsifiers were produced rather than commonly observed biosurfactants in the fermentation process, which was attributed to the extracellular degradation of hydrocarbons. Core flooding tests demonstrated 20.5% oil recovery by microbial enhancement, and 59.8% viscosity reduction, showing potential of strain HB-4 for application in the oil industry, especially in enhanced heavy oil recovery.
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Affiliation(s)
- Cong-Yu Ke
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Guo-Min Lu
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Ying-Lin Wei
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Wu-Juan Sun
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Jun-Feng Hui
- School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China
| | - Xiao-Yan Zheng
- School of Chemical Engineering, Northwest University, Xi'an 710069, Shaanxi, China
| | - Qun-Zheng Zhang
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Xun-Li Zhang
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China.
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9
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Iqbal A, Arshad M, Karthikeyan R, Gentry TJ, Rashid J, Ahmed I, Schwab AP. Diesel degrading bacterial endophytes with plant growth promoting potential isolated from a petroleum storage facility. 3 Biotech 2019; 9:35. [PMID: 30622873 DOI: 10.1007/s13205-018-1561-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 12/29/2018] [Indexed: 12/15/2022] Open
Abstract
Thirteen (13) endophytic bacterial strains were isolated from Echinochloa crus-galli (Cockspur grass) and Cynodon dactylon (Bermuda grass) growing in an oil-contaminated site at a petroleum storage and transportation facility. Of the 13 strains assessed for their potential to degrade monoaromatic compounds (phenol, toluene, and xylene) and diesel and for their plant growth promoting (PGP) ability (phosphate solubilization, siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase production), isolate J10 (identified as Pseudomonas sp. by 16S rRNA gene sequencing) was found to the best diesel biodegrader with the best PGP traits. The Monod model used for Pseudomonas sp. J10 growth kinetics on diesel fuel as the sole carbon source showed that the maximum specific bacterial growth rate was 0.0644 h- 1 and the half velocity constant (K s ) was estimated as 4570 mg L- 1. The overall growth yield coefficient and apparent growth yield were determined to be 0.271 g h- 1 and 0.127 g cells/g substrate, respectively. Pseudomonas sp. J10 removed 69% diesel in four days as determined by gas chromatographic (GC) analysis. These findings could assist in developing an endophyte assisted efficient diesel biodegradation system using Pseudomonas sp. J10 isolated from Echinochloa crus-galli.
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Affiliation(s)
- Aneela Iqbal
- 1Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Sector H-12, Islamabad, 44000 Pakistan
- 2Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77843 USA
- 3Soil and Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Muhammad Arshad
- 1Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Sector H-12, Islamabad, 44000 Pakistan
| | - Raghupathy Karthikeyan
- 2Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77843 USA
| | - Terry J Gentry
- 3Soil and Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jamshaid Rashid
- 4Department of Environmental Science, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320 Pakistan
| | - Iftikhar Ahmed
- 5Bio-resource Conservation Institute (BCI), National Culture Collection of Pakistan (NCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500 Pakistan
| | - Arthur Paul Schwab
- 3Soil and Crop Sciences, Texas A&M University, College Station, TX 77843 USA
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10
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Belbahri L, Chenari Bouket A, Rekik I, Alenezi FN, Vallat A, Luptakova L, Petrovova E, Oszako T, Cherrad S, Vacher S, Rateb ME. Comparative Genomics of Bacillus amyloliquefaciens Strains Reveals a Core Genome with Traits for Habitat Adaptation and a Secondary Metabolites Rich Accessory Genome. Front Microbiol 2017; 8:1438. [PMID: 28824571 PMCID: PMC5541019 DOI: 10.3389/fmicb.2017.01438] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 07/17/2017] [Indexed: 12/04/2022] Open
Abstract
The Gram positive, non-pathogenic endospore-forming soil inhabiting prokaryote Bacillus amyloliquefaciens is a plant growth-promoting rhizobacterium. Bacillus amyloliquefaciens processes wide biocontrol abilities and numerous strains have been reported to suppress diverse bacterial, fungal and fungal-like pathogens. Knowledge about strain level biocontrol abilities is warranted to translate this knowledge into developing more efficient biocontrol agents and bio-fertilizers. Ever-expanding genome studies of B. amyloliquefaciens are showing tremendous increase in strain-specific new secondary metabolite clusters which play key roles in the suppression of pathogens and plant growth promotion. In this report, we have used genome mining of all sequenced B. amyloliquefaciens genomes to highlight species boundaries, the diverse strategies used by different strains to promote plant growth and the diversity of their secondary metabolites. Genome composition of the targeted strains suggest regions of genomic plasticity that shape the structure and function of these genomes and govern strain adaptation to different niches. Our results indicated that B. amyloliquefaciens: (i) suffer taxonomic imprecision that blurs the debate over inter-strain genome diversity and dynamics, (ii) have diverse strategies to promote plant growth and development, (iii) have an unlocked, yet to be delimited impressive arsenal of secondary metabolites and products, (iv) have large number of so-called orphan gene clusters, i.e., biosynthetic clusters for which the corresponding metabolites are yet unknown, and (v) have a dynamic pan genome with a secondary metabolite rich accessory genome.
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Affiliation(s)
- Lassaad Belbahri
- Laboratory of Soil Biology, University of NeuchatelNeuchatel, Switzerland.,NextBiotechAgareb, Tunisia
| | - Ali Chenari Bouket
- NextBiotechAgareb, Tunisia.,Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan.,Young Researchers and Elite Club, Tabriz Branch, Islamic Azad UniversityTabriz, Iran
| | | | | | - Armelle Vallat
- Neuchâtel Platform of Analytical Chemistry, Institute of Chemistry, University of NeuchâtelNeuchâtel, Switzerland
| | - Lenka Luptakova
- NextBiotechAgareb, Tunisia.,Department of Biology and Genetics, Institute of Biology, Zoology and Radiobiology, University of Veterinary Medicine and PharmacyKosice, Slovakia
| | - Eva Petrovova
- Institute of Anatomy, University of Veterinary Medicine and PharmacyKosice, Slovakia
| | | | | | | | - Mostafa E Rateb
- School of Science and Sport, University of the West of ScotlandPaisley, United Kingdom
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11
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Shen F, Li Y, Zhang M, Awasthi MK, Ali A, Li R, Wang Q, Zhang Z. Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA. Sci Rep 2016; 6:39148. [PMID: 27958371 PMCID: PMC5153631 DOI: 10.1038/srep39148] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/18/2016] [Indexed: 02/01/2023] Open
Abstract
In this study, we investigated the influence of heavy metals (HM) on total soil bacterial population and its diversity pattern from 10 km distance of a Zinc smelter in Feng County, Qinling Mountain, China. We characterized and identified the bacterial community in a HM polluted soil using 16S rDNA technology. Out results indicated that the maximum soil HM concentration and the minimum bacterial population were observed in S2 soil, whereas bacterial diversity raised with the sampling distance increased. The bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria in cornfield soils, except Fimicutes phylum which dominated in hilly area soil. The soil CEC, humic acid (HA)/fulvic acid (FA) and microbial OTUs increased with the sampling distance increased. Shewanella, Halomonas and Escherichia genera were highly tolerant to HM stress in both cultivated and non-cultivated soil. Finally, we found a consistent correlation of bacterial diversity with total HM and SOM along the sampling distance surrounding the zinc smelter, which could provide a new insight into the bacterial community-assisted and phytoremediation of HM contaminated soils.
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MESH Headings
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/growth & development
- Benzopyrans/toxicity
- Biodiversity
- Cadmium/toxicity
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Humic Substances/toxicity
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
- Soil Microbiology
- Soil Pollutants/chemistry
- Soil Pollutants/toxicity
- Zinc/toxicity
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Affiliation(s)
- Feng Shen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanxia Li
- School of Environment, Beijing Normal University, Beijing, China
| | - Min Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Amjad Ali
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
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12
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Zhang J, Xue Q, Gao H, Lai H, Wang P. Production of lipopeptide biosurfactants by Bacillus atrophaeus 5-2a and their potential use in microbial enhanced oil recovery. Microb Cell Fact 2016; 15:168. [PMID: 27716284 PMCID: PMC5048436 DOI: 10.1186/s12934-016-0574-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/28/2016] [Indexed: 12/02/2022] Open
Abstract
Background Lipopeptides are known as promising microbial surfactants and have been successfully used in enhancing oil recovery in extreme environmental conditions. A biosurfactant-producing strain, Bacillus atrophaeus 5-2a, was recently isolated from an oil-contaminated soil in the Ansai oilfield, Northwest China. In this study, we evaluated the crude oil removal efficiency of lipopeptide biosurfactants produced by B. atrophaeus 5-2a and their feasibility for use in microbial enhanced oil recovery. Results The production of biosurfactants by B. atrophaeus 5-2a was tested in culture media containing eight carbon sources and nitrogen sources. The production of a crude biosurfactant was 0.77 g L−1 and its surface tension was 26.52 ± 0.057 mN m−1 in a basal medium containing brown sugar (carbon source) and urea (nitrogen source). The biosurfactants produced by the strain 5-2a demonstrated excellent oil spreading activity and created a stable emulsion with paraffin oil. The stability of the biosurfactants was assessed under a wide range of environmental conditions, including temperature (up to 120 °C), pH (2–13), and salinity (0–50 %, w/v). The biosurfactants were found to retain surface-active properties under the extreme conditions. Additionally, the biosurfactants were successful in a test to simulate microbial enhanced oil recovery, removing 90.0 and 93.9 % of crude oil adsorbed on sand and filter paper, respectively. Fourier transform infrared spectroscopy showed that the biosurfactants were a mixture of lipopeptides, which are powerful biosurfactants commonly produced by Bacillus species. Conclusions The study highlights the usefulness of optimization of carbon and nitrogen sources and their effects on the biosurfactants production and further emphasizes on the potential of lipopeptide biosurfactants produced by B. atrophaeus 5-2a for crude oil removal. The favorable properties of the lipopeptide biosurfactants make them good candidates for application in the bioremediation of oil-contaminated sites and microbial enhanced oil recovery process.
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Affiliation(s)
- Junhui Zhang
- College of Natural Resources and Environment, Northwest A & F University, 3 Taicheng Road, 712100, Yangling, China
| | - Quanhong Xue
- College of Natural Resources and Environment, Northwest A & F University, 3 Taicheng Road, 712100, Yangling, China.
| | - Hui Gao
- College of Natural Resources and Environment, Northwest A & F University, 3 Taicheng Road, 712100, Yangling, China
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A & F University, 3 Taicheng Road, 712100, Yangling, China
| | - Ping Wang
- College of Earth Sciences and Resources, Chang'an University, 710055, Xi'an, China
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