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Pinto OHB, Costa FS, Rodrigues GR, da Costa RA, da Rocha Fernandes G, Júnior ORP, Barreto CC. Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids. Microb Ecol 2021; 81:169-179. [PMID: 32617619 DOI: 10.1007/s00248-020-01548-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.
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Affiliation(s)
- Otávio Henrique Bezerra Pinto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
- Laboratory of Enzymology, Institute of Biological Sciences, Department of Cell Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Flávio Silva Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Gisele Regina Rodrigues
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
| | - Rosiane Andrade da Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
| | - Gabriel da Rocha Fernandes
- Research Center René Rachou, Oswaldo Cruz Foundation (Fiocruz), Avenida Augusto de Lima 1715, Barro Preto, Belo Horizonte, 30190-002, Brazil
| | - Osmindo Rodrigues Pires Júnior
- Department of Physiological Sciences, Institute of Biological Sciences, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Cristine Chaves Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil.
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Yuan L, Wang L, Li ZH, Zhang MQ, Shao W, Sheng GP. Antibiotic resistance and microbiota in the gut of Chinese four major freshwater carp from retail markets. Environ Pollut 2019; 255:113327. [PMID: 31600703 DOI: 10.1016/j.envpol.2019.113327] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/22/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
Fish-associated antibiotic resistance genes (ARGs) have attracted increasing attention due to their potential risks to human beings via the food chain. However, data are scarce regarding the antibiotic resistance in fish themselves. Herein, the antibiotic resistance genes (ARGs) were assessed in the gut of four major Chinese freshwater carp (i.e., silver carp, grass carp, bighead carp, and crucian carp) from food retail markets. Results show that the abundances of target ARGs (e.g., tetA, tetO, tetQ, tetW, sulI, sulII, and blaTEM-1) and class 1 integrase (intI1) were in the range 9.4 × 10-6 - 1.6 × 10-1 and 6.7 × 10-5 - 5.2 × 10-2 gene copies per 16S rRNA gene, respectively. The sulI, sulII, and tetQ strongly correlated with silver and mercury resistance genes (e.g., silE and merR). The microbial taxa of fish gut could be partly separated among retail markets based on the PCA analysis. About 15.0% of the OTUs in fish gut were shared and 74.5% of the shared OTUs were identified as Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, and Proteobacteria. These phyla may constitute the core microbiota in the guts of the four Chinese freshwater carp. The possible ARG hosts were revealed based on the network analysis, and the presence of pathogen-associated resistant genera in fish gut highlights the need to fully understand their potential human health risks.
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Affiliation(s)
- Li Yuan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Li Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Zheng-Hao Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Ming-Qi Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Wei Shao
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Guo-Ping Sheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei 230026, China.
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Uddin M, Chen J, Qiao X, Tian R, Arafat Y, Yang X. Bacterial community variations in paddy soils induced by application of veterinary antibiotics in plant-soil systems. Ecotoxicol Environ Saf 2019; 167:44-53. [PMID: 30292975 DOI: 10.1016/j.ecoenv.2018.09.101] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
Soil bacterial communities have complex regulatory networks, which are mainly associated with soil fertility and ecological functions, and are likely to be disturbed due to antibiotics applications. The impact of antibiotics, particularly in mixtures form, on bacterial communities in different paddy soils is poorly understood. Using pyrosequencing techniques of 16 S rRNA genes, this study investigated the synergistic effects of veterinary antibiotics (sulfadiazine, sulfamethoxazole, trimethoprim, florfenicol, and clarithromycin) on bacterial communities in a soil-bacteria-plant system. Rice was grown under controlled greenhouse conditions where unplanted and planted treatments were doped with 200 µg kg-1 of combined antibiotics over a period of 3 months. Bacterial richness remained unaltered, while a significant decline was observed in bacterial diversity due to antibiotics in the four paddy soils. Bacteroidetes and Acidobacteria were increased, while Actinobacteria and Firmicutes decreased under antibiotics exposure. Despite antibiotics perturbation, compositional variations were mainly attributed to the different paddy soils which harbor distinct bacterial communities. Haliangium and Gaiella were among the sensitive genera that were negatively correlated to antibiotics perturbation. Additionally, electrical conductivity, total organic carbon, and total nitrogen of soil solution were the key physiochemical indices which significantly influenced the structure of bacterial communities in the paddy soils. These findings expanded our knowledge of effects from synergistic antibiotics application and variations in bacterial communities among different paddy soils.
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Affiliation(s)
- Misbah Uddin
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xianliang Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Run Tian
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yasir Arafat
- Key Laboratory of Fujian Province for Agroecological Process and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou 35002, China
| | - Xiaojing Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Liu B, Zhang R, Xia X, Zhang W, Gao M, Lu Q, Lin K. Toxicity responses of bacterial community as a biological indicator after repeated exposure to lead (Pb) in the presence of decabromodiphenyl ether (BDE209). Environ Sci Pollut Res Int 2018; 25:36278-36286. [PMID: 30368700 DOI: 10.1007/s11356-018-3342-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
Continuous exposure of chemicals could cause various environmental impacts. Decabromodiphenyl ether (BDE209) and lead (Pb) can co-exist and are discharged simultaneously at e-waste recycling sites (EWRSs). Extensive concerns have been attracted by their toxic effects on soil microorganisms. Thus, by using high-throughput sequencing, this study explored bacterial community responses in a soil system after repeated Pb exposure in the presence of BDE209 in the laboratory during 90-day indoor incubation period. Gene sequencing of 16S rDNA performed on an Illumina MiSeq platform proved that one-off Pb exposure caused higher microbial abundance and community diversity. Additionally, both repetitive Pb treatment and exogenous BDE209 input could change bacterial community composition. Twenty-three different bacterial phyla were detected in the soil samples, while more than 90% of the sequences in each treatment belonged to a narrow variety. The sequence analyses elucidated that Proteobacteria, Acidobacteria, and Bacteroidetes were the top three dominant phyla. Our observations could provide a few insights into the ecological risks of Pb and BDE209 co-existed contamination in soils at EWRSs.
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Affiliation(s)
- Bo Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Pharmaceutical School, Shanghai, 200135, China
| | - Rong Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiaoqian Xia
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wei Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
| | - Mengwen Gao
- Baowu Group Environmental Resources Technology Co., Ltd., Shanghai, 200439, China
| | - Qiang Lu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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Delgado-Balbuena L, Bello-López JM, Navarro-Noya YE, Rodríguez-Valentín A, Luna-Guido ML, Dendooven L. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils. PLoS One 2016; 11:e0160991. [PMID: 27727277 PMCID: PMC5058544 DOI: 10.1371/journal.pone.0160991] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 07/28/2016] [Indexed: 01/13/2023] Open
Abstract
Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the effect of application of carrot residue, earthworms or the surfactant on the bacterial community structure was more accentuated in the arable soil than in the pasture soil. It was found that removal of anthracene was not linked to changes in the bacterial community structure.
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Affiliation(s)
| | | | | | | | | | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, D.F., Mexico
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Cai Z, Ma J, Wang J, Cai J, Yang G, Zhao X. Impact of the novel neonicotinoid insecticide Paichongding on bacterial communities in yellow loam and Huangshi soils. Environ Sci Pollut Res Int 2016; 23:5134-5142. [PMID: 26552792 DOI: 10.1007/s11356-015-5733-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/03/2015] [Indexed: 06/05/2023]
Abstract
Insecticides are widely sprayed in modern agriculture for ensuring the crop yield, which could also lead to contamination and insecticide residue in soils. Paichongding (IPP) is a novel neonicotinoid insecticide and was developed recently in China. Soil bacterial community, diversity, and community composition vary widely depending on environmental factors. As for now, little is known about bacterial species thriving, bacterial community diversity, and structure in IPP-spraying soils. In present study, IPP degradation in yellow loam and Huangshi soils was investigated, and bacterial communities and diversity were examined in soil without IPP spray and with IPP spray through pyrosequencing of 16S ribosomal RNA (rRNA) gene amplicons. The degradation ratio of IPP at 60 days after treatment (DAT) reached 51.22 and 34.01 % in yellow loam and Huangshi soil, respectively. A higher richness of operational taxonomic units (OTUs) was found in yellow loam soil (867 OTUs) and Huangshi soil (762 OTUs) without IPP spray while OUTs were relatively low in IPP-spraying soils. The community composition also differed both in phyla and genus level between these two environmental conditions. Proteobacteria, Firmicutes, Planctomycetes, Chloroflexi, Armatimonadetes, and Chlorobi were stimulated to increase after IPP application, while IPP inhibited the phyla of Bacteroidetes, Actinobacteria, and Acidobacteria.
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Affiliation(s)
- Zhiqiang Cai
- Laboratory of Applied Microbiology, School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, 213164, China.
| | - Jiangtao Ma
- Laboratory of Applied Microbiology, School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, 213164, China
| | - Jing Wang
- Laboratory of Applied Microbiology, School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, 213164, China
| | - Jinyan Cai
- Laboratory of Applied Microbiology, School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, 213164, China
| | - Guanghua Yang
- Laboratory of Applied Microbiology, School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, 213164, China
| | - Xiyue Zhao
- Laboratory of Applied Microbiology, School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou, 213164, China.
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Liu X, Cheng X, Wang H, Wang K, Qiao K. Effect of fumigation with 1,3-dichloropropene on soil bacterial communities. Chemosphere 2015; 139:379-385. [PMID: 26210186 DOI: 10.1016/j.chemosphere.2015.07.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 05/20/2023]
Abstract
1,3-Dichloropropene (1,3-D) is a potential candidate as a soil fumigant because of the restriction of methyl bromide (MB) in soil fumigation. So far, little is known about the bacteria diversity in 1,3-D fumigated soil. Therefore, the impact of 1,3-D on soil bacterial community was determined by the 16S rRNA gene amplicon 454 sequencing. A total of 230,617 valid reads and 19,366 OTUs were obtained from the thirteen samples. 454 sequencing results revealed that Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria and Firmicutes were predominant phylum in soils. Bacterial diversity was affected initially, while recovered in the later treatments and soils from 1,3-D treatment plots had a higher bacterial diversity. The results of this study demonstrated that 1,3-D had only a short-term and transitory impact on the indigenous soil microbial community. Our study would provide useful information for evaluating ecological safety of 1,3-D in China.
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Affiliation(s)
- Xiumei Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Xingkai Cheng
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Hongyan Wang
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, People's Republic of China.
| | - Kaiyun Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
| | - Kang Qiao
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, People's Republic of China.
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Abed RMM, Al-Kindi S, Al-Kharusi S. Diversity of bacterial communities along a petroleum contamination gradient in desert soils. Microb Ecol 2015; 69:95-105. [PMID: 25103912 DOI: 10.1007/s00248-014-0475-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P < 0.0001) and shared less than 20 % of their operational taxonomic units (OTUs). OTU richness was relatively higher in the soils with the higher oil pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.
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Affiliation(s)
- Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P.O. Box: 36, 123 Al Khoud, Muscat, Sultanate of Oman,
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