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Zhang X, Zhang G, Yan Q, Ahmad B, Pei J, Huang L. Quality variation and salt-alkali-tolerance mechanism of Cynomorium songaricum: Interacting from microbiome-transcriptome-metabolome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170801. [PMID: 38340858 DOI: 10.1016/j.scitotenv.2024.170801] [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: 11/24/2023] [Revised: 01/22/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Addressing soil salinization and implementing sustainable practices for cultivating cash crops on saline-alkali land is a prominent global challenge. Cynomorium songaricum is an important salt-alkali tolerant medicinal plant capable of adapting to saline-alkali environments. In this study, two typical ecotypes of C. songaricum from the desert-steppe (DS) and saline-alkali land (SAL) habitats were selected. Through the integration of multi-omics with machine learning, the rhizosphere microbial communities, genetic maps, and metabolic profiles of two ecotypes were created and the crucial factors for the adaptation of C. songaricum to saline-alkali stress were identified, including 7 keystone OTUs (i.e. Novosphingobium sp., Sinorhizobium meliloti, and Glycomyces sp.), 5 core genes (cell wall-related genes), and 10 most important metabolites (i.e. cucurbitacin D and 3-Hydroxybutyrate) were identified. Our results indicated that under saline-alkali environments, the microbial competition might become more intense, and the microbial community network had the simple but stable structure, accompanied by the changes in the gene expression related to cell wall for adaptation. However, this regulation led to the reduction in active ingredients, such as the accumulation of flavonoids and organic acid, and enhanced the synthesis of bitter substances (cucurbitacin D), resulting in the decrease in the quality of C. songaricum. Therefore, compared to the SAL ecotype, the DS was more suitable for the subsequent development of medicinal and edible products of C. songaricum. Furthermore, to explore the reasons for this quality variation, we constructed a comprehensive microbial-genetic-metabolic regulatory network, revealing that the metabolism of C. songaricum was primarily influenced by genetic factors. These findings not only offer new insights for future research into plant salt-alkali tolerance strategies but also provide a crucial understanding for cultivating high-quality medicinal plants.
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Affiliation(s)
- Xinke Zhang
- Key lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Guoshuai Zhang
- Key lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Qi Yan
- Key lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Bashir Ahmad
- Center for Biotechnology & Microbiology, University of Peshawar, 25000 Peshawar, Pakistan
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China.
| | - Linfang Huang
- Key lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
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2
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Gomeiz AT, Sun Y, Newborn A, Wang ZW, Angelotti B, Van Aken B. Metagenomic Analysis of a Continuous-Flow Aerobic Granulation System for Wastewater Treatment. Microorganisms 2023; 11:2328. [PMID: 37764172 PMCID: PMC10535324 DOI: 10.3390/microorganisms11092328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Aerobic granulation is an emerging process in wastewater treatment that has the potential to accelerate sedimentation of the microbial biomass during secondary treatment. Aerobic granulation has been difficult to achieve in the continuous flow reactors (CFRs) used in modern wastewater treatment plants. Recent research has demonstrated that the alternation of nutrient-abundant (feast) and nutrient-limiting (famine) conditions is able to promote aerobic granulation in a CFR. In this study, we conducted a metagenomic analysis with the objective of characterizing the bacterial composition of the granular biomass developed in three simulated plug flow reactors (PFRs) with different feast-to-famine ratios. Phylogenetic analyses revealed a clear distinction between the bacterial composition of aerobic granules in the pilot simulated PFRs as compared with conventional activated sludge. Larger and denser granules, showing improved sedimentation properties, were observed in the PFR with the longest famine time and were characterized by a greater proportion of bacteria producing abundant extracellular polymeric substances (EPS). Functional metagenomic analysis based on KEGG pathways indicated that the large and dense aerobic granules in the PFR with the longest famine time showed increased functionalities related to secretion systems and quorum sensing, which are characteristics of bacteria in biofilms and aerobic granules. This study contributes to a further understanding of the relationship between aerobic granule morphology and the bacterial composition of the granular biomass.
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Affiliation(s)
- Alison T. Gomeiz
- School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA;
| | - Yewei Sun
- Hazen and Sawyer, 4035 Ridge Top Road, Fairfax, VA 22030, USA;
| | - Aaron Newborn
- Department of Chemistry and Biochemistry, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
| | - Zhi-Wu Wang
- Department of Biological Systems Engineering, Virginia Tech, 1230 Washington St. SW, Blacksburg, VA 24061, USA;
| | - Bob Angelotti
- Upper Occoquan Service Authority, 14631 Compton Rd, Centreville, VA 20121, USA;
| | - Benoit Van Aken
- Department of Chemistry and Biochemistry, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
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3
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Yuan C, Davis AP, Kaya D, Kjellerup BV. Distribution and biodegradation potential of polycyclic aromatic hydrocarbons (PAHs) accumulated in media of a stormwater bioretention. CHEMOSPHERE 2023:139188. [PMID: 37302503 DOI: 10.1016/j.chemosphere.2023.139188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/13/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a group of organic compounds that can be captured and accumulate in the bioretention cell media, which may lead to secondary pollution and ecological risks. This research aimed to understand the spatial distribution of 16 priority PAHs in bioretention media, identify their sources, evaluate their ecological impact, and assess the potential for their aerobic biodegradation. The highest total PAH concentration (25.5 ± 1.7 μg/g) was observed 1.83 m from the inlet and 10-15 cm deep. The individual PAHs with the highest concentrations were benzo [g,h,i]perylene in February (1.8 ± 0.8 μg/g) and pyrene in June (1.8 ± 0.8 μg/g). Data indicated that primary sources of PAHs were fossil fuel combustion and petroleum. The ecological impact and toxicity of the media were assessed by probable effect concentrations (PECs) and benzo [a]pyrene total toxicity equivalent (BaP-TEQ). The results showed that the concentrations of pyrene and chrysene exceeded the PECs, and the average BaP-TEQ was 1.64 μg/g, primarily caused by benzo [a]pyrene. The functional gene (C12O) of PAH-ring cleaving dioxygenases (PAH-RCD) was present in the surface media, which indicated that aerobic biodegradation of PAHs was possible. Overall, this study revealed the PAHs accumulated most at medium distance and depth, where biodegradation may be limited. Thus, the accumulation of PAHs below the surface of the bioretention cell may need to be considered during long-term operation and maintenance.
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Affiliation(s)
- Chen Yuan
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Allen P Davis
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Devrim Kaya
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Birthe V Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA.
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Hu W, Li Z, Ou H, Wang X, Wang Q, Tao Z, Huang S, Huang Y, Wang G, Pan X. Novosphingobium album sp. nov., Novosphingobium organovorum sp. nov. and Novosphingobium mangrovi sp. nov. with the organophosphorus pesticides degrading ability isolated from mangrove sediments. Int J Syst Evol Microbiol 2023; 73. [PMID: 37115596 DOI: 10.1099/ijsem.0.005843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Members of the genus Novosphingobium were frequently isolated from polluted environments and possess great bioremediation potential. Here, three species, designated B2637T, B2580T and B1949T, were isolated from mangrove sediments and might represent novel species in the genus Novosphingobium based on a polyphasic taxonomy study. Phylogenomic analysis revealed that strains B2580T, B1949T and B2637T clustered with Novosphingobium naphthalenivorans NBRC 102051T, 'N. profundi' F72 and N. decolorationis 502str22T, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolates and their closely related species were less than 94 and 54 %, respectively, all below the threshold of species discrimination. The sizes of the genomes of isolates B2580T, B2637T and B1949T ranged from 4.4 to 4.6 Mb, containing 63.3-66.4 % G+C content. Analysis of their genomic sequences identified genes related to pesticide degradation, heavy-metal resistance, nitrogen fixation, antibiotic resistance and sulphur metabolism, revealing the biotechnology potential of these isolates. Except for B2637T, B1949T and B2580T were able to grow in the presence of quinalphos. Results from these polyphasic taxonomic analyses support the affiliation of these strains to three novel species within the genus Novosphingobium, for which we propose the name Novosphingobium album sp. nov. B2580T (=KCTC 72967T=MCCC 1K04555T), Novosphingobium organovorum sp. nov. B1949T (=KCTC 92158T=MCCC 1K03763T) and Novosphingobium mangrovi sp. nov. B2637T (KCTC 72969T=MCCC 1K04460T).
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Affiliation(s)
- Wenjin Hu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Zhe Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Haisheng Ou
- Guangxi Normal University School of Physical Science and Technology, Guilin, 541004, PR China
| | - Xiaochun Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Qiaozhen Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Zhanhua Tao
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Shushi Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Yuanlin Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Guiwen Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Xinli Pan
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
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5
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Dell'Anno F, Joaquim van Zyl L, Trindade M, Buschi E, Cannavacciuolo A, Pepi M, Sansone C, Brunet C, Ianora A, de Pascale D, Golyshin PN, Dell'Anno A, Rastelli E. Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120772. [PMID: 36455775 DOI: 10.1016/j.envpol.2022.120772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.
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Affiliation(s)
- Filippo Dell'Anno
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Leonardo Joaquim van Zyl
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Marla Trindade
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Antonio Cannavacciuolo
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Milva Pepi
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, UK.
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
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6
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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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Long T, Wan H, Zhang J, Wu J, Liang JX, Zhu C. The High-Effective Catalytic Degradation of Benzo[a]pyrene by Mn-Corrolazine Regulated by Oriented External Electric Field: Insight From DFT Study. Front Chem 2022; 10:884105. [PMID: 35720998 PMCID: PMC9201028 DOI: 10.3389/fchem.2022.884105] [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: 02/28/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The degradation of BaP into hydroxybenzo[a]pyrene by Mn-corrolazine and its regulation by an oriented external electronic field (OEEF) were systematically studied using first-principle calculations. Extensive density function calculations showed that the degradation of BaP into hydroxybenzo[a]pyrene by Mn-corrolazine occurs via a three-step process in the absence of OEEF, in which a more toxic and stable epoxide intermediate is generated. However, upon application of OEEF along the intrinsic Mn-O reaction axis, the degradation of BaP into hydroxybenzo[a]pyrene is greatly simplified. The negative charge on the terminal O atom of Mn-OO corrolazine increases with an increase in the OEEF intensity. As the intensity of the OEEF increases over 0.004 a.u., the negatively charged terminal O atom has the ability to directly abstract the positively charged H atom of BaP and the degradation of BaP into hydroxybenzo[a]pyrene can be completed via a one-step process, avoiding the production of more toxic epoxide intermediates.
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Affiliation(s)
- Tairen Long
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, China
| | - Haiyan Wan
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, China
| | | | - Jie Wu
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, China
| | - Jin-Xia Liang
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, China
- *Correspondence: Jin-Xia Liang, ; Chun Zhu,
| | - Chun Zhu
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, China
- *Correspondence: Jin-Xia Liang, ; Chun Zhu,
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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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Ma XX, Jiang ZY, Wu P, Wang YF, Cheng H, Wang YS, Gu JD. Effect of mangrove restoration on sediment properties and bacterial community. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1672-1679. [PMID: 33864552 DOI: 10.1007/s10646-021-02370-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Mangrove reconstruction is an efficient approach for mangrove conservation and restoration. The present study aimed to explore the effects of mangrove reconstruction on sediment properties and bacterial community. The results showed that mangrove restoration greatly promoted sediment fertility, whereas the improvements were more obvious induced by Kandelia obovata when compared to Avicennia marina. In all the samples, the dominant top5 bacterial group were Proteobacteria (48.31-54.52%), Planctomycetes (5.98-8.48%), Bacteroidetes (4.49-11.14%) and Acidobacteria (5.69-8.16%). As for the differences among the groups, the relative abundance of Chloroflexi was higher in the sediments of K. obovata, while Bacteroidetes was more abundant in A. marina group. Furthermore, the two bacterial genera (Rhodoplanes and Novosphingobium) were more dominant in the sediments of K. obovata, while the sediments of A. marina contained higher abundance of Vibrio and Marinobacterium. Besides, bacterial community was highly correlated with mangrove species and sediment property and nutrient status. The results of this study would provide a better understanding of the ecological benefits of mangroves and highlighted the information on biogeochemical processes driven by mangrove restoration and microorganisms.
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Affiliation(s)
- Xiao-Xia Ma
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
- Department of Bioengineering, Jinan University, Guangzhou, 510632, China
| | - Zhao-Yu Jiang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Peng Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yong-Fei Wang
- Department of Bioengineering, Jinan University, Guangzhou, 510632, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
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10
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Ali SS, Jiao H, Mustafa AM, Koutra E, El-Sapagh S, Kornaros M, Elsamahy T, Khalil M, Bulgariu L, Sun J. Construction of a novel microbial consortium valued for the effective degradation and detoxification of creosote-treated sawdust along with enhanced methane production. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126091. [PMID: 34118544 DOI: 10.1016/j.jhazmat.2021.126091] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 04/29/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Lignocellulosic biomass represents an unlimited and ubiquitous energy source, which can effectively address current global challenges, including climate change, greenhouse gas emissions, and increased energy demand. However, lignocellulose recalcitrance hinders microbial degradation, especially in case of contaminated materials such as creosote (CRO)-treated wood, which necessitates appropriate processing in order to eliminate pollution. This study might be the first to explore a novel bacterial consortium SST-4, for decomposing birchwood sawdust, capable of concurrently degrading lignocellulose and CRO compounds. Afterwards, SST-4 which stands for molecularly identified bacterial strains Acinetobacter calcoaceticus BSW-11, Shewanella putrefaciens BSW-18, Bacillus cereus BSW-23, and Novosphingobium taihuense BSW-25 was evaluated in terms of biological sawdust pre-treatment, resulting in effective lignocellulose degradation and 100% removal of phenol and naphthalene. Subsequently, the maximum biogas production observed was 18.7 L/kg VS, while cumulative methane production was 162.8 L/kg VS, compared to 88.5 without microbial pre-treatment. The cumulative energy production from AD-I and AD-II through biomethanation was calculated as 3177.1 and 5843.6 KJ/kg, respectively. The pretreatment process exhibited a significant increase in the energy yield by 83.9%. Lastly, effective CRO detoxification was achieved with EC50 values exceeding 90%, showing the potential for an integrated process of effective contaminated wood management and bioenergy production.
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Affiliation(s)
- Sameh Samir Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
| | - Haixin Jiao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Ahmed M Mustafa
- State Key Laboratory of Pollution Control and Resourses Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Department of Agricultural Engineering, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - Eleni Koutra
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 1 Karatheodori Str., University Campus, Patras 26504, Greece; INVALOR: Research Infrastructure for Waste Valorization and Sustainable Management, University Campus, Patras 26504, Greece
| | - Shimaa El-Sapagh
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Michael Kornaros
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 1 Karatheodori Str., University Campus, Patras 26504, Greece; INVALOR: Research Infrastructure for Waste Valorization and Sustainable Management, University Campus, Patras 26504, Greece
| | - Tamer Elsamahy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Maha Khalil
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Laura Bulgariu
- Department of Environmental Engineering and Management, Cristofor Simionescu Faculty of Chemical Engineering and Environmental Protection, Gheorghe Asachi Technical University of Iasi, 700050 Iasi, Romania
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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Mishra B, Varjani S, Kumar G, Awasthi MK, Awasthi SK, Sindhu R, Binod P, Rene ER, Zhang Z. Microbial approaches for remediation of pollutants: Innovations, future outlook, and challenges. ENERGY & ENVIRONMENT 2021; 32:1029-1058. [DOI: 10.1177/0958305x19896781] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Environmental contamination with persistent organic pollutants has emerged as a serious threat of pollution. Bioremediation is a key to eliminate these harmful pollutants from the environment and has gained the interest of researchers during the past few decades. Scientific knowledge upon microbial interactions with individual pollutants over the past decades has helped to abate environmental pollution. Traditional bioremediation approaches have limitations for their applications; hence, it is essential to discover new bioremediation approaches with biotechnological interventions for best results. The developments in various methodologies are expected to increase the efficiency of bioremediation techniques and provide environmentally sound strategies. This paper deals with the profiling of microorganisms present in polluted sites using various techniques such as culture-based approaches and omics-based approaches. Besides this, it also provides up-to-date scientific literature on the microbial electrochemical technologies which are nowadays considered as the best approach for remediation of pollutants. Detailed information about future outlook and challenges to evaluate the effect of various treatment technologies for remediation of pollutants has been discussed.
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Affiliation(s)
- Bishwambhar Mishra
- Department of Biotechnology, Chaitanya Bharathi Institute of Technology, Hyderabad, India
| | - Sunita Varjani
- Paryavaran Bhavan, Gujarat Pollution Control Board, Gandhinagar, India
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
| | - Raveendran Sindhu
- CSIR–National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, India
| | - Parameswaran Binod
- CSIR–National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, India
| | - Eldon R Rene
- Department of Environmental Engineering and Water Technology, IHE Delft Institute of Water Education, Delft, The Netherlands
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
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12
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Laothamteep N, Kawano H, Vejarano F, Suzuki-Minakuchi C, Shintani M, Nojiri H, Pinyakong O. Effects of environmental factors and coexisting substrates on PAH degradation and transcriptomic responses of the defined bacterial consortium OPK. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116769. [PMID: 33676341 DOI: 10.1016/j.envpol.2021.116769] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 05/12/2023]
Abstract
The present study showed that syntrophic associations in a defined bacterial consortium, named OPK, containing Mycolicibacterium strains PO1 and PO2, Novosphingobium pentaromativorans PY1 and Bacillus subtilis FW1, led to effective pyrene degradation over a wide range of pH values, temperatures and salinities, as well as in the presence of a second polycyclic aromatic hydrocarbon (PAH). Anthracene, phenanthrene or fluorene facilitated complete pyrene degradation within 9 days, while fluoranthene delayed pyrene degradation. Interestingly, fluoranthene degradation was enhanced in the presence of pyrene. Transcriptome analysis confirmed that Mycolicibacterium strains were the key PAH-degraders during the cometabolism of pyrene and fluoranthene. Notably, the transcription of genes encoding pyrene-degrading enzymes were shown to be important for enhanced fluoranthene degradation. NidAB was the major initial oxygenase involved in the degradation of pyrene and fluoranthene mixture. Other functional genes encoding ribosomal proteins, an iron transporter, ABC transporters and stress response proteins were induced in strains PO1 and PO2. Furthermore, an intermediate pyrene-degrading Novosphingobium strain contributed to protocatechuate degradation. The results demonstrated that synergistic interactions among the bacterial members (PO1, PO2 and PY1) of the consortium OPK promoted the simultaneous degradation of two high molecular weight (HMW) PAHs.
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Affiliation(s)
- Natthariga Laothamteep
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Microbial Technology for Marine Pollution Treatment Research Unit, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hibiki Kawano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Felipe Vejarano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka, 432-8561, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Onruthai Pinyakong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Microbial Technology for Marine Pollution Treatment Research Unit, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand.
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13
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Gao H, Wang Y, Luo Q, Yang L, He X, Wu J, Kachanuban K, Wilaipun P, Zhu W, Wang Y. Bioactive Metabolites From Acid-Tolerant Fungi in a Thai Mangrove Sediment. Front Microbiol 2021; 11:609952. [PMID: 33552019 PMCID: PMC7862741 DOI: 10.3389/fmicb.2020.609952] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/23/2020] [Indexed: 01/04/2023] Open
Abstract
Despite being potentially useful extremophile resources, there have been few reports on acid-tolerant fungi and their bioactive metabolites. Acidophilic/aciduric fungi (n = 237) were isolated from Thai mangrove sediments in an acidic medium. Using fungal identification technology (including morphologic observation, chemical screening, and sequence comparisons) all the isolates were identified and 41 representative isolates were selected for analysis of the phylogenetic relationships (ITS rDNA, β-tubulin, calmodulin, and actin gene sequences). There were seven genera identified – Penicillium; Aspergillus; Talaromyces; Cladosporium; Allophoma; Alternaria; and Trichoderma – in four taxonomic orders of the phylum Ascomycota, and Penicillium, Aspergillus, and Talaromyces were the dominant genera. Acidity tolerance was evaluated and 95% of the isolates could grow under extremely acidic conditions (pH 2). Six strains were classed as acidophilic fungi that cannot survive under pH 7, all of which had an extraordinarily close genetic relationship and belonged to the genus Talaromyces. This is the first report on the acidophilic characteristics of this genus. The antimicrobial, anti-tumor, and antiviral activities of the fermentation extracts were evaluated. Nearly three-quarters of the extracts showed cytotoxic activity, while less than a quarter showed antimicrobial or anti-H1N1 activity. The typical aciduric fungus Penicillium oxalicum OUCMDZ-5207 showed similar growth but completely different chemical diversity at pH 3 and 7. The metabolites of OUCMDZ-5207 that were obtained only at pH 3 were identified as tetrahydroauroglaucin (1), flavoglaucin (2), and auroglaucin (3), among which auroglaucin showed strong selective inhibition of A549 cells with an IC50 value of 5.67 μM. These results suggest that acid stress can activate silent gene clusters to expand the diversity of secondary metabolites, and the bioprospecting of aciduric/acidophilic microorganism resources in Thai mangrove sediments may lead to the discovery of compounds with potential medicinal applications.
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Affiliation(s)
- Hai Gao
- School of Medicine and Pharmacy, Ocean University of China, Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yanan Wang
- School of Medicine and Pharmacy, Ocean University of China, Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qiao Luo
- School of Medicine and Pharmacy, Ocean University of China, Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liyuan Yang
- School of Medicine and Pharmacy, Ocean University of China, Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xingxing He
- School of Medicine and Pharmacy, Ocean University of China, Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jun Wu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | | | | | - Weiming Zhu
- School of Medicine and Pharmacy, Ocean University of China, Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yi Wang
- School of Medicine and Pharmacy, Ocean University of China, Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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14
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Leung MHY, Tong X, Bastien P, Guinot F, Tenenhaus A, Appenzeller BMR, Betts RJ, Mezzache S, Li J, Bourokba N, Breton L, Clavaud C, Lee PKH. Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants. MICROBIOME 2020; 8:100. [PMID: 32591010 PMCID: PMC7320578 DOI: 10.1186/s40168-020-00874-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/20/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing. RESULTS Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds. CONCLUSIONS The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.
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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | | | - Florent Guinot
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Arthur Tenenhaus
- CentraleSupelec-L2S-Laboratoire des signaux et systèmes, Brain and Spine Institute, Université Paris-Sud, Orsay, France
| | | | | | | | - Jing Li
- L’Oréal Research and Innovation, Pudong, China
| | | | - Lionel Breton
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Cécile Clavaud
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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15
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Dominguez JJA, Inoue C, Chien MF. Hydroponic approach to assess rhizodegradation by sudangrass (Sorghum x drummondii) reveals pH- and plant age-dependent variability in bacterial degradation of polycyclic aromatic hydrocarbons (PAHs). JOURNAL OF HAZARDOUS MATERIALS 2020; 387:121695. [PMID: 31780291 DOI: 10.1016/j.jhazmat.2019.121695] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/24/2019] [Accepted: 11/14/2019] [Indexed: 05/27/2023]
Abstract
Rhizodegradation of polycyclic aromatic hydrocarbons (PAHs) is a product of complex interactions between plant and bacteria. In this study, hydroponic culture of sudangrass was established in order to investigate the effects of the plant on PAHs degradation and vice versa through changes in rhizosphere bacterial community. Results showed a plant-induced variability in PAHs degradation dependent on a characteristic shift in bacterial community, with pH and plant age as driving factors. Moreover, bacterial communities with high diversity seemed to abate the phytotoxic effects of PAHs degradation as observed in the plant's gross health. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing revealed that regardless of plant age and culture conditions, the increase or decrease of Sphingobium sp. could dictate the PAHs degradation potential of the bacterial consortium. Overall, this study utilized hydroponic culture of sudangrass to show that plant even of same species can suppress, support, or enhance PAHs degradation of bacteria depending on specific factors.
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Affiliation(s)
- John Jewish A Dominguez
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Mei-Fang Chien
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
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Stable-Isotope Probing-Enabled Cultivation of the Indigenous Bacterium Ralstonia sp. Strain M1, Capable of Degrading Phenanthrene and Biphenyl in Industrial Wastewater. Appl Environ Microbiol 2019; 85:AEM.00511-19. [PMID: 31053587 DOI: 10.1128/aem.00511-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023] Open
Abstract
To identify and obtain the indigenous degraders metabolizing phenanthrene (PHE) and biphenyl (BP) from the complex microbial community within industrial wastewater, DNA-based stable-isotope probing (DNA-SIP) and cultivation-based methods were applied in the present study. DNA-SIP results showed that two bacterial taxa (Vogesella and Alicyclobacillus) were considered the key biodegraders responsible for PHE biodegradation only, whereas Bacillus and Cupriavidus were involved in BP degradation. Vogesella and Alicyclobacillus have not been linked with PHE degradation previously. Additionally, DNA-SIP helped reveal the taxonomic identity of Ralstonia-like degraders involved in both PHE and BP degradation. To target the separation of functional Ralstonia-like degraders from the wastewater, we modified the traditional cultivation medium and culture conditions. Finally, an indigenous PHE- and BP-degrading strain, Ralstonia pickettii M1, was isolated via a cultivation-dependent method, and its role in PHE and BP degradation was confirmed by enrichment of the 16S rRNA gene and distinctive dioxygenase genes in the DNA-SIP experiment. Our study has successfully established a program for the application of DNA-SIP in the isolation of the active functional degraders from an environment. It also deepens our insight into the diversity of indigenous PHE- and BP-degrading communities.IMPORTANCE The comprehensive treatment of wastewater in industrial parks suffers from the presence of multiple persistent organic pollutants (POPs), such as polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), which reduce the activity of activated sludge and are difficult to eliminate. Characterizing and applying active bacterial degraders metabolizing multiple POPs therefore helps to reveal the mechanisms of synergistic metabolism and to improve wastewater treatment efficiency in industrial parks. To date, SIP studies have successfully investigated the biodegradation of PAHs or PCBs in real-world habitats. DNA-SIP facilitates the isolation of target microorganisms that pose environmental concerns. Here, an indigenous phenanthrene (PHE)- and biphenyl (BP)-degrading strain in wastewater, Ralstonia pickettii M1, was isolated via a cultivation-dependent method, and its role in PHE and BP degradation was confirmed by DNA-SIP. Our study provides a routine protocol for the application of DNA-SIP in the isolation of the active functional degraders from an environment.
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Izzo SA, Quintana S, Espinosa M, Babay PA, Peressutti SR. First Characterization of PAH-degrading bacteria from Río de la Plata and high-resolution melting: an encouraging step toward bioremediation. ENVIRONMENTAL TECHNOLOGY 2019; 40:1250-1261. [PMID: 29261428 DOI: 10.1080/09593330.2017.1420104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
The Río de la Plata, one of the most important estuarine environments in South America that sustains valuable fisheries, is affected by PAH contamination associated with oil industry and port activities. A total of 95 bacteria with potential to degrade phenanthrene were obtained from water samples using traditional culture methods. PCR-RFLP analysis of 16S rDNA partial fragments was used as a screening tool for reducing the number of isolates during diversity studies, obtaining 42 strains with different fingerprint patterns. Phylogenetic analysis indicated that they were affiliated to 19 different genera of Gamma- and Alpha-Proteobacteria, and Actinobacteria. Some of them showed an efficient phenanthrene degradation by HPLC (between 83% and 97%) and surfactant production (between 40% and 55%). They could be an alternative for microbial selection in the degradation of PAHs in this estuarine system. In order to detect and monitor PAH-degrading bacteria in this highly productive area, rDNA amplicons of the 33 isolates, produced by PCR real time, were tested by the high-resolution melting (HRM) technique. After analyzing the generated melting curves, it was possible to accurately distinguish nine patterns corresponding to eight different genera. HRM analysis allowed a differentiation at the species level for genera Pseudomonas, Halomonas and Vibrio. The implementation of this method as a fast and sensitive scanning approach to identify PAH-degrading bacteria, avoiding the sequencing step, would mean an advance in bioremediation technologies.
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Affiliation(s)
- Silvina A Izzo
- a Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP) , Mar del Plata, Buenos Aires , Argentina
| | - Silvina Quintana
- b Área de Biología Molecular de Fares Taie , Instituto de Análisis , Rivadavia, Mar del Plata , Argentina
- c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires , Argentina
| | - Mariela Espinosa
- d Comisión Nacional de Energía Atómica , Buenos Aires , Argentina
| | - Paola A Babay
- d Comisión Nacional de Energía Atómica , Buenos Aires , Argentina
| | - Silvia R Peressutti
- a Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP) , Mar del Plata, Buenos Aires , Argentina
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Rathour R, Gupta J, Tyagi B, Kumari T, Thakur IS. Biodegradation of pyrene in soil microcosm by Shewanella sp. ISTPL2, a psychrophilic, alkalophilic and halophilic bacterium. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.biteb.2018.10.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Muangchinda C, Chamcheun C, Sawatsing R, Pinyakong O. Diesel oil removal by Serratia sp. W4-01 immobilized in chitosan-activated carbon beads. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:26927-26938. [PMID: 30008160 DOI: 10.1007/s11356-018-2742-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/09/2018] [Indexed: 04/16/2023]
Abstract
Serratia sp. W4-01 was immobilized in chitosan-activated carbon beads and used for diesel oil removal. The type and concentration of chitosan, activated carbon content, and bead diameter were investigated as factors affecting diesel oil removal. The results showed that 2% (w/v) squid pen chitosan beads modified with 1% activated carbon (w/v) and with a 3-mm diameter had a good spherical shape and strength as well as diesel oil removal capability. The immobilized W4-01 cells removed more than 40% of diesel oil after 7 days when the initial diesel oil concentration was 100 to 400 mg L-1, whereas 29-36% of diesel oil was removed after 14 days when the initial concentration was 800 to 1000 mg L-1. Additionally, the immobilized cells maintained the ability to remove diesel oil over a pH range of 5-11. The addition of a biosurfactant increased the diesel oil removal from 62 to 75%. The reusability tests revealed that the ability of immobilized cells to remove diesel oil was enhanced after reuse, and 50-90% of diesel oil was removed during 2 to 12 reuse cycles. The stability and survival of W4-01 cells was confirmed by scanning electron microscopy and confocal laser scanning microscopy. The results of this study showed the potential use of W4-01 cells immobilized in chitosan-activated carbon beads for future applications in remediating diesel contamination.
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Affiliation(s)
- Chanokporn Muangchinda
- Microbial Technology for Marine Pollution Treatment Research Unit, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chalinee Chamcheun
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rajitpitch Sawatsing
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Onruthai Pinyakong
- Microbial Technology for Marine Pollution Treatment Research Unit, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- 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), Bangkok, 10330, Thailand.
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Ping L, Zhang C, Cui H, Yuan X, Cui J, Shan S. Characterization and application of a newly isolated pyrene-degrading bacterium, Pseudomonas monteilii. 3 Biotech 2017; 7:309. [PMID: 28955606 DOI: 10.1007/s13205-017-0945-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/05/2017] [Indexed: 12/27/2022] Open
Abstract
Pseudomonas monteilii PL5 (PL5) was newly isolated from soil sample and was identified by 16S rDNA sequence analysis. The strain PL5 had a high potential to degrade pyrene (PYR) in both liquid solution and soil and was able to degrade 51.8% of PYR at 25 °C and pH 7.0 condition within 10 days. At 25 °C, the ability of strain PL5 to degrade PYR at different pH values followed the following order pH 6.0 > pH 7.0 > pH 8.0 > pH 9.0. Degradation of total PYR was 56.5 and 51.8% after 10 days at pH 6.0 and 7.0 with PYR half-lives of 8.8 and 9.2 days, respectively. The ability of strain PL5 degraded PYR under different temperatures was 35 > 25 > 15 °C at pH 6.0. Among the tested soils contaminated by PYR, the best degradation of PYR by strain PL5 occurred in paddy soil where the degradation was 57.5% after 10 days, and the half-life of PYR was reduced 19-fold in the presence of strain PL5. This study suggested that P. monteilii PL5 could be used for the bioremediation of the contaminated soil and water through the degradation of PYR.
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Affiliation(s)
- Lifeng Ping
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, 310023 China
- Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Chunrong Zhang
- Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - He Cui
- College of Resources and Environment, Jilin Agricultural University, Changchun, 130118 China
| | - Xiaoli Yuan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, 310023 China
| | - Juntao Cui
- College of Resources and Environment, Jilin Agricultural University, Changchun, 130118 China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, 310023 China
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Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing. Biodegradation 2017; 28:423-436. [PMID: 28956196 DOI: 10.1007/s10532-017-9806-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
The indigenous microorganisms responsible for degrading phenanthrene (PHE) in activated biosludge were identified using DNA-based stable isotope probing. Besides the well-known PHE degraders Burkholderia, Ralstonia, Sinobacteraceae and Arthrobacter, we for the first time linked the taxa Paraburkholderia and Kaistobacter with in situ PHE biodegradation. Analysis of PAH-RHDα gene detected in the heavy DNA fraction of 13C-PHE treatment suggested the mechanisms of horizontal gene transfer or inter-species hybridisation in PAH-RHD gene spread within the microbial community. Additionally, three cultivable PHE degraders, Microbacterium sp. PHE-1, Rhodanobacter sp. PHE-2 and Rhodococcus sp. PHE-3, were isolated from the same activated biosludge. Among them, Rhodanobacter sp. PHE-2 is the first identified strain in its genus with PHE-degrading ability. However, the involvement of these strains in PHE degradation in situ was questionable, due to their limited enrichment in the heavy DNA fraction of 13C-PHE treatment and lack of PAH-RHDα gene found in these isolates. Collectively, our findings provide a deeper understanding of the diversity and functions of indigenous microbes in PHE degradation.
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Qin W, Fan F, Zhu Y, Wang Y, Liu X, Ding A, Dou J. Comparative proteomic analysis and characterization of benzo(a)pyrene removal by Microbacterium sp. strain M.CSW3 under denitrifying conditions. Bioprocess Biosyst Eng 2017; 40:1825-1838. [PMID: 28913631 DOI: 10.1007/s00449-017-1836-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/03/2017] [Indexed: 01/30/2023]
Abstract
High-molecular-weight polycyclic aromatic hydrocarbons are persistent organic pollutants with great environmental and human health risks and the associated bioremediation activities have always been hampered by the lack of powerful bacterial species under redox conditions. A Microbacterium sp. strain capable of using benzo(a)pyrene as sole carbon and energy sources under denitrifying conditions was isolated. The difference in protein expression during BaP removal and removal characterization were investigated. A total of 146 proteins were differentially expressed, 44 proteins were significantly up-regulated and 102 proteins were markedly down-regulated. GO and COG analysis showed that BaP removal inhibited the expression of proteins related to glucose metabolism at different levels and activated other metabolic pathway. The proteins associated with catalytic activity and metabolic process were altered significantly. Furthermore, the BaP removal might be occurred in certain organelle of M.CSW3. The strain removed BaP with a speed of 0.0657-1.0072 mg/L/day over the concentrations range 2.5-100 mg/L. High removal rates (>70%) were obtained over the range of pH 7-11 in 14 days. Carbohydrates and organic acids which could be utilized by the strain, as well as heavy metal ions, reduced BaP removal efficiency. However, phenanthrene or pyrene addition enhanced the removal capability of M.CSW3. The strain was proved to have practical potential for bioremediation of PAHs-contaminated soil and this study provided a powerful platform for further application by improving production of associated proteins.
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Affiliation(s)
- Wei Qin
- College of Water Sciences, Beijing Normal University, No 19 Xinjiekou Wai Street, Haidian District, Beijing, 100875, China
| | - FuQiang Fan
- Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, 250101, Canada
| | - Yi Zhu
- College of Water Sciences, Beijing Normal University, No 19 Xinjiekou Wai Street, Haidian District, Beijing, 100875, China
| | - Yingying Wang
- College of Water Sciences, Beijing Normal University, No 19 Xinjiekou Wai Street, Haidian District, Beijing, 100875, China
| | - Xiang Liu
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, No 19 Xinjiekou Wai Street, Haidian District, Beijing, 100875, China
| | - Junfeng Dou
- College of Water Sciences, Beijing Normal University, No 19 Xinjiekou Wai Street, Haidian District, Beijing, 100875, China.
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Biodegradation of benzo(a)pyrene by Microbacterium sp. strain under denitrification: Degradation pathway and effects of limiting electron acceptors or carbon source. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.02.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Ping L, Guo Q, Chen X, Yuan X, Zhang C, Zhao H. Biodegradation of pyrene and benzo[a]pyrene in the liquid matrix and soil by a newly identified Raoultella planticola strain. 3 Biotech 2017; 7:56. [PMID: 28444597 DOI: 10.1007/s13205-017-0704-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/21/2017] [Indexed: 11/28/2022] Open
Abstract
In the current study, the PL7 strain was isolated from soil and identified as Raoultella planticola based on its physiological characteristics and 16S rDNA sequence. By the 10th day, the PL7 strain degraded 52.0% of the pyrene (PYR) content and 50.8% of the benzo[a]pyrene (BaP) content in 20 mg L-1 PYR and 10 mg L-1 BaP in the liquid matrix. The half-life of PYR and BaP by PL7 degradation was 8.59 and 9.46 days, respectively. At pH 8.0, the degradation rates of PYR and BaP by PL7 were significantly higher at 30 °C than at 20 and 40 °C. The degradation ability of PL7 differed in red soil, paddy soil and fluvo-aquic soil; red soil produced the fastest degradation rates. The half-life of PYR and BaP by PL7 degradation in red soil was 21.7 and 11.9 days, respectively; however, without PL7 the half-life of PYR in red soil was 91.2 days. This study demonstrated the significant potential of the PL7 strain for bioremediation applications in the liquid matrix and soil contaminated by PAHs.
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Affiliation(s)
- Lifeng Ping
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, 310023, China.
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Qian Guo
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoyang Chen
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoli Yuan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, 310023, China
| | - Chunrong Zhang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hua Zhao
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Singh P, Tiwary BN. Optimization of conditions for polycyclic aromatic hydrocarbons (PAHs) degradation by Pseudomonas stutzeri P2 isolated from Chirimiri coal mines. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.02.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Muangchinda C, Yamazoe A, Polrit D, Thoetkiattikul H, Mhuantong W, Champreda V, Pinyakong O. Biodegradation of high concentrations of mixed polycyclic aromatic hydrocarbons by indigenous bacteria from a river sediment: a microcosm study and bacterial community analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:4591-4602. [PMID: 27957694 DOI: 10.1007/s11356-016-8185-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023]
Abstract
This study assessed the biodegradation of mixtures of polycyclic aromatic hydrocarbons (PAHs) by indigenous bacteria in river sediment. Microcosms were constructed from sediment from the Chao Phraya River (the main river in Thailand) by supplementation with high concentrations of fluorene, phenanthrene, pyrene (300 mg kg-1 of each PAH), and acenaphthene (600 mg kg-1). Fluorene and phenanthrene were completely degraded, whereas 50% of the pyrene and acenaphthene were removed at the end of the incubation period (70 days). Community analyses revealed the dynamics of the bacterial profiles in the PAH-degrading microcosms after PAH exposure. Actinobacteria predominated and became significantly more abundant in the microcosms after 14 days of incubation at room temperature under aerobic conditions. Furthermore, the remaining PAHs and alpha diversity were positively correlated. The sequencing of clone libraries of the PAH-RHDα genes also revealed that the dioxygenase genes of Mycobacterium sp. comprised 100% of the PAH-RHDα library at the end of the microcosm setup. Moreover, two PAH-degrading Actinobacteria (Arthrobacter sp. and Rhodococcus ruber) were isolated from the original sediment sample and showed high activity in the degradation of phenanthrene and fluorene in liquid cultivation. This study reveals that indigenous bacteria had the ability to degrade high concentrations of mixed PAHs and provide clear evidence that Actinobacteria may be potential candidates to play a major role in PAH degradation in the river sediment.
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Affiliation(s)
- Chanokporn Muangchinda
- Bioremediation Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Atsushi Yamazoe
- Biological Resource Center, National Institute of Technology and Evaluation, 2-49-10 Nishihara, Shibuya-ku, Tokyo, 151-0066, Japan
| | - Duangporn Polrit
- Bioremediation Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Honglada Thoetkiattikul
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, 12120, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, 12120, Thailand
| | - Onruthai Pinyakong
- Bioremediation Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Center of Excellence on Hazardous Substance Management (HSM), Bangkok, 10330, Thailand.
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Gkorezis P, Daghio M, Franzetti A, Van Hamme JD, Sillen W, Vangronsveld J. The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective. Front Microbiol 2016; 7:1836. [PMID: 27917161 PMCID: PMC5116465 DOI: 10.3389/fmicb.2016.01836] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.
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Affiliation(s)
- Panagiotis Gkorezis
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Matteo Daghio
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
- Department of Biological Sciences, Thompson Rivers University, KamloopsBC, Canada
| | - Andrea Franzetti
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
| | | | - Wouter Sillen
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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Ruffini Castiglione M, Giorgetti L, Becarelli S, Siracusa G, Lorenzi R, Di Gregorio S. Polycyclic aromatic hydrocarbon-contaminated soils: bioaugmentation of autochthonous bacteria and toxicological assessment of the bioremediation process by means of Vicia faba L. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7930-7941. [PMID: 26769476 DOI: 10.1007/s11356-016-6049-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
Two bacterial strains, Achromobacter sp. (ACH01) and Sphingomonas sp. (SPH01), were isolated from a heavily polycyclic aromatic hydrocarbon (PAH)-contaminated soil (5431.3 ± 102.3 ppm) for their capacity to use a mixture of anthracene, pyrene, phenanthrene and fluorene as sole carbon sources for growth and for the capacity to produce biosurfactants. The two strains were exploited for bioaugmentation in a biopile pilot plant to increase the bioavailability and the degradation of the residual PAH contamination (99.5 ± 7.1 ppm) reached after 9 months of treatment. The denaturing gel gradient electrophoresis (DGGE) profile of the microbial ecology of the soil during the experimentation showed that the bioaugmentation approach was successful in terms of permanence of the two strains in the soil in treatment. The bioaugmentation of the two bacterial isolates positively correlated with the PAH depletion that reached 7.9 ± 2 ppm value in 2 months of treatment. The PAH depletion was assessed by the loss of the phyto-genotoxicity of soil elutriates on the model plant Vicia faba L., toxicological assessment adopted also to determine the minimum length of the decontamination process for obtaining both the depletion of the PAH contamination and the detoxification of the soil at the end of the process. The intermediate phases of the bioremediation process were the most significant in terms of toxicity, inducing genotoxic effects and selective DNA fragmentation in the stem cell niche of the root tip. The selective DNA fragmentation can be related to the selective induction of cell death of mutant stem cells that can compromise offsprings.
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Affiliation(s)
| | - Lucia Giorgetti
- National Research Council (CNR), Institute of Biology and Agricultural Biotechnology (IBBA), Research Unit of Pisa, Via Moruzzi 1, 56124, Pisa, Italy
| | - Simone Becarelli
- Department of Biology, University of Pisa, via Ghini 13, 56126, Pisa, Italy
| | - Giovanna Siracusa
- Department of Biology, University of Pisa, via Ghini 13, 56126, Pisa, Italy
| | - Roberto Lorenzi
- Department of Biology, University of Pisa, via Ghini 13, 56126, Pisa, Italy
| | - Simona Di Gregorio
- Department of Biology, University of Pisa, via Ghini 13, 56126, Pisa, Italy.
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Yuan J, Lai Q, Sun F, Zheng T, Shao Z. The diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge. Front Microbiol 2015; 6:853. [PMID: 26379634 PMCID: PMC4548250 DOI: 10.3389/fmicb.2015.00853] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 08/05/2015] [Indexed: 12/03/2022] Open
Abstract
The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR). After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene, and pyrene), nine bacterial consortia were obtained from depths of 3946–4746 m. While the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene, and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE) analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium, and Rhodovulum occurred most frequently in different PAH-degrading consortia. By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis, and Stappia were found to be PAH degraders. To the best of our knowledge, this is the first time these bacteria have been identified in this context. In summary, this report revealed significant diversity among the PAH-degrading bacteria in the deep-sea water column. These bacteria may play a role in PAH removal in deep-sea environments.
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Affiliation(s)
- Jun Yuan
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
| | - Tianling Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of MOE for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University Xiamen, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Key Laboratory of Marine Genetic Resources of Fujian Province Xiamen, China ; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Xiamen, China
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Mhuantong W, Wongwilaiwalin S, Laothanachareon T, Eurwilaichitr L, Tangphatsornruang S, Boonchayaanant B, Limpiyakorn T, Pattaragulwanit K, Punmatharith T, McEvoy J, Khan E, Rachakornkij M, Champreda V. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing. PLoS One 2015; 10:e0128043. [PMID: 26020967 PMCID: PMC4447364 DOI: 10.1371/journal.pone.0128043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 04/21/2015] [Indexed: 11/18/2022] Open
Abstract
The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.
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Affiliation(s)
- Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sarunyou Wongwilaiwalin
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Thanaporn Laothanachareon
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Lily Eurwilaichitr
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- Genome Institute, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Benjaporn Boonchayaanant
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - Tawan Limpiyakorn
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - Kobchai Pattaragulwanit
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - Thantip Punmatharith
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - John McEvoy
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND 58108, United States of America
| | - Eakalak Khan
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, ND 58108, United States of America
| | - Manaskorn Rachakornkij
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
- Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Phayatai, Bangkok 10330, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
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31
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Ren G, Ren W, Teng Y, Li Z. Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil. Front Microbiol 2015; 6:22. [PMID: 25688237 PMCID: PMC4311681 DOI: 10.3389/fmicb.2015.00022] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/08/2015] [Indexed: 11/13/2022] Open
Abstract
Understanding the potential for Polycyclic aromatic hydrocarbons (PAH) degradation by indigenous microbiota and the influence of PAHs on native microbial communities is of great importance for bioremediation and ecological evaluation. Various studies have focused on the bacterial communities in the environment where obvious PAH degradation was observed, little is known about the microbiota in the soil where poor degradation was observed. Soil microcosms were constructed with a red soil by supplementation with a high-molecular-weight PAH (pyrene) at three dosages (5, 30, and 70 mg ⋅ kg(-1)). Real-time PCR was used to evaluate the changes in bacterial abundance and pyrene dioxygenase gene (nidA) quantity. Illumina sequencing was used to investigate changes in diversity, structure, and composition of bacterial communities. After 42 days of incubation, no evident degradation was observed. The poor degradation ability was associated with the stability or significant decrease of abundance of the nidA gene. Although the abundance of the bacterial 16S rRNA gene was not affected by pyrene, the bacterial richness and diversity were decreased with increasing dosage of pyrene and the community structure was changed. Phylotypes affected by pyrene were comprehensively surveyed: (1) at the high taxonomic level, seven of the abundant phyla/classes (relative abundance >1.0%) including Chloroflexi, AD3, WPS-2, GAL5, Alphaproteobacteria, Actinobacteria, and Deltaproteobacteria and one rare phylum Crenarchaeota were significantly decreased by at least one dosage of pyrene, while three phyla/classes (Acidobacteria, Betaproteobacteria, and Gammaproteobacteria) were significantly increased; and (2) at the lower taxonomic level, the relative abundances of twelve orders were significantly depressed, whereas those of nine orders were significantly increased. This work enhanced our understanding of the biodegradation potential of pyrene in red soil and the effect of pyrene on soil ecosystems at the microbial community level.
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Affiliation(s)
- Gaidi Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
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Ping L, Zhang C, Zhang C, Zhu Y, He H, Wu M, Tang T, Li Z, Zhao H. Isolation and characterization of pyrene and benzo[a]pyrene-degrading Klebsiella pneumonia PL1 and its potential use in bioremediation. Appl Microbiol Biotechnol 2014; 98:3819-28. [PMID: 24389667 DOI: 10.1007/s00253-013-5469-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 12/01/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), which are hard to degrade, are the main pollutants in the environment. Degradation of PAHs in the environment is becoming more necessary and urgent. In the current study, strain PL1 with degradation capability of pyrene (PYR) and benzo[a]pyrene (BaP) was isolated from soil and identified as Klebsiella pneumoniae by morphological and physiological characteristics as well as 16S rDNA sequence. With the presence of 20 mg L⁻¹ PYR and 10 mg L⁻¹ BaP in solution, the strain PL1 could degrade 63.4 % of PYR and 55.8 % of BaP in 10 days, respectively. The order of biodegradation of strain PL1 was pH 7.0 > pH 8.0 > pH 10.0 > pH 6.0 > pH 5.0. Strain PL1 degradation ability varied in different soil. The half-life of PYR in soil was respectively 16.9, 24.9, and 88.9 days in paddy soil, red soil, and fluvo-aquic soil by PL1 degradation; however, the half-lives of BaP were respectively 9.5, 9.5, and 34.0 days in paddy soil, red soil, and fluvo-aquic soil by PL1 degradation. The results demonstrate that the degradation capability on PYR and BaP by PL1 in paddy soil was relatively good, and K. pneumoniae PL1 was the new degradation bacterium of PYR and BaP. K. pneumoniae PL1 has potential application in PAH bioremediation.
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Affiliation(s)
- Lifeng Ping
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China,
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