1
|
Li J, Zhang D, Luo C, Li B, Zhang G. In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17087-17098. [PMID: 37823365 DOI: 10.1021/acs.est.3c04247] [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] [Indexed: 10/13/2023]
Abstract
The identification and in situ cultivation of functional yet uncultivable microorganisms are important to confirm inferences regarding their ecological functions. Here, we developed a new method that couples Raman-activated cell sorting (RACS), stable-isotope probing (SIP), and genome-directed cultivation (GDC)─namely, RACS-SIP-GDC─to identify, sort, and cultivate the active toluene degraders from a complex microbial community in petroleum-contaminated soil. Using SIP, we successfully identified the active toluene degrader Pigmentiphaga, the single cells of which were subsequently sorted and isolated by RACS. We further successfully assembled the genome of Pigmentiphaga based on the metagenomic sequencing of 13C-DNA and genomic sequencing of sorted cells, which was confirmed by gyrB gene comparison and average nucleotide identity determination. Additionally, the genotypes and phenotypes of this degrader were directly linked at the single-cell level, and its complete toluene metabolic pathways in petroleum-contaminated soil were reconstructed. Based on its unique metabolic properties uncovered by genome sequencing, we modified the traditional cultivation medium with antibiotics, amino acids, carbon sources, and growth factors (e.g., vitamins and metals), achieving the successful cultivation of RACS-sorted active degrader Pigmentiphaga sp. Our results implied that RACS-SIP-GDC is a state-of-the-art approach for the precise identification, targeted isolation, and cultivation of functional microbes from complex communities in natural habitats. RACS-SIP-GDC can be used to explore specific and targeted organic-pollution-degrading microorganisms at the single-cell level and provide new insights into their biodegradation mechanisms.
Collapse
Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, China
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bei Li
- State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 130033 Changchun, China
- HOOKE Instruments Ltd., 130033 Changchun, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| |
Collapse
|
2
|
Liang C, Ye Q, Huang Y, Wang Y, Zhang Z, Wang H. Shifts of the new functional marker gene (pahE) of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial population and its relationship with PAHs biodegradation. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129305. [PMID: 35709619 DOI: 10.1016/j.jhazmat.2022.129305] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/22/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Identification of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial populations and understanding their responses to PAHs are crucial for the designing of appropriate bioremediation strategies. In this study, the responses of PAHs-degrading bacterial populations to different PAHs were studied in terms of the compositions and abundance variations of their new functional marker gene (pahE) by gene-targeted metagenomic and qPCR analysis. Overall, PAHs species significantly affected the composition and abundance of pahE gene within the PAHs-degrading bacteria in each treatment and different pahE of PAHs-degrading bacteria involved in the different stages of PAHs degradation. Noted that new pahE genotypes were also discovered in all PAHs treatment groups, indicating that some potential new PAHs-degrading bacterial genera were also involved in PAHs degradation. Besides, all three PAH removal rates were significantly positively related with pahE gene abundances (R2 = 0.908 ~ 0.922, p < 0.01), demonstrating that pahE could be a good indicator of PAHs degradation activity or potential. This is the first study focusing on the dynamic changes of the pahE gene within PAHs-degrading bacterial community during the degradation of PAHs in mangrove sediment, providing novel insights into the use of pahE gene as the functional marker to indicate PAH degradation.
Collapse
Affiliation(s)
- Chengyue Liang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Quanhui Ye
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yong Huang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yun Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zuotao Zhang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
3
|
Lara-Moreno A, Morillo E, Merchán F, Villaverde J. A comprehensive feasibility study of effectiveness and environmental impact of PAH bioremediation using an indigenous microbial degrader consortium and a novel strain Stenotrophomonas maltophilia CPHE1 isolated from an industrial polluted soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112512. [PMID: 33848881 DOI: 10.1016/j.jenvman.2021.112512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/04/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
Polycyclic Aromatic Hydrocarbons (PAHs) are major toxic and recalcitrant pollutants in the environment. This study assessed the capacity of an isolated soil microbial consortium (OMC) to biodegrade PAHs. OMC was able to reach 100% biodegradation of naphthalene, acenaphthylene, acenaphthene, fluorene and phenanthrene in solution, and up to 76% and 50% of anthracene and fluoranthene, respectively, from a mix of 16 PAHs. To measure phenanthrene (PHE) mineralization, OMC and eight strains isolated from OMC were used and identified by PCR amplification of the gene 16S ribosomal RNA. A novel Stenotrophomonas maltophilia CPHE1, not previously described as a PAH degrader, was able to mineralize almost 40% PHE and biodegrade 90.5% in solution, in comparison to OMC that reached 100% PHE degradation, but only 18.8% mineralization. Based on metabolites identified during PHE degradation and on the detection of two genes (PAH RHDα and nahAc) in OMC consortium, two possible via were described for its degradation, through salicylic and phthalic acid. PAH RHDα, which codified the first step on PHE biodegradation pathway, was also found in the DNA of S. maltophilia CPHE1. An ecotoxicology study showed that PHE bioremediation after inoculating S. maltophilia CPHE1 for 30 days decreased by half the solution toxicity.
Collapse
Affiliation(s)
- Alba Lara-Moreno
- Institute of Natural Resources and Agrobiology of Seville, Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Science Research Council (IRNAS-CSIC), Seville, Spain; Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain.
| | - Esmeralda Morillo
- Institute of Natural Resources and Agrobiology of Seville, Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Science Research Council (IRNAS-CSIC), Seville, Spain
| | - Francisco Merchán
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Jaime Villaverde
- Institute of Natural Resources and Agrobiology of Seville, Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Science Research Council (IRNAS-CSIC), Seville, Spain
| |
Collapse
|
4
|
Rahmeh R, Akbar A, Kumar V, Al-Mansour H, Kishk M, Ahmed N, Al-Shamali M, Boota A, Al-Ballam Z, Shajan A, Al-Okla N. Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment. Evol Bioinform Online 2021; 17:11769343211016887. [PMID: 34163126 PMCID: PMC8191072 DOI: 10.1177/11769343211016887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/16/2021] [Indexed: 11/15/2022] Open
Abstract
Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi, and Acidobacteria groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.
Collapse
Affiliation(s)
- Rita Rahmeh
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Abrar Akbar
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Vinod Kumar
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Hamad Al-Mansour
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Mohamed Kishk
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Nisar Ahmed
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Mustafa Al-Shamali
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Anwar Boota
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Zainab Al-Ballam
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Anisha Shajan
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Naser Al-Okla
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| |
Collapse
|
5
|
Jiang L, Luo C, Zhang D, Song M, Mei W, Sun Y, Zhang G. Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:962-973. [PMID: 33371686 DOI: 10.1021/acs.est.0c04951] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plants usually promote pollutant bioremediation by several mechanisms including modifying the diversity of functional microbial species. However, conflicting results are reported that root exudates have no effects or negative effects on organic pollutant degradation. In this study, we investigated the roles of ryegrass in phenanthrene degradation in soils using DNA stable isotope probing (SIP) and metagenomics to reveal a potential explanation for conflicting results among phytoremediation studies. Phenanthrene biodegradation efficiency was improved by 8% after 14 days of cultivation. Twelve and ten operational taxonomic units (OTUs) were identified as active phenanthrene degraders in non-rhizosphere and rhizosphere soils, respectively. The active phenanthrene degraders exhibited higher average phylogenetic distances in rhizosphere soils (0.33) than non-rhizosphere soils (0.26). The Ka/Ks values (the ratio of nonsynonymous to synonymous substitutions) were about 10.37% higher in the rhizosphere treatment among >90% of all key carbohydrate metabolism-related genes, implying that ryegrass may be an important driver of microbial community variation in the rhizosphere by relieving the carbohydrate metabolism pressure and improving the survival ability of r-strategy microbes. Most Ka/Ks values of root-exudate-related metabolism genes exhibited little change, except for fumarate hydratase that increased 13-fold in the rhizosphere compared to that in the non-rhizosphere treatment. The Ka/Ks values of less than 50% phenanthrene-degradation-related genes were affected, 30% of which increased and 70% behaved oppositely. Genes with altered Ka/Ks values had a low percentage and followed an inconsistent changing tendency, indicating that phenanthrene and its metabolites are not major factors influencing the active degraders. These results suggested the importance of carbohydrate metabolism, especially fumaric acid, in rhizosphere community shift, and hinted at a new hypothesis that the rhizosphere effect on phenanthrene degradation efficiency depends on the existence of active degraders that have competitive advantages in carbohydrate and fumaric acid metabolism.
Collapse
Affiliation(s)
- Longfei Jiang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Mengke Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Weiping Mei
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yingtao Sun
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| |
Collapse
|
6
|
Li J, Peng K, Zhang D, Luo C, Cai X, Wang Y, Zhang G. Autochthonous bioaugmentation with non-direct degraders: A new strategy to enhance wastewater bioremediation performance. ENVIRONMENT INTERNATIONAL 2020; 136:105473. [PMID: 31999970 DOI: 10.1016/j.envint.2020.105473] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Autochthonous bioaugmentation (ABA) strategies are primarily carried out using a single, highly efficient type of bacteria that is capable of directly degrading the target compound. However, no studies have examined the use of non-direct degraders (NDDs), which are involved in the metabolic pathway of target compounds instead of direct degradation. Here, to evaluate the bioremediation efficiency and mechanism of ABA by NDDs, we demonstrated the use of an NDD on the biodegradation of biphenyl, a model compound used to study polychlorinated biphenyl (PCB) degradation. The NDD examined in this study, Marmoricola LJ-33, was isolated from activated sludge. Although Marmoricola LJ-33 alone did not directly degrade biphenyl under laboratory conditions, it did contribute to in situ biphenyl biodegradation in the activated sludge, as evidenced by DNA-stable-isotope-probing (DNA-SIP). Implementation of ABA with strain LJ-33 was shown to significantly accelerate biphenyl degradation efficiency, demonstrating the potential of NDD strains for degradation in ABA. More importantly, LJ-33 amendment altered the diversity of the microbial communities involved in biphenyl metabolism. Our findings suggest that a combination of pre-screening followed by DNA-SIP analysis is a practical strategy to precisely separate NDDs. Additionally, our work indicates a new mechanism of ABA strategy with NDDs as a promising in situ bioremediation strategy, broadening our concept in constructing functional consortia to enhance the biodegradation performance of activated sludge in wastewater treatment plants.
Collapse
Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Ke Peng
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Xixi Cai
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yujie Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| |
Collapse
|
7
|
Thomas F, Corre E, Cébron A. Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil. THE ISME JOURNAL 2019; 13:1814-1830. [PMID: 30872807 PMCID: PMC6775975 DOI: 10.1038/s41396-019-0394-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/08/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.
Collapse
Affiliation(s)
- François Thomas
- Université de Lorraine, CNRS, LIEC, 54500, Nancy, France
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54500, Nancy, France.
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Li J, Luo C, Zhang G, Zhang D. Coupling magnetic-nanoparticle mediated isolation (MMI) and stable isotope probing (SIP) for identifying and isolating the active microbes involved in phenanthrene degradation in wastewater with higher resolution and accuracy. WATER RESEARCH 2018; 144:226-234. [PMID: 30032019 DOI: 10.1016/j.watres.2018.07.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/05/2018] [Accepted: 07/14/2018] [Indexed: 06/08/2023]
Abstract
Stable isotope probing (SIP) is a cultivation-independent approach identifying the functional microbes in their natural habitats, possibly linking their identities to functions. DNA-SIP is well-established but suffers from the shift of 12C-DNA into the heavy DNA (13C-DNA) fraction, which significantly reduces the resolution and accuracy. In this study, we coupled magnetic-nanoparticle mediated isolation (MMI) and DNA-SIP, namely MMI-SIP, to identify the active microbes involved in phenanthrene degradation from PAH-contaminated wastewater. Microbes affiliated to Pseudomonas and Sphingobium were responsible for in situ phenanthrene metabolism from the SIP results, and Pigmentiphaga was only unraveled for phenanthrene degradation in the MMI and MMI-SIP microcosms. MMI-SIP also significantly increased the enrichment of the above microbes and genes encoding the alpha subunit of the PAH-ring hydroxylating dioxygenase (PAH-RHDα) in the heavy DNA fractions. Our findings suggest that MMI-SIP is a powerful tool, with higher resolution and accuracy, to distinguish the active microbes involved in phenanthrene metabolism in the wastewater, provide a more precise map of functional microbial communities, and offer suggestions for effective management for wastewater treatment plants.
Collapse
Affiliation(s)
- Jibing Li
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
10
|
Jiang L, Luo C, Zhang D, Song M, Sun Y, Zhang G. Biphenyl-Metabolizing Microbial Community and a Functional Operon Revealed in E-Waste-Contaminated Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8558-8567. [PMID: 29733586 DOI: 10.1021/acs.est.7b06647] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Primitive electronic waste (e-waste) recycling activities release massive amounts of persistent organic pollutants (POPs) and heavy metals into surrounding soils, posing a major threat to the ecosystem and human health. Microbes capable of metabolizing POPs play important roles in POPs remediation in soils, but their phylotypes and functions remain unclear. Polychlorinated biphenyls (PCBs), one of the main pollutants in e-waste contaminated soils, have drawn increasing attention due to their high persistence, toxicity, and bioaccumulation. In the present study, we employed the culture-independent method of DNA stable-isotope probing to identify active biphenyl and PCB degraders in e-waste-contaminated soil. A total of 19 rare operational taxonomic units and three dominant bacterial genera ( Ralstonia, Cupriavidus, and uncultured bacterium DA101) were enriched in the 13C heavy DNA fraction, confirming their functions in PCBs metabolism. Additionally, a 13.8 kb bph operon was amplified, containing a bphA gene labeled by 13C that was concentrated in the heavy DNA fraction. The tetranucleotide signature characteristics of the bph operon suggest that it originated from Ralstonia. The bph operon may be shared by horizontal gene transfer because it contains a transposon gene and is found in various bacterial species. This study gives us a deeper understanding of PCB-degrading mechanisms and provides a potential resource for the bioremediation of PCBs-contaminated soils.
Collapse
Affiliation(s)
- Longfei Jiang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640 , China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640 , China
- College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Dayi Zhang
- School of Environment , Tsinghua University , Beijing 100084 , China
| | - Mengke Song
- College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Yingtao Sun
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640 , China
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640 , China
| |
Collapse
|
11
|
Deng Y, Deng C, Yang J, Li B, Wang E, Yuan H. Novel Butane-Oxidizing Bacteria and Diversity of bmoX Genes in Puguang Gas Field. Front Microbiol 2018; 9:1576. [PMID: 30065710 PMCID: PMC6056644 DOI: 10.3389/fmicb.2018.01576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/25/2018] [Indexed: 11/13/2022] Open
Abstract
To investigate the diversity of butane-oxidizing bacteria in soils contaminated by long-term light hydrocarbon microseepage and the influence of butane on the soil microbial community, a quantitative study and identification of butane-oxidizing bacteria (BOB) in soils at the Puguang gas field were performed by DNA-based stable isotope probing (DNA-SIP). For the first time, two phylotypes corresponding to the genera Giesbergeria and Ramlibacter were identified as being directly involved in butane oxidation, in addition to the well-known light hydrocarbon degrader Pseudomonas. Furthermore, bmoX genes were strongly labeled by 13C-butane, and their abundances in gas field soils increased by 43.14-, 17.39-, 21.74-, and 30.14-fold when incubated with butane for 6, 9, 12, and 14 days, respectively, indicating that these bmoX-harboring bacteria could use butane as the sole carbon and energy source and they play an important role in butane degradation. We also found that the addition of butane rapidly shaped the bacterial community and reduced the diversity of bmoX genes in the gas field soils. These findings improve our understanding of BOB in the gas field environment and reveal the potential for their applications in petroleum exploration and bioremediation.
Collapse
Affiliation(s)
- Yue Deng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chunping Deng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Baozhen Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| |
Collapse
|
12
|
Li J, Luo C, Zhang D, Song M, Cai X, Jiang L, Zhang G. Autochthonous Bioaugmentation-Modified Bacterial Diversity of Phenanthrene Degraders in PAH-Contaminated Wastewater as Revealed by DNA-Stable Isotope Probing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:2934-2944. [PMID: 29378393 DOI: 10.1021/acs.est.7b05646] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
To reveal the mechanisms of autochthonous bioaugmentation (ABA) in wastewater contaminated with polycyclic aromatic hydrocarbons (PAHs), DNA-stable-isotope-probing (SIP) was used in the present study with the addition of an autochthonous microorganism Acinetobacter tandoii LJ-5. We found LJ-5 inoculum produced a significant increase in phenanthrene (PHE) mineralization, but LJ-5 surprisingly did not participate in indigenous PHE degradation from the SIP results. The improvement of PHE biodegradation was not explained by the engagement of LJ-5 but attributed to the remarkably altered diversity of PHE degraders. Of the major PHE degraders present in ambient wastewater ( Rhodoplanes sp., Mycobacterium sp., Xanthomonadaceae sp. and Enterobacteriaceae sp.), only Mycobacterium sp. and Enterobacteriaceae sp. remained functional in the presence of strain LJ-5, but five new taxa Bacillus, Paenibacillus, Ammoniphilus, Sporosarcina, and Hyphomicrobium were favored. Rhodoplanes, Ammoniphilus, Sporosarcina, and Hyphomicrobium were directly linked to, for the first time, indigenous PHE biodegradation. Sequences of functional PAH-RHDα genes from heavy fractions further proved the change in PHE degraders by identifying distinct PAH-ring hydroxylating dioxygenases between ambient degradation and ABA. Our findings indicate a new mechanism of ABA, provide new insights into the diversity of PHE-degrading communities, and suggest ABA as a promising in situ bioremediation strategy for PAH-contaminated wastewater.
Collapse
Affiliation(s)
- Jibing Li
- Guangzhou Institute of Geochemistry , Chinese Academy of Sciences , Guangzhou 510640 , China
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry , Chinese Academy of Sciences , Guangzhou 510640 , China
- College of Natural Resources and Environment , South China Agricultural University , Guangzhou , 510642 , China
| | - Dayi Zhang
- School of Environment , Tsinghua University , Beijing 100084 , China
| | - Mengke Song
- College of Natural Resources and Environment , South China Agricultural University , Guangzhou , 510642 , China
| | - Xixi Cai
- College of Resources and Environment , Fujian Agriculture and Forestry University , Fuzhou , 350002 , China
| | - Longfei Jiang
- Guangzhou Institute of Geochemistry , Chinese Academy of Sciences , Guangzhou 510640 , China
| | - Gan Zhang
- Guangzhou Institute of Geochemistry , Chinese Academy of Sciences , Guangzhou 510640 , China
| |
Collapse
|
13
|
Jiang B, Jin N, Xing Y, Su Y, Zhang D. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP). Crit Rev Biotechnol 2018; 38:1025-1048. [DOI: 10.1080/07388551.2018.1427697] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Naifu Jin
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Yuping Su
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
- School of Environment, Tsinghua University, Beijing, PR China
| |
Collapse
|
14
|
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.
Collapse
|
15
|
Li J, Luo C, Song M, Dai Q, Jiang L, Zhang D, Zhang G. Biodegradation of Phenanthrene in Polycyclic Aromatic Hydrocarbon-Contaminated Wastewater Revealed by Coupling Cultivation-Dependent and -Independent Approaches. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3391-3401. [PMID: 28181806 DOI: 10.1021/acs.est.6b04366] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The indigenous microorganisms responsible for degrading phenanthrene (PHE) in polycyclic aromatic hydrocarbons (PAHs)-contaminated wastewater were identified by DNA-based stable isotope probing (DNA-SIP). In addition to the well-known PHE degraders Acinetobacter and Sphingobium, Kouleothrix and Sandaracinobacter were found, for the first time, to be directly responsible for indigenous PHE biodegradation. Additionally, a novel PHE degrader, Acinetobacter tandoii sp. LJ-5, was identified by DNA-SIP and direct cultivation. This is the first report and reference to A. tandoii involved in the bioremediation of PAHs-contaminated water. A PAH-RHDα gene involved in PHE metabolism was detected in the heavy fraction of 13C treatment, but the amplification of PAH-RHDα gene failed in A. tandoii LJ-5. Instead, the strain contained catechol 1,2-dioxygenase and the alpha/beta subunits of protocatechuate 3,4-dioxygenase, indicating use of the β-ketoadipate pathway to degrade PHE and related aromatic compounds. These findings add to our current knowledge on microorganisms degrading PHE by combining cultivation-dependent and cultivation-independent approaches and provide deeper insight into the diversity of indigenous PHE-degrading communities.
Collapse
Affiliation(s)
- Jibing Li
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640, China
- University of Chinese Academy of Sciences , Beijing, 100039, China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640, China
| | - Mengke Song
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640, China
| | - Qing Dai
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640, China
- University of Chinese Academy of Sciences , Beijing, 100039, China
| | - Longfei Jiang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640, China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University , Lancaster, LA1 4YQ, United Kingdom
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640, China
| |
Collapse
|
16
|
Carroll SM, Peacock AD, Zimbron J, Alepidis KN, Clock JA. Demonstrating Contaminant Degradation at an MGP Site With Metabolic Gas Flux and Radio Carbon Dating. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/rem.21508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
17
|
Obi CC, Adebusoye SA, Amund OO, Ugoji EO, Ilori MO, Hedman CJ, Hickey WJ. Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment. Appl Microbiol Biotechnol 2017; 101:4299-4314. [PMID: 28190100 DOI: 10.1007/s00253-017-8151-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/18/2017] [Accepted: 01/22/2017] [Indexed: 01/12/2023]
Abstract
Coastal sediments contaminated by polycyclic aromatic hydrocarbons (PAHs) can be candidates for remediation via an approach like land farming. Land farming converts naturally anaerobic sediments to aerobic environments, and the response of microbial communities, in terms of community structure alterations and corresponding effects on biodegradative activities, is unknown. A key goal of this study was to determine if different sediments exhibited common patterns in microbial community responses that might serve as indicators of PAH biodegradation. Sediments from three stations in the Lagos Lagoon (Nigeria) were used in microcosms, which were spiked with a mixture of four PAH, then examined for PAH biodegradation and for shifts in microbial community structure by analysis of diversity in PAH degradation genes and Illumina sequencing of 16S rRNA genes. PAH biodegradation was similar in all sediments, yet each exhibited unique microbiological responses and there were no microbial indicators of PAH bioremediation common to all sediments.
Collapse
Affiliation(s)
- Chioma C Obi
- Department of Microbiology, University of Lagos, Lagos, Nigeria.
- O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison, Madison, WI, USA.
| | | | | | - Esther O Ugoji
- Department of Microbiology, University of Lagos, Lagos, Nigeria
| | - Mathew O Ilori
- Department of Microbiology, University of Lagos, Lagos, Nigeria
| | | | - William J Hickey
- O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
18
|
Song M, Jiang L, Zhang D, Luo C, Wang Y, Yu Z, Yin H, Zhang G. Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil. JOURNAL OF HAZARDOUS MATERIALS 2016; 308:50-57. [PMID: 26808242 DOI: 10.1016/j.jhazmat.2016.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/30/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.
Collapse
Affiliation(s)
- Mengke Song
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Longfei Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
| | - Yan Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhiqiang Yu
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Hua Yin
- College of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| |
Collapse
|
19
|
Cupples AM. Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201500479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|