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Li J, Luo C, Cai X, Dai Y, Zhang D, Zhang G. Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC). ENVIRONMENT INTERNATIONAL 2024; 185:108555. [PMID: 38458119 DOI: 10.1016/j.envint.2024.108555] [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: 12/14/2023] [Revised: 01/28/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024]
Abstract
High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from 13C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from 13C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.
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Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xixi Cai
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 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 130021, China; College of New Energy and Environment, Jilin University, Changchun 130021, China; Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang 110044, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Maszenan AM, Bessarab I, Williams RBH, Petrovski S, Seviour RJ. The phylogeny, ecology and ecophysiology of the glycogen accumulating organism (GAO) Defluviicoccus in wastewater treatment plants. WATER RESEARCH 2022; 221:118729. [PMID: 35714465 DOI: 10.1016/j.watres.2022.118729] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/22/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
This comprehensive review looks critically what is known about members of the genus Defluviicoccus, an example of a glycogen accumulating organism (GAO), in wastewater treatment plants, but found also in other habitats. It considers the operating conditions thought to affect its performance in activated sludge plants designed to remove phosphorus microbiologically, including the still controversial view that it competes with the polyphosphate accumulating bacterium Ca. Accumulibacter for readily biodegradable substrates in the anaerobic zone receiving the influent raw sewage. It looks at its present phylogeny and what is known about it's physiology and biochemistry under the highly selective conditions of these plants, where the biomass is recycled continuously through alternative anaerobic (feed); aerobic (famine) conditions encountered there. The impact of whole genome sequence data, which have revealed considerable intra- and interclade genotypic diversity, on our understanding of its in situ behaviour is also addressed. Particular attention is paid to the problems in much of the literature data based on clone library and next generation DNA sequencing data, where Defluviicoccus identification is restricted to genus level only. Equally problematic, in many publications no attempt has been made to distinguish between Defluviicoccus and the other known GAO, especially Ca. Competibacter, which, as shown here, has a very different ecophysiology. The impact this has had and continues to have on our understanding of members of this genus is discussed, as is the present controversy over its taxonomy. It also suggests where research should be directed to answer some of the important research questions raised in this review.
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Affiliation(s)
- Abdul M Maszenan
- E2S2, NUS Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 117456, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 117456, Singapore
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, 3086 Victoria, Australia
| | - Robert J Seviour
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, 3086 Victoria, Australia.
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Onetto CA, Grbin PR, McIlroy SJ, Eales KL. Genomic insights into the metabolism of ‘CandidatusDefluviicoccus seviourii’, a member ofDefluviicoccuscluster III abundant in industrial activated sludge. FEMS Microbiol Ecol 2018; 95:5210054. [DOI: 10.1093/femsec/fiy231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/24/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Cristobal A Onetto
- Department of Wine & Food Science, University of Adelaide, Adelaide 5064, Australia
| | - Paul R Grbin
- Department of Wine & Food Science, University of Adelaide, Adelaide 5064, Australia
| | - Simon J McIlroy
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Brisbane, Australia
| | - Kathryn L Eales
- Department of Wine & Food Science, University of Adelaide, Adelaide 5064, Australia
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