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Basik AA, Gibu N, Kawagiwa Y, Ng SM, Yeo TC, Sudesh K, Kasai D. Genomic insights into Dactylosporangium sp. AC04546, a rubber degrader with three latex clearing proteins. Front Microbiol 2024; 15:1378082. [PMID: 38873160 PMCID: PMC11169899 DOI: 10.3389/fmicb.2024.1378082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024] Open
Abstract
With more than 100 rubber-degrading strains being reported, only 9 Lcp proteins isolated from Nocardia, Gordonia, Streptomyces, Rhodococcus, Actinoplanes, and Solimonas have been purified and biochemically characterized. A new strain, Dactylosporangium sp. AC04546 (strain JCM34239), isolated from soil samples collected in Sarawak Forest, was able to grow and utilize natural or synthetic rubber as the sole carbon source. Complete genome of Strain AC04546 was obtained from the hybrid assembly of PacBio Sequel II and Illumina MiSeq. Strain AC04546 has a large circular genome of 13.08 Mb with a G+C content of 72.1%. The genome contains 11,865 protein-coding sequences with 3 latex clearing protein (lcp) genes located on its chromosome. The genetic organization of the lcp gene cluster is similar to two other reported rubber-degrading strains-Actinoplanes sp. OR16 and Streptomyces sp. CFMR 7. All 3 Lcp from strain AC04546 were expressed in Escherichia coli and exhibited degrading activity against natural rubber. The distinctiveness of strain AC04546, along with other characterized rubber-degrading strains, is reported here.
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Affiliation(s)
| | - Namiko Gibu
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yukimura Kawagiwa
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Siuk-Mun Ng
- Codon Genomics S/B, Seri Kembangan, Selangor, Malaysia
| | | | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia
| | - Daisuke Kasai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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Prasert Y, Surachat K, Chukamnerd A, Umsakul K. Investigation of potential rubber-degrading bacteria and genes involved. Arch Microbiol 2024; 206:71. [PMID: 38252137 DOI: 10.1007/s00203-023-03781-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/22/2023] [Accepted: 11/30/2023] [Indexed: 01/23/2024]
Abstract
COVID-19 pandemic has generated high demand for natural rubber gloves (NR) leading to crucial issues of rubber waste and waste management such as burning, dumping, stockpiling, discarding waste in landfills. Hence, rubber biodegradation by microorganisms is an alternative solution to the problem. The biodegradation method is environmentally friendly but normally extremely slow. Numerous microorganisms can degrade NR as a source of carbon and energy. In this study, Rhodococcus pyridinivorans KU1 was isolated from the consortium CK from previous study. The 40% rubber weight loss was detected after incubated for 2 months. The bacterial colonization and cavities on the surface of rubber were identified using a scanning electron microscope (SEM). The result demonstrated the critical degradation of the rubber surface, indicating that bacteria can degrade rubber and use it as their sole carbon source. The result of whole-genome sequencing (WGS) revealed a gene that is 99.9% identical to lcp which is responsible for poly (cis-1,4-isoprene) degradation. The results from Meta16S rRNA sequencing showed that the microbial communities were slightly shifted during the 2-month degradation, depending on the presence of monomers or oligomers appeared during the degradation process. The majority of species were soil bacteria such as phylum Proteobacteria, Actinobacteria, and Firmicutes. Members of Pseudoxanthomonas seemed to be the dominant degraders throughout the degradation.
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Affiliation(s)
- Yaninee Prasert
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Translational Medicine Research Center, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Arnon Chukamnerd
- Division of Infectious Diseases, Department of Internal Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Kamontam Umsakul
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
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Cui C, Jiang M, Zhang C, Zhang N, Jin FJ, Li T, Lee HG, Jin L. Assembly strategies for rubber-degrading microbial consortia based on omics tools. Front Bioeng Biotechnol 2023; 11:1326395. [PMID: 38125306 PMCID: PMC10731047 DOI: 10.3389/fbioe.2023.1326395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Numerous microorganisms, including bacteria and fungus, have been identified as capable of degrading rubber. Rubber biodegradation is still understudied due to its high stability and the lack of well-defined pathways and efficient enzymes involved in microorganism metabolism. However, rubber products manufacture and usage cause substantial environmental issues, and present physical-chemical methods involve dangerous chemical solvents, massive energy, and trash with health hazards. Eco-friendly solutions are required in this context, and biotechnological rubber treatment offers considerable promise. The structural and functional enzymes involved in poly (cis-1,4-isoprene) rubber and their cleavage mechanisms have been extensively studied. Similarly, novel bacterial strains capable of degrading polymers have been investigated. In contrast, relatively few studies have been conducted to establish natural rubber (NR) degrading bacterial consortia based on metagenomics, considering process optimization, cost effective approaches and larger scale experiments seeking practical and realistic applications. In light of the obstacles encountered during the constructing NR-degrading consortia, this study proposes the utilization of multi-omics tools to discern the underlying mechanisms and metabolites of rubber degradation, as well as associated enzymes and effective synthesized microbial consortia. In addition, the utilization of omics tool-based methods is suggested as a primary research direction for the development of synthesized microbial consortia in the future.
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Affiliation(s)
- Chengda Cui
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Mengke Jiang
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Chengxiao Zhang
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Naxue Zhang
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Taihua Li
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Long Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
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Leong SY, Lee SY, Koh TY, Ang DTC. 4R of rubber waste management: current and outlook. JOURNAL OF MATERIAL CYCLES AND WASTE MANAGEMENT 2022; 25:37-51. [PMID: 36466440 PMCID: PMC9703434 DOI: 10.1007/s10163-022-01554-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Excessive accumulation of rubber waste necessitates the need to revisit the effectiveness of the existing rubber waste management system. This review provides an overview of the legislative frameworks, techniques, challenges, and trends of rubber waste management in various countries. The 4R (reduce, reuse, recycle and recover) framework applied in waste management system in some countries appears to be viable for the processing of rubber waste. Certain countries especially some of the European Union (EU) members have implemented extended producer responsibility (EPR) system to manage the collection of rubber waste, particularly used tires. The processing of rubber waste in each level of the 4R hierarchy was then discussed, with detailed elaboration on the most practiced 'R', recycling which encompasses the direct recycling of products, as well as material recycling via physical and/or chemical means. The challenges faced in the implementation of rubber waste management system in different countries were highlighted and recommendations for a more sustainable rubber consumption were provided at the end of this review.
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Affiliation(s)
- Seng-Yi Leong
- Tunku Abdul Rahman University of Management and Technology, Jalan Genting Kelang, Wilayah Persekutuan Kuala Lumpur, 53300 Kuala Lumpur, Malaysia
| | - Siang-Yin Lee
- Technology and Engineering Division (BTK), RRIM Sungai Buloh Research Station, Malaysian Rubber Board (MRB), 47000 Selangor, Sungai Buloh Malaysia
| | - Thiam-Young Koh
- Tunku Abdul Rahman University of Management and Technology, Jalan Genting Kelang, Wilayah Persekutuan Kuala Lumpur, 53300 Kuala Lumpur, Malaysia
| | - Desmond Teck-Chye Ang
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
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