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Vural C, Ettadili H. Biodegradation of phthalic acid and terephthalic acid by Comamonas testosteroni strains. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01176-x. [PMID: 38809402 DOI: 10.1007/s12223-024-01176-x] [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: 12/04/2023] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Phthalic acid isomers are the monomers of phthalate molecules, also known as phthalic acid esters, widely employed in the plastics industry. This study aims to investigate the biodegradation of phthalic acid (PA) and terephthalic acid (TPA) by five industry-borne Comamonas testosteroni strains: 3APTOL, 3ABBK, 2B, 3A1, and C8. To assess the ability of C. testosteroni strains to biodegrade phthalic acid isomers in fermentation media, an analytical method was employed, consisting of high-performance liquid chromatography (HPLC) analyses. Subsequently, molecular screening of the genomic and plasmid DNA was conducted to identify the degradative genes responsible for the breakdown of these chemicals. The genes of interest, including ophA2, tphA2, tphA3, pmdA, and pmdB, were screened by real-time PCR. The five C. testosteroni strains effectively degraded 100% of 100 mg/L PA (p = 0.033) and TPA (p = 0.0114). Molecular analyses indicated that all C. testosteroni strains contained the pertinent genes at different levels within their genomes and plasmids, as reflected in the threshold cycle (Ct) values. Additionally, DNA temperature of melting (Tm) analyses uncovered minor differences between groups of genes in genomic and plasmid DNA. C. testosteroni strains could be excellent candidates for the removal of phthalic acid isomers from environmental systems.
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Affiliation(s)
- Caner Vural
- Department of Biology, Molecular Biology Section, Pamukkale University, 20160, Denizli, Turkey.
| | - Hamza Ettadili
- Department of Biology, Molecular Biology Section, Pamukkale University, 20160, Denizli, Turkey
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Cao Z, Xia W, Wu S, Ma J, Zhou X, Qian X, Xu A, Dong W, Jiang M. Bioengineering Comamonas testosteroni CNB-1: a robust whole-cell biocatalyst for efficient PET microplastic degradation. BIORESOUR BIOPROCESS 2023; 10:94. [PMID: 38647778 PMCID: PMC10992048 DOI: 10.1186/s40643-023-00715-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/10/2023] [Indexed: 04/25/2024] Open
Abstract
The escalating crisis of polyethylene terephthalate (PET) microplastic contamination in biological wastewater treatment systems is a pressing environmental concern. These microplastics inevitably accumulate in sewage sludge due to the absence of effective removal technologies. Addressing this urgent issue, this study introduces a novel approach using DuraPETase, a potent enzyme with enhanced PET hydrolytic activity at ambient temperatures. Remarkably, this enzyme was successfully secreted from Comamonas testosteroni CNB-1, a dominant species in the active sludge. The secreted DuraPETase showed significant hydrolytic activity toward p-NPB and PET nanoplastics. Furthermore, the CNB-1 derived whole-cell biocatalyst was able to depolymerize PET microplastics under ambient temperature, achieving a degradation efficiency of 9% within 7 days. The CNB-1-based whole biocatalysts were also capable of utilizing PET degradation intermediates, such as terephthalic acid (TPA) and ethylene glycol (EG), and bis(2-hydroxyethyl)-TPA (BHET), for growth. This indicates that it can completely mineralize PET, as opposed to merely breaking it down into smaller molecules. This research highlights the potential of activated sludge as a potent source for insitu microplastic removal.
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Affiliation(s)
- Zhanqing Cao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Wei Xia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Shilei Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Jiale Ma
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xiaoli Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xiujuan Qian
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Anming Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, Nanjing Tech University, Nanjing, 211816, China.
| | - Min Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, Nanjing Tech University, Nanjing, 211816, China
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Hamese S, Mugwanda K, Takundwa M, Prinsloo E, Thimiri Govinda Raj DB. Recent advances in genome annotation and synthetic biology for the development of microbial chassis. J Genet Eng Biotechnol 2023; 21:156. [PMID: 38038785 PMCID: PMC10692039 DOI: 10.1186/s43141-023-00598-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
This article provides an overview of microbial host selection, synthetic biology, genome annotation, metabolic modeling, and computational methods for predicting gene essentiality for developing a microbial chassis. This article focuses on lactic acid bacteria (LAB) as a microbial chassis and strategies for genome annotation of the LAB genome. As a case study, Lactococcus lactis is chosen based on its well-established therapeutic applications such as probiotics and oral vaccine development. In this article, we have delineated the strategies for genome annotations of lactic acid bacteria. These strategies also provide insights into streamlining genome reduction without compromising the functionality of the chassis and the potential for minimal genome chassis development. These insights underscore the potential for the development of efficient and sustainable synthetic biology systems using streamlined microbial chassis with minimal genomes.
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Affiliation(s)
- Saltiel Hamese
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, Next Generation Health Cluster, CSIR Pretoria, South Africa
- Biotechnology Innovation Centre, Rhodes University, PO Box 94, Makhanda, 6140, South Africa
| | - Kanganwiro Mugwanda
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, Next Generation Health Cluster, CSIR Pretoria, South Africa
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Mutsa Takundwa
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, Next Generation Health Cluster, CSIR Pretoria, South Africa
| | - Earl Prinsloo
- Biotechnology Innovation Centre, Rhodes University, PO Box 94, Makhanda, 6140, South Africa
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, Next Generation Health Cluster, CSIR Pretoria, South Africa.
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Ma XC, Wang K, Gao XL, Li XK, Liu GG, Chen HY, Piao CY, You SJ. Deciphering the fate of osmotic stress priming on enhanced microorganism acclimation for purified terephthalic acid wastewater treatment with high salinity and organic load. BIORESOURCE TECHNOLOGY 2023; 374:128656. [PMID: 36690216 DOI: 10.1016/j.biortech.2023.128656] [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: 10/13/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Osmotic stress priming (OSP) was an effective management strategy for improving microbial acclimation to salt stress. In this study, the interaction between pollutants and microbiota, and microbial osmoregulation were investigated triggered by OSP (alternately increasing salinity and organic loading). Results showed that OSP significantly improved COD removal from 31.53 % to 67.99 % and mitigated the terephthalate inhibition produced by toluate, decreasing from 1908.08 mg/L to 837.16 mg/L compared with direct priming. Due to an increase in salinity, Pelotomaculum and Mesotoga were enriched to facilitate terephthalate degradation and syntrophic acetate oxidation (SAO). And organic load promoted acetate formation through syntrophic metabolism of Syntrophorhabdus/Pelotomaculum and SAO-dependent hydrogenotrophic methanogenesis. K+ absorbing, proline and trehalose synthesis participated in osmoregulation at 0.5 % salinity, while only ectoine alleviated intracellular osmolarity under 1.0 % salinity with OLR of 0.44 kg COD /m3. This study provided in-depth insight for microbial acclimation process of anaerobic priming of saline wastewater.
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Affiliation(s)
- Xiao-Chen Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ke Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; National Engineering Research Center for Safe Sludge Disposal and Resource Recovery, Harbin Institute of Technology, Harbin 150090, China; Harbin Institute of Technology National Engineering Research Center of Water Resources Co., Ltd, Guangdong Yuehai Water Investment Co., Ltd, Harbin 150090, China
| | - Xin-Lei Gao
- Harbin Institute of Technology National Engineering Research Center of Water Resources Co., Ltd, Guangdong Yuehai Water Investment Co., Ltd, Harbin 150090, China
| | - Xiang-Kun Li
- School of Civil and Transportation, Hebei University of Technology, Tianjin 300401, China.
| | - Gai-Ge Liu
- School of Civil and Transportation, Hebei University of Technology, Tianjin 300401, China
| | - Hong-Ying Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chen-Yu Piao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shi-Jie You
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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Ma XC, Wang K, Gao XL, Li XK, Liu GG, Chen HY, Piao CY, You SJ. Temperature-regulated and starvation-induced refractory para-toluic acid anaerobic biotransformation. CHEMOSPHERE 2023; 311:137008. [PMID: 36377119 DOI: 10.1016/j.chemosphere.2022.137008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/04/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Little research was focused on the anerobic degradation of refractory para-toluic acid at present. Thus, temperature-regulated anaerobic system of para-toluic acid fed as sole substrate was built and investigated via microbiota, metabolism intermediates, and function prediction in this study. Results showed that low methane yield was produced in para-toluic acid anaerobic system at alkaline condition. And the causes were owing to anaerobic methane oxidation and potentially H2S production at 37 °C, N2 production by denitrification before starvation and propionic acid occurrence after starvation at 27 °C, and production of N2 and free ammonia, and accumulation of acetic acid at 52 °C. Simultaneously, hydrogenotrophic methanogenesis dependent on syntrophic acetate oxidation (SAO) was predominant, facilitating the removal of para-toluic acid at 52 °C. Moreover, the key intermediate changed from phthalic acid of 37 °C and 27 °C before starvation to terephthalic acid of 52 °C. Starvation promoted removal of para-toluic acid through benzoyl-CoA pathway by Syntrophorhabdus, enrichment of syntrophic propionate degraders of Bacteroidetes and Ignavibacteriaceae, and increase of methylotrophic methanogens.
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Affiliation(s)
- Xiao-Chen Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ke Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; National Engineering Research Center for Safe Sludge Disposal and Resource Recovery, Harbin Institute of Technology, Harbin, 150090, China; Harbin Institute of Technology National Engineering Research Center of Water Resources Co., Ltd, Guangdong Yuehai Water Investment Co., Ltd, Harbin, 150090, China.
| | - Xin-Lei Gao
- Harbin Institute of Technology National Engineering Research Center of Water Resources Co., Ltd, Guangdong Yuehai Water Investment Co., Ltd, Harbin, 150090, China
| | - Xiang-Kun Li
- School of Civil and Transportation, Hebei University of Technology, Tianjin, 300401, China.
| | - Gai-Ge Liu
- School of Civil and Transportation, Hebei University of Technology, Tianjin, 300401, China
| | - Hong-Ying Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Chen-Yu Piao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Shi-Jie You
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
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Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
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Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
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