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Lee GH, Kim DW, Jin YH, Kim SM, Lim ES, Cha MJ, Ko JK, Gong G, Lee SM, Um Y, Han SO, Ahn JH. Biotechnological Plastic Degradation and Valorization Using Systems Metabolic Engineering. Int J Mol Sci 2023; 24:15181. [PMID: 37894861 PMCID: PMC10607142 DOI: 10.3390/ijms242015181] [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: 09/22/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Various kinds of plastics have been developed over the past century, vastly improving the quality of life. However, the indiscriminate production and irresponsible management of plastics have led to the accumulation of plastic waste, emerging as a pressing environmental concern. To establish a clean and sustainable plastic economy, plastic recycling becomes imperative to mitigate resource depletion and replace non-eco-friendly processes, such as incineration. Although chemical and mechanical recycling technologies exist, the prevalence of composite plastics in product manufacturing complicates recycling efforts. In recent years, the biodegradation of plastics using enzymes and microorganisms has been reported, opening a new possibility for biotechnological plastic degradation and bio-upcycling. This review provides an overview of microbial strains capable of degrading various plastics, highlighting key enzymes and their role. In addition, recent advances in plastic waste valorization technology based on systems metabolic engineering are explored in detail. Finally, future perspectives on systems metabolic engineering strategies to develop a circular plastic bioeconomy are discussed.
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Affiliation(s)
- Ga Hyun Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Do-Wook Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Yun Hui Jin
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sang Min Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Eui Seok Lim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Min Ji Cha
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jung Ho Ahn
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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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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Junghare M, Frey J, Naji KM, Spiteller D, Vaaje-Kolstad G, Schink B. Isophthalate:coenzyme A ligase initiates anaerobic degradation of xenobiotic isophthalate. BMC Microbiol 2022; 22:227. [PMID: 36171563 PMCID: PMC9516798 DOI: 10.1186/s12866-022-02630-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Environmental contamination from synthetic plastics and their additives is a widespread problem. Phthalate esters are a class of refractory synthetic organic compounds which are widely used in plastics, coatings, and for several industrial applications such as packaging, pharmaceuticals, and/or paints. They are released into the environment during production, use and disposal, and some of them are potential mutagens and carcinogens. Isophthalate (1,3-benzenedicarboxylic acid) is a synthetic chemical that is globally produced at a million-ton scale for industrial applications and is considered a priority pollutant. Here we describe the biochemical characterization of an enzyme involved in anaerobic degradation of isophthalate by the syntrophically fermenting bacterium Syntrophorhabdus aromaticivorans strain UI that activate isophthalate to isophthalyl-CoA followed by its decarboxylation to benzoyl-CoA. Results Isophthalate:Coenzyme A ligase (IPCL, AMP-forming) that activates isophthalate to isophthalyl-CoA was heterologously expressed in E. coli (49.6 kDa) for biochemical characterization. IPCL is homologous to phenylacetate-CoA ligase that belongs to the family of ligases that form carbon-sulfur bonds. In the presence of coenzyme A, Mg2+ and ATP, IPCL converts isophthalate to isophthalyl-CoA, AMP and pyrophosphate (PPi). The enzyme was specifically induced after anaerobic growth of S. aromaticivorans in a medium containing isophthalate as the sole carbon source. Therefore, IPCL exhibited high substrate specificity and affinity towards isophthalate. Only substrates that are structurally related to isophthalate, such as glutarate and 3-hydroxybenzoate, could be partially converted to the respective coenzyme A esters. Notably, no activity could be measured with substrates such as phthalate, terephthalate and benzoate. Acetyl-CoA or succinyl-CoA did not serve as CoA donors. The enzyme has a theoretical pI of 6.8 and exhibited optimal activity between pH 7.0 to 7.5. The optimal temperature was between 25 °C and 37 °C. Denaturation temperature (Tm) of IPCL was found to be at about 63 °C. The apparent KM values for isophthalate, CoA, and ATP were 409 μM, 642 μM, and 3580 μM, respectively. Although S. aromaticivorans is a strictly anaerobic bacterium, the enzyme was found to be oxygen-insensitive and catalysed isophthalyl-CoA formation under both anoxic and oxic conditions. Conclusion We have successfully cloned the ipcl gene, expressed and characterized the corresponding IPCL enzyme, which plays a key role in isophthalate activation that initiates its activation and further degradation by S. aromaticivorans. Its biochemical characterization represents an important step in the elucidation of the complete degradation pathway of isophthalate. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02630-x.
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Affiliation(s)
- Madan Junghare
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany. .,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway.
| | - Jasmin Frey
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Khalid M Naji
- Chemical Ecology and Biological Chemistry, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Dieter Spiteller
- Chemical Ecology and Biological Chemistry, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway
| | - Bernhard Schink
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany
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Kuroda K, Narihiro T, Shinshima F, Yoshida M, Yamaguchi H, Kurashita H, Nakahara N, Nobu MK, Noguchi TQP, Yamauchi M, Yamada M. High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation. WATER RESEARCH 2022; 219:118581. [PMID: 35584587 DOI: 10.1016/j.watres.2022.118581] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Polyethylene terephthalate (PET) is produced worldwide, mainly as material for plastic drink bottles. PET is produced by polymerization of purified terephthalate (PTA) or dimethyl terephthalate (DMT) with ethylene glycol. During the synthetic manufacturing processes of PTA and DMT, high organic loading wastewater is produced, which is typically treated separately by anaerobic wastewater treatment technologies. Given the high demand for PET, manufacturing plants are expanding globally, which will result in an increase in the amounts of PTA and DMT wastewater in need of treatment. In terms of effective treatment, the cotreatment of PTA and DMT wastewater has several advantages, including lower area and energy requirements. In this study, we examined the performance of an upflow anaerobic sludge blanket (UASB) reactor in cotreating PTA and DMT wastewater with high organic loading, evaluating its removal characteristics after 518 days of continuous operation. In addition, we performed a microbiome analysis of the UASB granular sludge to uncover the microbial interactions and metabolic functions within the reactor. By continuous operation, we achieved an organic removal rate of 6.6 kg m-3 day-1. In addition, we confirmed that aromatic compounds in the complex wastewater from the PTA and DMT manufacturing processes are biodegradable in the following order: benzoate > orthophthalate > terephthalate > isophthalate > p-toluic acid. 16S rRNA gene-based network analysis shows that anaerobic Woesearchaeales belonging to phylum Nanoarchaeota has a positive correlation with Methanoregula, Candidatus Methanofastidiosum, and Methanosarcina, suggesting a symbiotic relationship with methanogens in granular sludge. Shotgun metagenomic analysis revealed that terephthalate, isophthalate/orthophthalate, and benzoate were degraded by different members of Pelotomaculaceae and Syntrophorhabdaceae. According to the genomic information, we propose two new possible routes for orthophthalate degradation by the Syntrophorhabdaceae organism.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517 Japan.
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517 Japan.
| | - Futaba Shinshima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517 Japan; Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki 885-8567, Japan
| | - Mio Yoshida
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki 885-8567, Japan
| | - Haruka Yamaguchi
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki 885-8567, Japan
| | - Hazuki Kurashita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517 Japan; Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki 885-8567, Japan
| | - Nozomi Nakahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Taro Q P Noguchi
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki 885-8567, Japan
| | - Masahito Yamauchi
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College, 1460-1 Shinkou, Hayato, Kirishima, Kagoshima 899-5193, Japan
| | - Masayoshi Yamada
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College, 1460-1 Shinkou, Hayato, Kirishima, Kagoshima 899-5193, Japan
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Natural Source Zone Depletion (NSZD) Quantification Techniques: Innovations and Future Directions. SUSTAINABILITY 2022. [DOI: 10.3390/su14127027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Natural source zone depletion (NSZD) is an emerging technique for sustainable and cost-effective bioremediation of light non-aqueous phase liquid (LNAPL) in oil spill sites. Depending on regulatory objectives, NSZD has the potential to be used as either the primary or sole LNAPL management technique. To achieve this goal, NSZD rate (i.e., rate of bulk LNAPL mass depletion) should be quantified accurately and precisely. NSZD has certain characteristic features that have been used as surrogates to quantify the NSZD rates. This review highlights the most recent trends in technology development for NSZD data collection and rate estimation, with a focus on the operational and technical advantages and limitations of the associated techniques. So far, four principal techniques are developed, including concentration gradient (CG), dynamic closed chamber (DCC), CO2 trap and thermal monitoring. Discussions revolving around two techniques, “CO2 trap” and “thermal monitoring”, are expanded due to the particular attention to them in the current industry. The gaps of knowledge relevant to the NSZD monitoring techniques are identified and the issues which merit further research are outlined. It is hoped that this review can provide researchers and practitioners with sufficient information to opt the best practice for the research and application of NSZD for the management of LNAPL impacted sites.
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Gao R, Pan H, Kai L, Han K, Lian J. Microbial degradation and valorization of poly(ethylene terephthalate) (PET) monomers. World J Microbiol Biotechnol 2022; 38:89. [PMID: 35426614 DOI: 10.1007/s11274-022-03270-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/23/2022] [Indexed: 12/22/2022]
Abstract
The polyethylene terephthalate (PET) is one of the major plastics with a huge annual production. Alongside with its mass production and wide applications, PET pollution is threatening and damaging the environment and human health. Although mechanical or chemical methods can deal with PET, the process suffers from high cost and the hydrolyzed monomers will cause secondary pollution. Discovery of plastic-degrading microbes and the corresponding enzymes emerges new hope to cope with this issue. Combined with synthetic biology and metabolic engineering, microbial cell factories not only provide a promising approach to degrade PET, but also enable the conversion of its monomers, ethylene glycol (EG) and terephthalic acid (TPA), into value-added compounds. In this way, PET wastes can be handled in environment-friendly and more potentially cost-effective processes. While PET hydrolases have been extensively reviewed, this review focuses on the microbes and metabolic pathways for the degradation of PET monomers. In addition, recent advances in the biotransformation of TPA and EG into value-added compounds are discussed in detail.
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Affiliation(s)
- Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 310027, Hangzhou, China
| | - Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China
| | - Lei Kai
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, 22116, Xuzhou, China.,Jiangsu Keybio Co. LTD, 22116, Xuzhou, China
| | - Kun Han
- Jiangsu Keybio Co. LTD, 22116, Xuzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China. .,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 310027, Hangzhou, China.
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Tiwari N, Bansal M, Santhiya D, Sharma JG. Insights into microbial diversity on plastisphere by multi-omics. Arch Microbiol 2022; 204:216. [PMID: 35316402 DOI: 10.1007/s00203-022-02806-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Plastic pollution is a major concern in marine environment as it takes many years to degrade and is one of the greatest threats to marine life. Plastic surface, referred to as plastisphere, provides habitat for growth and proliferation of various microorganisms. The discovery of these microbes is necessary to identify significant genes, enzymes and bioactive compounds that could help in bioremediation and other commercial applications. Conventional culture techniques have been successful in identifying few microbes from these habitats, leaving majority of them yet to be explored. As such, to recognize the vivid genetic diversity of microbes residing in plastisphere, their structure and corresponding ecological roles within the ecosystem, an emerging technique, called metagenomics has been explored. The technique is expected to provide hitherto unknown information on microbes from the plastisphere. Metagenomics along with next generation sequencing provides comprehensive knowledge on microbes residing in plastisphere that identifies novel microbes for plastic bioremediation, bioactive compounds and other potential benefits. The following review summarizes the efficiency of metagenomics and next generation sequencing technology over conventionally used methods for culturing microbes. It attempts to illustrate the workflow mechanism of metagenomics to elucidate diverse microbial profiles. Further, importance of integrated multi-omics techniques has been highlighted in discovering microbial ecology residing on plastisphere for wider applications.
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Affiliation(s)
- Neha Tiwari
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Megha Bansal
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Deenan Santhiya
- Department of Applied Chemistry, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, Delhi, 110042, India.
| | - Jai Gopal Sharma
- Department of Biotechnology, Delhi Technological University, Delhi, India
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Lin K, Han S, Zheng S. Application of Corynebacterium glutamicum engineering display system in three generations of biorefinery. Microb Cell Fact 2022; 21:14. [PMID: 35090458 PMCID: PMC8796525 DOI: 10.1186/s12934-022-01741-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/09/2022] [Indexed: 11/29/2022] Open
Abstract
The fermentation production of platform chemicals in biorefineries is a sustainable alternative to the current petroleum refining process. The natural advantages of Corynebacterium glutamicum in carbon metabolism have led to C. glutamicum being used as a microbial cell factory that can use various biomass to produce value-added platform chemicals and polymers. In this review, we discussed the use of C. glutamicum surface display engineering bacteria in the three generations of biorefinery resources, and analyzed the C. glutamicum engineering display system in degradation, transport, and metabolic network reconstruction models. These engineering modifications show that the C. glutamicum engineering display system has great potential to become a cell refining factory based on sustainable biomass, and further optimizes the inherent properties of C. glutamicum as a whole-cell biocatalyst. This review will also provide a reference for the direction of future engineering transformation.
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Affiliation(s)
- Kerui Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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10
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Fuller AJ, Leary P, Gray ND, Davies HS, Mosselmans JFW, Cox F, Robinson CH, Pittman JK, McCann CM, Muir M, Graham MC, Utsunomiya S, Bower WR, Morris K, Shaw S, Bots P, Livens FR, Law GTW. Organic complexation of U(VI) in reducing soils at a natural analogue site: Implications for uranium transport. CHEMOSPHERE 2020; 254:126859. [PMID: 32957279 DOI: 10.1016/j.chemosphere.2020.126859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/07/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Understanding the long-term fate, stability, and bioavailability of uranium (U) in the environment is important for the management of nuclear legacy sites and radioactive wastes. Analysis of U behavior at natural analogue sites permits evaluation of U biogeochemistry under conditions more representative of long-term equilibrium. Here, we have used bulk geochemical and microbial community analysis of soils, coupled with X-ray absorption spectroscopy and μ-focus X-ray fluorescence mapping, to gain a mechanistic understanding of the fate of U transported into an organic-rich soil from a pitchblende vein at the UK Needle's Eye Natural Analogue site. U is highly enriched in the Needle's Eye soils (∼1600 mg kg-1). We show that this enrichment is largely controlled by U(VI) complexation with soil organic matter and not U(VI) bioreduction. Instead, organic-associated U(VI) seems to remain stable under microbially-mediated Fe(III)-reducing conditions. U(IV) (as non-crystalline U(IV)) was only observed at greater depths at the site (>25 cm); the soil here was comparatively mineral-rich, organic-poor, and sulfate-reducing/methanogenic. Furthermore, nanocrystalline UO2, an alternative product of U(VI) reduction in soils, was not observed at the site, and U did not appear to be associated with Fe-bearing minerals. Organic-rich soils appear to have the potential to impede U groundwater transport, irrespective of ambient redox conditions.
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Affiliation(s)
- Adam J Fuller
- Centre for Radiochemistry Research, Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK
| | - Peter Leary
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Neil D Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Helena S Davies
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | | | - Filipa Cox
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Clare H Robinson
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Jon K Pittman
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Clare M McCann
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Michael Muir
- School of Geoscience, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Margaret C Graham
- School of Geoscience, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Satoshi Utsunomiya
- School of Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - William R Bower
- Centre for Radiochemistry Research, Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK; Radiochemistry Unit, Department of Chemistry, The University of Helsinki, 00014, Finland
| | - Katherine Morris
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Samuel Shaw
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Pieter Bots
- Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Francis R Livens
- Centre for Radiochemistry Research, Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK; Research Centre for Radwaste Disposal, and Williamson Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Gareth T W Law
- Centre for Radiochemistry Research, Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK; Radiochemistry Unit, Department of Chemistry, The University of Helsinki, 00014, Finland.
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11
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Moura AGL, Centurion VB, Okada DY, Motteran F, Delforno TP, Oliveira VM, Varesche MBA. Laundry wastewater and domestic sewage pilot-scale anaerobic treatment: Microbial community resilience regarding sulfide production. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 251:109495. [PMID: 31539699 DOI: 10.1016/j.jenvman.2019.109495] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 05/07/2023]
Abstract
In this study, the removal of anionic surfactant Linear Alkylbenzene Sulfonate (LAS) from laundry wastewater was evaluated in co-digestion with domestic sewage, using a pilot-scale Expanded Granular Sludge Bed reactor. Surfactant influent concentration was enhanced from 5 ± 3 mg LAS L-1 (stage I) to 19 ± 10 mg LAS L-1 (stage II) and 36 ± 19 mg LAS L-1 (stage III) throughout reactor operation. Sulfide levels higher than 20 mg L-1 influenced LAS removal efficiency, which decreased from 71% to 55% and 32% in stage I, II and III, respectively. Acclimation of microbial population was verified and higher relative abundance of the genera similar to Cytophaga, Bacteroides, Syntrophus and Syntrophobacter in the early stages (adaptation and stage I) was replaced by higher relative abundance of the genera Anaerophaga, Nitrosovibrio, Sulfurovum and Desulfovibrio in the last stages (stage II and III).
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Affiliation(s)
- A G L Moura
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP, Brazil.
| | - V B Centurion
- Microbial Resources Division, Research Centre for Chemistry, Biology and Agriculture (CPQBA), Campinas University, UNICAMP, Campinas, SP, Brazil.
| | - D Y Okada
- School of Technology, Division of Technology in Environment Sanitation, Campinas University, UNICAMP, Limeira, SP, Brazil.
| | - F Motteran
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP, Brazil.
| | - T P Delforno
- Microbial Resources Division, Research Centre for Chemistry, Biology and Agriculture (CPQBA), Campinas University, UNICAMP, Campinas, SP, Brazil.
| | - V M Oliveira
- Microbial Resources Division, Research Centre for Chemistry, Biology and Agriculture (CPQBA), Campinas University, UNICAMP, Campinas, SP, Brazil.
| | - M B A Varesche
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP, Brazil.
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12
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Reis AC, Kolvenbach BA, Chami M, Gales L, Egas C, Corvini PFX, Nunes OC. Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. BMC Genomics 2019; 20:885. [PMID: 31752666 PMCID: PMC6868719 DOI: 10.1186/s12864-019-6206-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/21/2019] [Indexed: 02/01/2023] Open
Abstract
Background Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified. Results Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements. Conclusions Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.
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Affiliation(s)
- Ana C Reis
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.,Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Mohamed Chami
- BioEM lab, C-Cina, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Luís Gales
- Instituto de Investigação e Inovação em Saúde - i3S, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Biologia Molecular e Celular - IBMC, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar - ICBAS, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Faculty of Medicine, Rua Larga, Pólo I, 3004-504, Coimbra, Portugal
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Olga C Nunes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
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13
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Identification of naphthalene carboxylase subunits of the sulfate-reducing culture N47. Biodegradation 2019; 30:147-160. [DOI: 10.1007/s10532-019-09872-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/26/2019] [Indexed: 11/26/2022]
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14
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Reis AC, Čvančarová M, Liu Y, Lenz M, Hettich T, Kolvenbach BA, Corvini PFX, Nunes OC. Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP. Appl Microbiol Biotechnol 2018; 102:10299-10314. [PMID: 30294753 DOI: 10.1007/s00253-018-9411-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 11/26/2022]
Abstract
In the last decade, biological degradation and mineralization of antibiotics have been increasingly reported feats of environmental bacteria. The most extensively described example is that of sulfonamides that can be degraded by several members of Actinobacteria and Proteobacteria. Previously, we reported sulfamethoxazole (SMX) degradation and partial mineralization by Achromobacter denitrificans strain PR1, isolated from activated sludge. However, further studies revealed an apparent instability of this metabolic trait in this strain. Here, we investigated this instability and describe the finding of a low-abundance and slow-growing actinobacterium, thriving only in co-culture with strain PR1. This organism, named GP, shared highest 16S rRNA gene sequence similarity (94.6-96.9%) with the type strains of validly described species of the genus Leucobacter. This microbial consortium was found to harbor a homolog to the sulfonamide monooxygenase gene (sadA) also found in other sulfonamide-degrading bacteria. This gene is overexpressed in the presence of the antibiotic, and evidence suggests that it codes for a group D flavin monooxygenase responsible for the ipso-hydroxylation of SMX. Additional side reactions were also detected comprising an NIH shift and a Baeyer-Villiger rearrangement, which indicate an inefficient biological transformation of these antibiotics in the environment. This work contributes to further our knowledge in the degradation of this ubiquitous micropollutant by environmental bacteria.
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Affiliation(s)
- Ana C Reis
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Monika Čvančarová
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Ying Liu
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Markus Lenz
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Timm Hettich
- Institute for Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Olga C Nunes
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
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15
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Chau ATT, Lee M, Adrian L, Manefield MJ. Syntrophic Partners Enhance Growth and Respiratory Dehalogenation of Hexachlorobenzene by Dehalococcoides mccartyi Strain CBDB1. Front Microbiol 2018; 9:1927. [PMID: 30186256 PMCID: PMC6113397 DOI: 10.3389/fmicb.2018.01927] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/30/2018] [Indexed: 11/19/2022] Open
Abstract
This study investigated syntrophic interactions between chlorinated benzene respiring Dehalococcoides mccartyi strain CBDB1 and fermenting partners (Desulfovibrio vulgaris, Syntrophobacter fumaroxidans, and Geobacter lovleyi) during hexachlorobenzene respiration. Dechlorination rates in syntrophic co-cultures were enhanced 2-3 fold compared to H2 fed CBDB1 pure cultures (0.23 ± 0.04 μmol Cl− day−1). Syntrophic partners were also able to supply cobalamins to CBDB1, albeit with 3–10 fold lower resultant dechlorination activity compared to cultures receiving exogenous cyanocobalamin. Strain CBDB1 pure cultures accumulated ~1 μmol of carbon monoxide per 87.5 μmol Cl− released during hexachlorobenzene respiration resulting in decreases in dechlorination activity. The syntrophic partners investigated were shown to consume carbon monoxide generated by CBDB1, thus relieving carbon monoxide autotoxicity. Accumulation of lesser chlorinated chlorobenzene congeners (1,3- and 1,4-dichlorobenzene and 1,3,5-trichlorobenzene) also inhibited dechlorination activity and their removal from the headspace through adsorption to granular activated carbon was shown to restore activity. Proteomic analysis revealed co-culturing strain CBDB1 with Geobacter lovleyi upregulated CBDB1 genes associated with reductive dehalogenases, hydrogenases, formate dehydrogenase, and ribosomal proteins. These data provide insight into CBDB1 ecology and inform strategies for application of CBDB1 in ex situ hexachlorobenzene destruction technologies.
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Affiliation(s)
- Anh T T Chau
- College of Agriculture and Applied Biology, Cantho University, Can Tho, Vietnam.,School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Michael J Manefield
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia.,School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
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16
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Liu M, Wang S, Nobu MK, Bocher BTW, Kaley SA, Liu WT. Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater. WATER RESEARCH 2017; 122:308-316. [PMID: 28614743 DOI: 10.1016/j.watres.2017.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/08/2017] [Accepted: 06/03/2017] [Indexed: 06/07/2023]
Abstract
Up-flow anaerobic sludge blanket (UASB) processes treating purified terephthalic acid (PTA) wastewater often face challenges associated with biomass loss. As excessive biomass loss could lead to deterioration of PTA removal, biostimulation and bioaugmentation were often practiced without understanding the microbial impact in UASB. Three laboratory-scale UASB reactors were operated with synthetic PTA wastewater as the feed, with two added with co-substrate (glucose or molasses) on Day 170 for 90 days, and one with external granules on Day 118. Throughout the operation, treatment performance was measured together with the analysis of microbial communities of biomass samples using 16S rRNA-based gene Illumina sequencing. Glucose amendment destabilized both terephthalic acid and para-toluic acid removal, while molasses amendment improved para-toluic acid removal. Both substrate addition generally led to decreases in the abundances of syntrophs and methanogens and increases in carbohydrate-fermenting bacteria in the granular sludge. Regarding bioaugmentation, paper mill granule addition led to a temporary crash of terephthalic acid removal for 42 days, and deterioration of para-toluic acid removal throughout the operation. Syntrophs and methanogens were observed to colonize on the paper mill granules after three months, meanwhile growth of methanogens were stimulated on the PTA granules added initially. Overall, proper level of molasses amendment and external granule inoculation could be promising strategies to make up for biomass loss during the operation of PTA-degrading UASB.
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Affiliation(s)
- Miaomiao Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Shanquan Wang
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Masaru Konishi Nobu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | | | - Scott A Kaley
- BP America, Petrochemicals Technology, Naperville, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA.
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17
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Kuroda K, Nobu MK, Mei R, Narihiro T, Bocher BTW, Yamaguchi T, Liu WT. A Single-Granule-Level Approach Reveals Ecological Heterogeneity in an Upflow Anaerobic Sludge Blanket Reactor. PLoS One 2016; 11:e0167788. [PMID: 27936088 PMCID: PMC5147981 DOI: 10.1371/journal.pone.0167788] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
Abstract
Upflow anaerobic sludge blanket (UASB) reactor has served as an effective process to treat industrial wastewater such as purified terephthalic acid (PTA) wastewater. For optimal UASB performance, balanced ecological interactions between syntrophs, methanogens, and fermenters are critical. However, much of the interactions remain unclear because UASB have been studied at a “macro”-level perspective of the reactor ecosystem. In reality, such reactors are composed of a suite of granules, each forming individual micro-ecosystems treating wastewater. Thus, typical approaches may be oversimplifying the complexity of the microbial ecology and granular development. To identify critical microbial interactions at both macro- and micro- level ecosystem ecology, we perform community and network analyses on 300 PTA–degrading granules from a lab-scale UASB reactor and two full-scale reactors. Based on MiSeq-based 16S rRNA gene sequencing of individual granules, different granule-types co-exist in both full-scale reactors regardless of granule size and reactor sampling depth, suggesting that distinct microbial interactions occur in different granules throughout the reactor. In addition, we identify novel networks of syntrophic metabolic interactions in different granules, perhaps caused by distinct thermodynamic conditions. Moreover, unseen methanogenic relationships (e.g. “Candidatus Aminicenantes” and Methanosaeta) are observed in UASB reactors. In total, we discover unexpected microbial interactions in granular micro-ecosystems supporting UASB ecology and treatment through a unique single-granule level approach.
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Affiliation(s)
- Kyohei Kuroda
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, North Mathews Ave, Urbana, Illinois, United States of America
- Department of Environmental systems Engineering, Nagaoka University of Technology, Kami-tomioka, Nagaoka, Niigata, Japan
| | - Masaru K. Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, North Mathews Ave, Urbana, Illinois, United States of America
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, North Mathews Ave, Urbana, Illinois, United States of America
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, North Mathews Ave, Urbana, Illinois, United States of America
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central, Higashi, Tsukuba, Ibaraki, Japan
| | - Benjamin T. W. Bocher
- Petrochemicals Technology, BP America, Naperville, Illinois, United States of America
| | - Takashi Yamaguchi
- Department of Environmental systems Engineering, Nagaoka University of Technology, Kami-tomioka, Nagaoka, Niigata, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, North Mathews Ave, Urbana, Illinois, United States of America
- * E-mail:
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18
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Hamilton TL, Bovee RJ, Sattin SR, Mohr W, Gilhooly WP, Lyons TW, Pearson A, Macalady JL. Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria. Front Microbiol 2016; 7:598. [PMID: 27199928 PMCID: PMC4846661 DOI: 10.3389/fmicb.2016.00598] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Mahoney Lake in British Columbia is an extreme meromictic system with unusually high levels of sulfate and sulfide present in the water column. As is common in strongly stratified lakes, Mahoney Lake hosts a dense, sulfide-oxidizing phototrophic microbial community where light reaches the chemocline. Below this "plate," the euxinic hypolimnion is anoxic, eutrophic, saline, and rich in sulfide, polysulfides, elemental sulfur, and other sulfur intermediates. While much is known regarding microbial communities in sunlit portions of euxinic systems, the composition and genetic potential of organisms living at aphotic depths have rarely been studied. Metagenomic sequencing of samples from the hypolimnion and the underlying sediments of Mahoney Lake indicate that multiple taxa contribute to sulfate reduction below the chemocline and that the hypolimnion and sediments each support distinct populations of sulfate reducing bacteria (SRB) that differ from the SRB populations observed in the chemocline. After assembling and binning the metagenomic datasets, we recovered near-complete genomes of dominant populations including two Deltaproteobacteria. One of the deltaproteobacterial genomes encoded a 16S rRNA sequence that was most closely related to the sulfur-disproportionating genus Dissulfuribacter and the other encoded a 16S rRNA sequence that was most closely related to the fatty acid- and aromatic acid-degrading genus Syntrophus. We also recovered two near-complete genomes of Firmicutes species. Analysis of concatenated ribosomal protein trees suggests these genomes are most closely related to extremely alkaliphilic genera Alkaliphilus and Dethiobacter. Our metagenomic data indicate that these Firmicutes contribute to carbon cycling below the chemocline. Lastly, we recovered a nearly complete genome from the sediment metagenome which represents a new genus within the FCB (Fibrobacteres, Chlorobi, Bacteroidetes) superphylum. Consistent with the geochemical data, we found little or no evidence for organisms capable of sulfide oxidation in the aphotic zone below the chemocline. Instead, comparison of functional genes below the chemocline are consistent with recovery of multiple populations capable of reducing oxidized sulfur. Our data support previous observations that at least some of the sulfide necessary to support the dense population of phototrophs in the chemocline is supplied from sulfate reduction in the hypolimnion and sediments. These studies provide key insights regarding the taxonomic and functional diversity within a euxinic environment and highlight the complexity of biogeochemical carbon and sulfur cycling necessary to maintain euxinia.
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Affiliation(s)
- Trinity L Hamilton
- Department of Biological Sciences, University of Cincinnati Cincinnati, OH, USA
| | - Roderick J Bovee
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Sarah R Sattin
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Wiebke Mohr
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - William P Gilhooly
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis Indianapolis, IN, USA
| | - Timothy W Lyons
- Department of Earth Sciences, University of California Riverside, CA, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Jennifer L Macalady
- Penn State Astrobiology Research Center, Department of Geosciences, Pennsylvania State University University Park, TX, USA
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19
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Perz V, Hromic A, Baumschlager A, Steinkellner G, Pavkov-Keller T, Gruber K, Bleymaier K, Zitzenbacher S, Zankel A, Mayrhofer C, Sinkel C, Kueper U, Schlegel K, Ribitsch D, Guebitz GM. An Esterase from Anaerobic Clostridium hathewayi Can Hydrolyze Aliphatic-Aromatic Polyesters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2899-907. [PMID: 26878094 DOI: 10.1021/acs.est.5b04346] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recently, a variety of biodegradable polymers have been developed as alternatives to recalcitrant materials. Although many studies on polyester biodegradability have focused on aerobic environments, there is much less known on biodegradation of polyesters in natural and artificial anaerobic habitats. Consequently, the potential of anaerobic biogas sludge to hydrolyze the synthetic compostable polyester PBAT (poly(butylene adipate-co-butylene terephthalate) was evaluated in this study. On the basis of reverse-phase high-performance liquid chromatography (RP-HPLC) analysis, accumulation of terephthalic acid (Ta) was observed in all anaerobic batches within the first 14 days. Thereafter, a decline of Ta was observed, which occurred presumably due to consumption by the microbial population. The esterase Chath_Est1 from the anaerobic risk 1 strain Clostridium hathewayi DSM-13479 was found to hydrolyze PBAT. Detailed characterization of this esterase including elucidation of the crystal structure was performed. The crystal structure indicates that Chath_Est1 belongs to the α/β-hydrolases family. This study gives a clear hint that also micro-organisms in anaerobic habitats can degrade manmade PBAT.
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Affiliation(s)
- Veronika Perz
- Austrian Centre of Industrial Biotechnology ACIB , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
| | - Altijana Hromic
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz , Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Armin Baumschlager
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Tea Pavkov-Keller
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Karl Gruber
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz , Humboldtstrasse 50/III, 8010 Graz, Austria
| | - Klaus Bleymaier
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Sabine Zitzenbacher
- Austrian Centre of Industrial Biotechnology ACIB , Petersgasse 14, 8010 Graz, Austria
| | - Armin Zankel
- Institute of Electron Microscopy and Nanoanalysis, Graz University of Technology , Steyrergasse 17/III, 8010 Graz, Austria
| | - Claudia Mayrhofer
- Institute of Electron Microscopy and Nanoanalysis, Graz University of Technology , Steyrergasse 17/III, 8010 Graz, Austria
| | - Carsten Sinkel
- BASF SE , Carl-Bosch-Straße 38, 67056 Ludwigshafen, Germany
| | - Ulf Kueper
- BASF SE , Carl-Bosch-Straße 38, 67056 Ludwigshafen, Germany
| | | | - Doris Ribitsch
- Austrian Centre of Industrial Biotechnology ACIB , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
| | - Georg M Guebitz
- Austrian Centre of Industrial Biotechnology ACIB , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna , Konrad Lorenz Strasse 20, 3430 Tulln, Austria
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20
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Kantor RS, van Zyl AW, van Hille RP, Thomas BC, Harrison STL, Banfield JF. Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol 2015; 17:4929-41. [DOI: 10.1111/1462-2920.12936] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Rose S. Kantor
- Department of Plant and Microbial Biology; University of California; Berkeley CA USA
| | - A. Wynand van Zyl
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Robert P. van Hille
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Brian C. Thomas
- Department of Earth and Planetary Sciences; University of California; Berkeley CA USA
| | - Susan T. L. Harrison
- Center for Bioprocess Engineering Research; Department of Chemical Engineering; University of Cape Town; Cape Town South Africa
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences; University of California; Berkeley CA USA
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
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21
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Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME JOURNAL 2015; 9:1710-22. [PMID: 25615435 DOI: 10.1038/ismej.2014.256] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/20/2014] [Accepted: 11/24/2014] [Indexed: 11/09/2022]
Abstract
Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4.
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22
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Primers: Functional Genes and 16S rRNA Genes for Methanogens. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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23
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Auffret MD, Yergeau E, Labbé D, Fayolle-Guichard F, Greer CW. Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis. Appl Microbiol Biotechnol 2014; 99:2419-30. [PMID: 25343979 DOI: 10.1007/s00253-014-6159-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/12/2014] [Indexed: 11/29/2022]
Abstract
A bacterial consortium (Mix3) composed of microorganisms originating from different environments (soils and wastewater) was obtained after enrichment in the presence of a mixture of 16 hydrocarbons, gasoline, and diesel oil additives. After addition of the mixture, the development of the microbial composition of Mix3 was monitored at three different times (35, 113, and 222 days) using fingerprinting method and dominant bacterial species were identified. In parallel, 14 bacteria were isolated after 113 days and identified. Degradation capacities for Mix3 and the isolated bacterial strains were characterized and compared. At day 113, we induced the expression of catabolic genes in Mix3 by adding the substrate mixture to resting cells and the metatranscriptome was analyzed. After addition of the substrate mixture, the relative abundance of Actinobacteria increased at day 222 while a shift between Rhodococcus and Mycobacterium was observed after 113 days. Mix3 was able to degrade 13 compounds completely, with partial degradation of isooctane and 2-ethylhexyl nitrate, but tert-butyl alcohol was not degraded. Rhodococcus wratislaviensis strain IFP 2016 isolated from Mix3 showed almost the same degradation capacities as Mix3: these results were not observed with the other isolated strains. Transcriptomic results revealed that Actinobacteria and in particular, Rhodococcus species, were major contributors in terms of total and catabolic gene transcripts while other species were involved in cyclohexane degradation. Not all the microorganisms identified at day 113 were active except R. wratislaviensis IFP 2016 that appeared to be a major player in the degradation activity observed in Mix3.
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Affiliation(s)
- Marc D Auffret
- Institut Français du Pétrole (IFP), 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France,
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24
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Porter AW, Young LY. Benzoyl-CoA, a universal biomarker for anaerobic degradation of aromatic compounds. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:167-203. [PMID: 24767428 DOI: 10.1016/b978-0-12-800260-5.00005-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Aromatic compounds are a major component of the global carbon pool and include a diverse range of compounds such as humic acid, lignin, amino acids, and industrial contaminants. Due to the prevalence of aromatic compounds in the environment, aerobic and anaerobic microorganisms have evolved mechanisms by which to metabolize that available carbon. Less well understood are the anaerobic pathways. We now know that anaerobic metabolism of a variety of monoaromatic compounds can be initiated in a number of different ways, and a key metabolite for these pathways is benzoyl-CoA. Chemicals can have different upstream anaerobic degradation pathways yet can still be assessed by targeting the downstream benzoyl-CoA pathway. In this pathway, we propose that the ring opening hydrolase, encoded by the bamA gene, is especially useful because, in contrast to the benzoyl-CoA reductase, it is detected under a number of respiratory settings, including denitrifying, iron-reducing, sulfate-reducing, and fermentative conditions, and has a wide distribution in the environment. This review examines the bamA gene in enrichment cultures and environmental DNA extracts to consider whether it can be used as a biomarker for anaerobic aromatic degradation. Given the number of potential upstream inputs from natural and man-made monoaromatic compounds, the benzoyl-CoA pathway and the bamA gene in particular may play an important role in the global carbon cycle that has thus far been overlooked.
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Affiliation(s)
- Abigail W Porter
- Department of Environmental Science, School of Biological and Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA.
| | - Lily Y Young
- Department of Environmental Science, School of Biological and Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
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25
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Total protein extraction for metaproteomics analysis of methane producing biofilm: the effects of detergents. Int J Mol Sci 2014; 15:10169-84. [PMID: 24914765 PMCID: PMC4100146 DOI: 10.3390/ijms150610169] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/23/2014] [Accepted: 05/23/2014] [Indexed: 02/07/2023] Open
Abstract
Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents for the metaproteomics analysis of a terephthalate-degrading methanogenic biofilm using an on-line two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) system. Totally, 1018 non-repeated proteins were identified with the four treatments. On the whole, each treatment could recover the biofilm proteins with specific distributions of molecular weight, hydrophobicity, and isoelectric point. The extraction buffers containing zwitterionic and anionic detergents were found to harvest the proteins with better efficiency and quality, allowing identification up to 76.2% of total identified proteins with the LC-MS/MS analysis. According to the annotation with a relevant metagenomic database, we further observed different taxonomic profiles of bacterial and archaeal members and discriminable patterns of the functional expression among the extraction buffers used. Overall, the finding of the present study provides first insight to the effect of the detergents on the characteristics of extractable proteins from biofilm and the developed protocol combined with nano 2D-LC/MS/MS analysis can improve the metaproteomics studies on microbial functionality of biofilms in the wastewater treatment systems.
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26
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Gieg LM, Fowler SJ, Berdugo-Clavijo C. Syntrophic biodegradation of hydrocarbon contaminants. Curr Opin Biotechnol 2014; 27:21-9. [DOI: 10.1016/j.copbio.2013.09.002] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/30/2022]
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27
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Nobu MK, Narihiro T, Hideyuki T, Qiu YL, Sekiguchi Y, Woyke T, Goodwin L, Davenport KW, Kamagata Y, Liu WT. The genome ofSyntrophorhabdus aromaticivoransstrain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol 2014; 17:4861-72. [DOI: 10.1111/1462-2920.12444] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/21/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Masaru K. Nobu
- Department of Civil and Environmental Engineering; University of Illinois at Urbana-Champaign; Urbana IL USA
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering; University of Illinois at Urbana-Champaign; Urbana IL USA
- Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Ibaraki Japan
| | - Tamaki Hideyuki
- Department of Civil and Environmental Engineering; University of Illinois at Urbana-Champaign; Urbana IL USA
- Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Ibaraki Japan
| | - Yan-Ling Qiu
- Key Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao Shandong Province China
| | - Yuji Sekiguchi
- Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Ibaraki Japan
| | - Tanja Woyke
- DOE Joint Genome Institute; Walnut Creek CA USA
| | | | | | - Yoichi Kamagata
- Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Ibaraki Japan
- Bioproduction Research Institute; National Institute of Advanced Industrial Science and Technology (AIST); Toyohira-ku Sapporo Hokkaido Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering; University of Illinois at Urbana-Champaign; Urbana IL USA
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28
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Bakker MG, Schlatter DC, Otto-Hanson L, Kinkel LL. Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome. Mol Ecol 2013; 23:1571-1583. [DOI: 10.1111/mec.12571] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 09/20/2013] [Accepted: 09/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew G. Bakker
- Center for Rhizosphere Biology; Colorado State University; Fort Collins CO 80523-1173 USA
| | - Daniel C. Schlatter
- Department of Plant Pathology; University of Minnesota; Saint Paul MN 55108 USA
| | - Lindsey Otto-Hanson
- Department of Plant Pathology; University of Minnesota; Saint Paul MN 55108 USA
| | - Linda L. Kinkel
- Department of Plant Pathology; University of Minnesota; Saint Paul MN 55108 USA
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29
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Use of a hierarchical oligonucleotide primer extension approach for multiplexed relative abundance analysis of methanogens in anaerobic digestion systems. Appl Environ Microbiol 2013; 79:7598-609. [PMID: 24077716 DOI: 10.1128/aem.02450-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we established a rapid multiplex method to detect the relative abundances of amplified 16S rRNA genes from known cultivatable methanogens at hierarchical specificities in anaerobic digestion systems treating industrial wastewater and sewage sludge. The method was based on the hierarchical oligonucleotide primer extension (HOPE) technique and combined with a set of 27 primers designed to target the total archaeal populations and methanogens from 22 genera within 4 taxonomic orders. After optimization for their specificities and detection sensitivity under the conditions of multiple single-nucleotide primer extension reactions, the HOPE approach was applied to analyze the methanogens in 19 consortium samples from 7 anaerobic treatment systems (i.e., 513 reactions). Among the samples, the methanogen populations detected with order-level primers accounted for >77.2% of the PCR-amplified 16S rRNA genes detected using an Archaea-specific primer. The archaeal communities typically consisted of 2 to 7 known methanogen genera within the Methanobacteriales, Methanomicrobiales, and Methanosarcinales and displayed population dynamic and spatial distributions in anaerobic reactor operations. Principal component analysis of the HOPE data further showed that the methanogen communities could be clustered into 3 distinctive groups, in accordance with the distribution of the Methanosaeta, Methanolinea, and Methanomethylovorans, respectively. This finding suggested that in addition to acetotrophic and hydrogenotrophic methanogens, the methylotrophic methanogens might play a key role in the anaerobic treatment of industrial wastewater. Overall, the results demonstrated that the HOPE approach is a specific, rapid, and multiplexing platform to determine the relative abundances of targeted methanogens in PCR-amplified 16S rRNA gene products.
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