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Nieto EE, Jurburg SD, Steinbach N, Festa S, Morelli IS, Coppotelli BM, Chatzinotas A. DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories. MICROBIOME 2024; 12:146. [PMID: 39113100 PMCID: PMC11305082 DOI: 10.1186/s40168-024-01865-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/26/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation. RESULTS Inoculation effectively increased PAH removal in the short-term, but not in the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil. CONCLUSION Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.
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Affiliation(s)
- Esteban E Nieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina.
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
| | - Stephanie D Jurburg
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nicole Steinbach
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
| | - Irma S Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
- Comisión de Investigaciones Científicas de La Provincia de Buenos Aires, La Plata, Argentina
| | - Bibiana M Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
| | - Antonis Chatzinotas
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Meng S, Peng T, Liu Y, Zhang S, Qian Z, Huang T, Xie Q, Gu JD, Hu Z. Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133907. [PMID: 38471380 DOI: 10.1016/j.jhazmat.2024.133907] [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: 10/09/2023] [Revised: 02/18/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024]
Abstract
Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Yongjin Liu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Shan Zhang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Zhihui Qian
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Qingyi Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, PR China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion -Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China; Offshore Environmental Pollution Control Engineering Research, Shantou University, Shantou, Guangdong 515063, PR China.
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Wang SY, Wang YX, Yue SS, Shi XC, Lu FY, Wu SQ, Herrera-Balandrano DD, Laborda P. G-site residue S67 is involved in the fungicide-degrading activity of a tau class glutathione S-transferase from Carica papaya. J Biol Chem 2024; 300:107123. [PMID: 38417796 PMCID: PMC10958117 DOI: 10.1016/j.jbc.2024.107123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/01/2024] Open
Abstract
Thiram is a toxic fungicide extensively used for the management of pathogens in fruits. Although it is known that thiram degrades in plant tissues, the key enzymes involved in this process remain unexplored. In this study, we report that a tau class glutathione S-transferase (GST) from Carica papaya can degrade thiram. This enzyme was easily obtained by heterologous expression in Escherichia coli, showed low promiscuity toward other thiuram disulfides, and catalyzed thiram degradation under physiological reaction conditions. Site-directed mutagenesis indicated that G-site residue S67 shows a key influence for the enzymatic activity toward thiram, while mutation of residue S13, which reduced the GSH oxidase activity, did not significantly affect the thiram-degrading activity. The formation of dimethyl dithiocarbamate, which was subsequently converted into carbon disulfide, and dimethyl dithiocarbamoylsulfenic acid as the thiram degradation products suggested that thiram undergoes an alkaline hydrolysis that involves the rupture of the disulfide bond. Application of the GST selective inhibitor 4-chloro-7-nitro-2,1,3-benzoxadiazole reduced papaya peel thiram-degrading activity by 95%, indicating that this is the main degradation route of thiram in papaya. GST from Carica papaya also catalyzed the degradation of the fungicides chlorothalonil and thiabendazole, with residue S67 showing again a key influence for the enzymatic activity. These results fill an important knowledge gap in understanding the catalytic promiscuity of plant GSTs and reveal new insights into the fate and degradation products of thiram in fruits.
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Affiliation(s)
- Su-Yan Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Yan-Xia Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Sheng-Shuo Yue
- School of Life Sciences, Nantong University, Nantong, China
| | - Xin-Chi Shi
- School of Life Sciences, Nantong University, Nantong, China
| | - Feng-Yi Lu
- School of Life Sciences, Nantong University, Nantong, China
| | - Si-Qi Wu
- School of Life Sciences, Nantong University, Nantong, China
| | | | - Pedro Laborda
- School of Life Sciences, Nantong University, Nantong, China.
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Liu H, Yang H, Yin X, Wang S, Fang S, Zhang H. A novel pbd gene cluster responsible for pyrrole and pyridine ring cleavage in Rhodococcus ruber A5. JOURNAL OF HAZARDOUS MATERIALS 2024; 464:132992. [PMID: 37976859 DOI: 10.1016/j.jhazmat.2023.132992] [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: 08/29/2023] [Revised: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Pyridine and pyrrole, which are regarded as recalcitrant chemicals, are released into the environment as a result of industrial manufacturing processes, posing serious hazards to both the environment and human health. However, the pyrrole degradation mechanism and the pyridine-degrading gene in Rhodococcus are unknown. Herein, a highly efficient pyridine and pyrrole degradation strain Rhodococcus ruber A5 was isolated. Strain A5 completely degraded 1000 mg/L pyridine in a mineral salt medium within 24 h. The pyridine degradation of strain A5 was optimized using the BoxBehnken design. The optimum degradation conditions were found to be pH 7.15, temperature 28.06 ℃, and inoculation amount 1290.94 mg/L. The pbd gene clusters involved in pyridine degradation were discovered via proteomic analysis. The initial ring cleavage of pyridine and pyrrole in strain A5 was carried out by the two-component flavin-dependent monooxygenase PbdA/PbdE. The degradation pathways of pyridine and pyrrole were proposed by the identification of metabolites and comparisons of homologous genes. Additionally, homologous pbd gene clusters were found to exist in different bacterial genomes. Our study revealed the ring cleavage mechanisms of pyrrole and pyridine, and strain A5 was identified as a promising resource for pyridine bioremediation.
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Affiliation(s)
- Hongming Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Hao Yang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Xiaye Yin
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Siwen Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Shangping Fang
- School of Anesthesiology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Hao Zhang
- Key Laboratory of Metallurgical Emission Reduction and Comprehensive Utilization of Resources, Ministry of Education (Anhui University of Technology), Ma'anshan 243002, Anhui, China.
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Yi S, Zhu Z, Li F, Zhu L, Wu C, Ge F, Ji X, Tian J. Metagenomic and proteomic insights into the self-adaptive cell surface hydrophobicity of Sphingomonas sp. strain PAH02 reducing the migration of cadmium-phenanthrene co-pollutant in rice. Environ Microbiol 2024; 26:e16577. [PMID: 38183371 DOI: 10.1111/1462-2920.16577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
Cell surface hydrophobicity (CSH) dominates the interactions between rhizobacteria and pollutants at the soil-water interface, which is critical for understanding the dissipation of pollutants in the rhizosphere microzone of rice. Herein, we explored the effects of self-adaptive CSH of Sphingomonas sp. strain PAH02 on the translocation and biotransformation behaviour of cadmium-phenanthrene (Cd-Phe) co-pollutant in rice and rhizosphere microbiome. We evidenced that strain PAH02 reduced the adsorption of Cd-Phe co-pollutant on the rice root surface while enhancing the degradation of Phe and adsorption of Cd via its self-adaptive CSH in the hydroponic experiment. The significant upregulation of key protein expression levels such as MerR, ARHDs and enoyl-CoA hydratase/isomerase, ensures self-adaptive CSH to cope with the stress of Cd-Phe co-pollutant. Consistently, the bioaugmentation of strain PAH02 promoted the formation of core microbiota in the rhizosphere soil of rice (Oryza sativa L.), such as Bradyrhizobium and Streptomyces and induced gene enrichment of CusA and PobA that are strongly associated with pollutant transformation. Consequently, the contents of Cd and Phe in rice grains at maturity decreased by 17.2% ± 0.2% and 65.7% ± 0.3%, respectively, after the bioaugmentation of strain PAH02. These findings present new opportunities for the implementation of rhizosphere bioremediation strategies of co-contaminants in paddy fields.
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Affiliation(s)
- Shengwei Yi
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Zhongnan Zhu
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Feng Li
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Chen Wu
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Fei Ge
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
| | - Xionghui Ji
- Hunan Institute of Agro-Environment and Ecology, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jiang Tian
- College of Environment and Resources, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan University, Xiangtan, China
- Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan University, Xiangtan, China
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Kim J, Hwangbo M, Shih CH, Chu KH. Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation. WATER RESEARCH X 2023; 20:100187. [PMID: 37671037 PMCID: PMC10477051 DOI: 10.1016/j.wroa.2023.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 09/07/2023]
Abstract
Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.
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Affiliation(s)
- Jinha Kim
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
- School of Earth, Environmental and Marine Sciences, The University of Texas – Rio Grande Valley, Brownsville, TX, USA
| | - Chih-Hsuan Shih
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843-3136, USA
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You SM, Lee SS, Ryu MH, Song HM, Kang MS, Jung YJ, Song EC, Sung BH, Park SJ, Joo JC, Kim HT, Cha HG. β-Ketoadipic acid production from poly(ethylene terephthalate) waste via chemobiological upcycling. RSC Adv 2023; 13:14102-14109. [PMID: 37180017 PMCID: PMC10168023 DOI: 10.1039/d3ra02072j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
The upcycling of poly(ethylene terephthalate) (PET) waste can simultaneously produce value-added chemicals and reduce the growing environmental impact of plastic waste. In this study, we designed a chemobiological system to convert terephthalic acid (TPA), an aromatic monomer of PET, to β-ketoadipic acid (βKA), a C6 keto-diacid that functions as a building block for nylon-6,6 analogs. Using microwave-assisted hydrolysis in a neutral aqueous system, PET was converted to TPA with Amberlyst-15, a conventional catalyst with high conversion efficiency and reusability. The bioconversion process of TPA into βKA used a recombinant Escherichia coli βKA expressing two conversion modules for TPA degradation (tphAabc and tphB) and βKA synthesis (aroY, catABC, and pcaD). To improve bioconversion, the formation of acetic acid, a deleterious factor for TPA conversion in flask cultivation, was efficiently regulated by deleting the poxB gene along with operating the bioreactor to supply oxygen. By applying two-stage fermentation consisting of the growth phase in pH 7 followed by the production phase in pH 5.5, a total of 13.61 mM βKA was successfully produced with 96% conversion efficiency. This efficient chemobiological PET upcycling system provides a promising approach for the circular economy to acquire various chemicals from PET waste.
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Affiliation(s)
- Sang-Mook You
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT) Ulsan 44429 Republic of Korea
| | - Si Seon Lee
- Department of Biotechnology, The Catholic University of Korea Bucheon-si Gyeonggi-do 14662 Republic of Korea
| | - Mi Hee Ryu
- Green Carbon Research Center Korea Research Institute of Chemical Technology (KRICT) Daejeon 34114 Republic of Korea
| | - Hye Min Song
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science & Engineering, Ewha Woman's University Seoul 03760 Republic of Korea
| | - Min Soo Kang
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT) Ulsan 44429 Republic of Korea
| | - Ye Jean Jung
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT) Ulsan 44429 Republic of Korea
| | - Eun Chae Song
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University Daejeon 34134 Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science & Engineering, Ewha Woman's University Seoul 03760 Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea Bucheon-si Gyeonggi-do 14662 Republic of Korea
| | - Hee Taek Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University Daejeon 34134 Republic of Korea
| | - Hyun Gil Cha
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT) Ulsan 44429 Republic of Korea
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