1
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Pan L, Yuan B, Li Q, Ouyang J, Yang J, Zhou Y, Cui C. Efficient biodegradation of chlorobenzene via monooxygenation pathways by Pandoraea sp. XJJ-1 with high potential for groundwater bioremediation. Int Microbiol 2024:10.1007/s10123-024-00544-4. [PMID: 38900217 DOI: 10.1007/s10123-024-00544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/15/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Chlorobenzene (CB), extensively used in industrial processes, has emerged as a significant contaminant in soil and groundwater. The eco-friendly and cost-effective microbial remediation has been increasingly favored to address this environmental challenge. In this study, a degrading bacterium was isolated from CB-contaminated soil at a pesticide plant, identified as Pandoraea sp. XJJ-1 (CCTCC M 2021057). This strain completely degraded 100 mg·L-1 CB and showed extensive degradability across a range of pH (5.0-9.0), temperature (10-37 °C), and CB concentrations (100-600 mg·L-1). Notably, the degradation efficiency was 85.2% at 15 °C, and the strain could also degrade six other aromatic hydrocarbons, including benzene, toluene, ethylbenzene, and xylene (o-, m-, p-). The metabolic pathway of CB was inferred using ultraperformance liquid chromatography, gas chromatography-mass spectrometry, and genomic analysis. In strain XJJ-1, CB was metabolized to o-chlorophenol and 3-chloroxychol by CB monooxygenase, followed by ortho-cleavage by the action of 3-chlorocatechol 1,2-dioxygenase. Moreover, the presence of the chlorobenzene monooxygenation pathway metabolism in strain XJJ-1 is reported for the first time in Pandoraea. As a bacterium with low-temperature resistance and composite pollutant degradation capacity, strain XJJ-1 has the potential application prospects in the in-situ bioremediation of CB-contaminated sites.
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Affiliation(s)
- Lixu Pan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bo Yuan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qingqing Li
- State Environment Protection Engineering Center for Urban Soil Contamination Control and Remediation, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Ji Ouyang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jie Yang
- State Environment Protection Engineering Center for Urban Soil Contamination Control and Remediation, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Yan Zhou
- Sinopec Fifth Construction Co., Ltd, Guangzhou, 510145, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control On Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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2
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Yuan S, Guo S, Huang X, Meng F. Time-lagged interspecies interactions prevail during biofilm development in moving bed biofilm reactor. Biotechnol Bioeng 2022; 119:2770-2783. [PMID: 35837838 DOI: 10.1002/bit.28177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/27/2022] [Accepted: 07/10/2022] [Indexed: 11/09/2022]
Abstract
Clarifying the essential succession dynamics of interspecies interactions during biofilm development is crucial for the regulation and application of biofilm-based processes. In this study, regular and time-series phylogenetic molecular ecological networks (pMENs) were constructed to investigate ordinary and time-lagged interspecies interactions during biofilm development in a moving bed biofilm reactor (MBBR). Positive interactions dominated both regular (89.78%) and time-series (77.04%) ecological networks, suggesting that extensive cooperative behaviors facilitated biofilm development. The pronounced directional interactions (72.52%) in the time-series network further indicated that time-lagged interspecies interactions prevailed in the biofilm development process. Specifically, the proportion of directional negative interactions was higher than that of positive interactions, implying that interspecific competition preferred to be time-lagged. The time-series network revealed that module hubs exhibited extensive time-lagged positive interactions with their neighbors, and most of them exhibited altruistic behaviors. Keystone species possessing more positive interactions were positively correlated with biofilm biomass, NO3 - -N concentrations, and the removal efficiencies of NH4 + -N and COD. However, keystone species and peripherals that were negatively targeted by their neighbors showed positive correlations with the concentrations of NO2 - -N, polysaccharides, and proteins in the soluble microbial products. The data highlight that the time-series network can provide directional microbial interactions along with the biofilm development process, which would help to predict the tendency of community shifts and propose efficient strategies for the regulation of biofilm-based processes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shasha Yuan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Sixian Guo
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Xihao Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
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3
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Öztürk B, Werner J, Meier-Kolthoff JP, Bunk B, Spröer C, Springael D. Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax. Genome Biol Evol 2021; 12:827-841. [PMID: 32359160 PMCID: PMC7313664 DOI: 10.1093/gbe/evaa085] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 01/07/2023] Open
Abstract
Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight into the mechanisms of genetic adaptation toward linuron metabolism. Whole-genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated that they unlikely originate from a common ancestral linuron degrader. The linuron degraders differentiated from Variovorax strains that do not degrade linuron by the presence of multiple plasmids of 20–839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed 1) high conservation and synteny and 2) strain-dependent distribution among the different plasmids. Most of them were bordered by IS1071 elements forming composite transposon structures, often in a multimeric array configuration, appointing IS1071 as a key element in the recruitment of linuron catabolic genes in Variovorax. Most of the strains carried at least one (catabolic) broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1 Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire regarding both catabolic functions and vehicles to acquire linuron biodegradation.
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Affiliation(s)
- Başak Öztürk
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Division of Soil and Water Management, KU Leuven, Belgium
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Jan P Meier-Kolthoff
- Department Bioinformatics and Databases, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics and Databases, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Belgium
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4
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Li M, Shi Y, Li Y, Sun Y, Song C, Huang Z, Yang Z, Han Y. Shift of microbial diversity and function in high-efficiency performance biotrickling filter for gaseous xylene treatment. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2019; 69:1059-1069. [PMID: 31050600 DOI: 10.1080/10962247.2019.1600603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/21/2019] [Accepted: 03/22/2019] [Indexed: 05/26/2023]
Abstract
Xylene is the main component of many volatile industrial pollution sources, and the use of biotechnology to remove volatile organic compounds (VOCs) has become a growing trend. In this study, a biotrickling filter for gaseous xylene treatment was developed using activated sludge as raw material to study the biodegradation process of xylene. Reaction conditions were optimized, and long-term operation was performed. The optimal pH was 7.0, gas-liquid ratio was 15:1 (v/v), and temperature was 25 °C. High-throughput sequencing technique was carried out to analyze microbial communities in the top, middle, and bottom layers of the reactor. Characteristics of microbial diversity were elucidated, and microbial functions were predicted. The result showed that the removal efficiency (RE) was stable at 86%-91%, the maximum elimination capacity (EC) was 303.61 g·m-3·hr-1, residence time was 33.75 sec, and the initial inlet xylene concentration was 3000 mg·m-3, which was the highest known degradation concentration reported. Kinetic analysis of the xylene degradation indicated that it was a very high-efficiency-activity bioprocess. The rmax was 1059.8 g·m-3·hr-1, and Ks value was 4.78 g·m-3 in stationary phase. In addition, microbial community structures in the bottom and top layers were significantly different: Pseudomonas was the dominant genus in the bottom layer, whereas Sphingobium was dominant in the top layer. The results showed that intermediate metabolites of xylene could affect the distribution of community structure. Pseudomonas sp. can adapt to high concentration xylene-contaminated environments. Implications: We combined domesticated active sludge and reinforced microbial agent on biotrickling filter. This system performed continuously under a reduced residence time at 33.75 sec and high elimination capacity at 303.61 g·m-3·hr-1 in the biotrickling reactor for about 260 days. In this case, predomestication combined with reinforcing of microorganisms was very important to obtaining high-efficiency results. Analysis of microbial diversity and functional prediction indicated a gradient distribution along with the concentration of xylene. This implied a rational design of microbial reagent and optimizing the inoculation of different sites of reactor could reduce the preparation period of the technology.
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Affiliation(s)
- Mingxue Li
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology , Tianjin , People's Republic of China
| | - Yantao Shi
- R&D Department, SwanShine (Tianjin) Biotechnology & Development Ltd , Tianjin , People's Republic of China
| | - Yixuan Li
- R&D Department, SwanShine (Tianjin) Biotechnology & Development Ltd , Tianjin , People's Republic of China
| | - Yizhe Sun
- College of Chemical Engineering and Materials Science, Tianjin University of Science & Technology , Tianjin , People's Republic of China
| | - Chunhui Song
- Key Laboratory of Western China's Mineral Resources of Gansu Province, School of Earth Sciences, University of Lanzhou , Lanzhou , Gansu , People's Republic of China
| | - Zhiyong Huang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin , People's Republic of China
| | - Zongzheng Yang
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-utilization, Tianjin University of Science & Technology , Tianjin , People's Republic of China
| | - Yifan Han
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin , People's Republic of China
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5
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Chao HJ, Chen YY, Wu J, Yan DZ, Zhou NY. Complete Genome Sequence of a Chlorobenzene Degrader, Pandoraea pnomenusa MCB032. Curr Microbiol 2019; 76:1235-1237. [PMID: 31432211 DOI: 10.1007/s00284-019-01760-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022]
Abstract
Chlorobenzenes are ubiquitously distributed, highly persistent, and toxic environmental contaminants. Pandoraea pnomenusa MCB032 was isolated as a new dominant chlorobenzene-utilizing strain from a functionally stable bioreactor during the treatment of chlorobenzenes when strain Burkholderia sp. JS150 disappeared. In study, we report the complete genome sequence of strain MCB032 which consists of a circular chromosome and three plasmids, which are ~ 6 Mb in length with 5450 open reading frames-12 encoding rRNAs and 77 encoding tRNAs. We further identified 17 putative genes encoding the enzymes involved in the methyl-accepting chemotaxis proteins in sensing chemical gradients during chemotaxis. The annotated complete genome sequence of this strain will provide genetic insights into the degradation of chlorinated aromatic compounds. The information will empower the elucidation of chlorobenzene affinity hierarchy and species succession in the bioreactor.
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Affiliation(s)
- Hong-Jun Chao
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China.,Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yuan-Yuan Chen
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jing Wu
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Da-Zhong Yan
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China.
| | - Ning-Yi Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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6
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Mir-Tutusaus JA, Parladé E, Villagrasa M, Barceló D, Rodríguez-Mozaz S, Martínez-Alonso M, Gaju N, Sarrà M, Caminal G. Long-term continuous treatment of non-sterile real hospital wastewater by Trametes versicolor. J Biol Eng 2019; 13:47. [PMID: 31160922 PMCID: PMC6542094 DOI: 10.1186/s13036-019-0179-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/15/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Hospital wastewater is commonly polluted with high loads of pharmaceutically active compounds, which pass through wastewater treatment plants (WWTPs) and end up in water bodies, posing ecological and health risks. White-rot fungal treatments can cope with the elimination of a wide variety of micropollutants while remaining ecologically and economically attractive. Unfortunately, bacterial contamination has impeded so far a successful implementation of fungal treatment for real applications. RESULTS This work embodied a 91-day long-term robust continuous fungal operation treating real non-sterile hospital wastewater in an air pulsed fluidized bed bioreactor retaining the biomass. The hydraulic retention time was 3 days and the ageing of the biomass was avoided through partial periodic biomass renovation resulting in a cellular retention time of 21 days. Evolution of microbial community and Trametes abundance were evaluated. CONCLUSIONS The operation was able to maintain an average pharmaceutical load removal of over 70% while keeping the white-rot fungus active and predominant through the operation.
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Affiliation(s)
- Josep Anton Mir-Tutusaus
- Departament d’Enginyeria Química Biològica i Ambiental, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Eloi Parladé
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Marta Villagrasa
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, H2O Building, Emili Grahit 101, 17003 Girona, Spain
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, H2O Building, Emili Grahit 101, 17003 Girona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish Council for Scientific Research (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Sara Rodríguez-Mozaz
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, H2O Building, Emili Grahit 101, 17003 Girona, Spain
| | - Maira Martínez-Alonso
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Núria Gaju
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Montserrat Sarrà
- Departament d’Enginyeria Química Biològica i Ambiental, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Glòria Caminal
- Institut de Química Avançada de Catalunya (IQAC) CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
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7
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Wu X, Wu X, Shen L, Li J, Yu R, Liu Y, Qiu G, Zeng W. Whole Genome Sequencing and Comparative Genomics Analyses of Pandoraea sp. XY-2, a New Species Capable of Biodegrade Tetracycline. Front Microbiol 2019; 10:33. [PMID: 30761094 PMCID: PMC6361800 DOI: 10.3389/fmicb.2019.00033] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium Pandoraea sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of Pandoraea sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of Pandoraea sp. XY-2 and other Pandoraea spp. revealed that Pandoraea sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 Pandoraea strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of Pandoraea sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six tetA(48) genes and two specificgenes tetG and tetR in Pandoraea sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to Paraburkholderia, Burkholderia, Caballeronia, Salmonella, Vibrio, Proteobacteria, Pseudomonas, Acinetobacter, Flavimaricola, and some unidentified sources. As a new species, Pandoraea sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jiaokun Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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8
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Zhang S, Ying Z, You J, Ye J, Cheng Z, Chen D, Chen J. Superior performance and mechanism of chlorobenzene degradation by a novel bacterium. RSC Adv 2019; 9:15004-15012. [PMID: 35516324 PMCID: PMC9064227 DOI: 10.1039/c9ra01229j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 05/05/2019] [Indexed: 01/08/2023] Open
Abstract
A newly isolated strain was identified as Ochrobactrum sp. by 16S rRNA sequence analysis and named as ZJUTCB-1.
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Affiliation(s)
- Shihan Zhang
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Zanyun Ying
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
| | - Juping You
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
| | - Jiexu Ye
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Zhuowei Cheng
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Dongzhi Chen
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Jianmeng Chen
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
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9
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da Costa PB, Granada CE, Ambrosini A, Moreira F, de Souza R, dos Passos JFM, Arruda L, Passaglia LMP. A model to explain plant growth promotion traits: a multivariate analysis of 2,211 bacterial isolates. PLoS One 2014; 9:e116020. [PMID: 25542031 PMCID: PMC4277451 DOI: 10.1371/journal.pone.0116020] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 12/01/2014] [Indexed: 11/19/2022] Open
Abstract
Plant growth-promoting bacteria can greatly assist sustainable farming by improving plant health and biomass while reducing fertilizer use. The plant-microorganism-environment interaction is an open and complex system, and despite the active research in the area, patterns in root ecology are elusive. Here, we simultaneously analyzed the plant growth-promoting bacteria datasets from seven independent studies that shared a methodology for bioprospection and phenotype screening. The soil richness of the isolate's origin was classified by a Principal Component Analysis. A Categorical Principal Component Analysis was used to classify the soil richness according to isolate's indolic compound production, siderophores production and phosphate solubilization abilities, and bacterial genera composition. Multiple patterns and relationships were found and verified with nonparametric hypothesis testing. Including niche colonization in the analysis, we proposed a model to explain the expression of bacterial plant growth-promoting traits according to the soil nutritional status. Our model shows that plants favor interaction with growth hormone producers under rich nutrient conditions but favor nutrient solubilizers under poor conditions. We also performed several comparisons among the different genera, highlighting interesting ecological interactions and limitations. Our model could be used to direct plant growth-promoting bacteria bioprospection and metagenomic sampling.
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Affiliation(s)
- Pedro Beschoren da Costa
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Adriana Ambrosini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fernanda Moreira
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rocheli de Souza
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - João Frederico M. dos Passos
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Empresa de Pesquisa e Extensão Agropecuária de Santa Catarina (EPAGRI), Lages, SC, Brazil
| | - Letícia Arruda
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luciane M. P. Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- * E-mail:
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10
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Yu J, Cai W, Cheng Z, Chen J. Degradation of dichloromethane by an isolated strain Pandoraea pnomenusa and its performance in a biotrickling filter. J Environ Sci (China) 2014; 26:1108-1117. [PMID: 25079641 DOI: 10.1016/s1001-0742(13)60538-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 09/27/2013] [Accepted: 11/23/2013] [Indexed: 06/03/2023]
Abstract
A strain Pandoraea pnomenusa LX-1 that uses dichloromethane (DCM) as sole carbon and energy source has been isolated and identified in our laboratory. The optimum aerobic biodegradation of DCM in batch culture was evaluated by response surface methodology. Maximum biodegradation (5.35 mg/(L·hr)) was achieved under cultivation at 32.8°C, pH 7.3, and 0.66% NaCl. The growth and biodegradation processes were well fitted by Haldane's kinetic model, yielding maximum specific growth and degradation rates of 0.133 hr(-1) and 0.856 hr(-1), respectively. The microorganism efficiently degraded a mixture of DCM and coexisting components (benzene, toluene and chlorobenzene). The carbon recovery (52.80%-94.59%) indicated that the targets were predominantly mineralized and incorporated into cell materials. Electron acceptors increased the DCM biodegradation rate in the following order: mixed > oxygen > iron > sulfate > nitrate. The highest dechlorination rate was 0.365 mg Cl(-)/(hr·mg biomass), obtained in the presence of mixed electron acceptors. Removal was achieved in a continuous biotrickling filter at 56%-85% efficiency, with a mineralization rate of 75.2%. Molecular biology techniques revealed the predominant strain as P. pnomenusa LX-1. These results clearly demonstrated the effectiveness of strain LX-1 in treating DCM-containing industrial effluents. As such, the strain is a strong candidate for remediation of DCM coexisting with other organic compounds.
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Affiliation(s)
- Jianming Yu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310032, China.
| | - Wenji Cai
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhuowei Cheng
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China.
| | - Jianmeng Chen
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
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Zhao H, Geng Y, Fan J, Tao K, Hou T. Isolation and identification of Paracoccus sp. FD3 and evaluation of its formaldehyde degradation kinetics. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0449-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Muñoz R, Daugulis AJ, Hernández M, Quijano G. Recent advances in two-phase partitioning bioreactors for the treatment of volatile organic compounds. Biotechnol Adv 2012; 30:1707-20. [DOI: 10.1016/j.biotechadv.2012.08.009] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/24/2012] [Accepted: 08/25/2012] [Indexed: 12/01/2022]
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Degradation of chlorobenzene by strain Ralstonia pickettii L2 isolated from a biotrickling filter treating a chlorobenzene-contaminated gas stream. Appl Microbiol Biotechnol 2011; 91:407-15. [DOI: 10.1007/s00253-011-3255-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 02/20/2011] [Accepted: 03/16/2011] [Indexed: 10/18/2022]
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Integrating microbial ecology in bioprocess understanding: the case of gas biofiltration. Appl Microbiol Biotechnol 2011; 90:837-49. [PMID: 21424795 DOI: 10.1007/s00253-011-3191-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 02/25/2011] [Accepted: 02/27/2011] [Indexed: 10/18/2022]
Abstract
Biofilters are packed-bed bioreactors where contaminants, once transferred from the gas phase to the biofilm, are oxidized by diverse and complex communities of attached microorganisms. Over the last decade, more and more studies aimed at opening the back box of biofiltration by unraveling the biodiversity-ecosystem function relationship. In this review, we report the insights provided by the microbial ecology approach in biofilters and we emphasize the parallels existing with other engineered ecosystems used for wastewater treatment, as they all constitute relevant model ecosystems to explore ecological issues. We considered three characteristic ecological indicators: the density, the diversity, and the structure of the microbial community. Special attention was paid to the temporal and spatial dynamics of each indicator, insofar as it can disclose the potential relationship, or absence of relation, with any operating or functional parameter. We also focused on the impact of disturbance regime on the microbial community structure, in terms of resistance, resilience, and memory. This literature review led to mitigated conclusions in terms of biodiversity-ecosystem function relationship. Depending on the environmental system itself and the way it is investigated, the spatial and temporal dynamics of the microbial community can be either correlated (e.g., spatial stratification) or uncoupled (e.g., temporal instability) to the ecosystem function. This lack of generality shows the limits of current 16S approach in complex ecosystems, where a functional approach may be more suitable.
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Littlejohns JV, McAuley KB, Daugulis AJ. Model for a solid-liquid stirred tank two-phase partitioning bioscrubber for the treatment of BTEX. JOURNAL OF HAZARDOUS MATERIALS 2010; 175:872-882. [PMID: 19959280 DOI: 10.1016/j.jhazmat.2009.10.091] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 10/08/2009] [Accepted: 10/22/2009] [Indexed: 05/28/2023]
Abstract
A dynamic mathematical model has been developed to predict the performance of a stirred tank, solid-liquid two-phase partitioning bioreactor (SL-TPPB) for the treatment of benzene, toluene, ethylbenzene and o-xylene (BTEX) contaminated gases. The SL-TPPB system consists of an aqueous phase containing a bacterial consortium and a solid phase of silicone rubber beads (10%; v/v) with a high affinity for BTEX compounds. The silicone rubber beads serve to sequester and release BTEX according to thermodynamic equilibrium, which increases mass transfer from the gas phase and reduces aqueous phase concentrations of these toxic compounds during fluctuating inlet loadings. The model was developed from mass balances on BTEX components in the gas, aqueous and polymer phases, and biomass in the aqueous phase. Dynamic experimental data from this system were used to fit model parameters and to assess the accuracy of the model. A detailed estimability analysis of model parameters and initial conditions was completed to identify uncertain parameters that are most influential for the model predictions and to determine the parameters and initial conditions that should be targeted for estimation using the dynamic data. It was found that the developed model, with estimated parameters and initial conditions, has the ability to predict experimental off-gas BTEX concentrations with reasonable accuracy, which are the outputs of greatest importance.
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Affiliation(s)
- Jennifer V Littlejohns
- Department of Chemical Engineering, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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Wang L, Jin Y, Zhao L, Pang X, Zhang X. ERIC-PCR-based strain-specific detection of phenol-degrading bacteria in activated sludge of wastewater treatment systems. Lett Appl Microbiol 2009; 49:522-8. [PMID: 19708883 DOI: 10.1111/j.1472-765x.2009.02696.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To evaluate the use of Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR)-derived probes and primers to specifically detect bacterial strains in an activated sludge microbial community. METHODS AND RESULTS ERIC-PCR was performed on two phenol-degrading bacterial strains, Arthrobacter nicotianae P1-7 and Klebsiella sp. P8-14. Their amplicons were DIG labelled for use as probes and then hybridized with ERIC-PCR fingerprints. The results showed the distinct band patterns for both bacterial strains. Strain-specific PCR primers were designed based on the sequences of ERIC-PCR bands. The DNA of each of these strains was successfully detected from its mixture with activated sludge DNA, either by using their respective ERIC-PCR-based probes for hybridization or by using species-specific primers for amplification, with higher sensitivity by latter method. CONCLUSIONS Two phenol-degrading bacterial strains were identified from a mixture of activated sludge by using ERIC-PCR-based methods. SIGNIFICANCE AND IMPACT OF THE STUDY The study demonstrated that the bacteria, which have important functions in complex wastewater treatment microbial communities, could be specifically detected by using ERIC-PCR fingerprint-based hybridization or amplification.
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Affiliation(s)
- L Wang
- Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Jiang XW, Liu H, Xu Y, Wang SJ, Leak DJ, Zhou NY. Genetic and biochemical analyses of chlorobenzene degradation gene clusters in Pandoraea sp. strain MCB032. Arch Microbiol 2009; 191:485-92. [DOI: 10.1007/s00203-009-0476-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 03/09/2009] [Accepted: 03/27/2009] [Indexed: 11/30/2022]
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