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Li X, Lu C, Dai Y, Yu Z, Gu W, Li T, Li X, Li X, Wang X, Su Z, Xu M, Zhang H. Characterizing the Microbial Consortium L1 Capable of Efficiently Degrading Chlorimuron-Ethyl via Metagenome Combining 16S rDNA Sequencing. Front Microbiol 2022; 13:912312. [PMID: 35814706 PMCID: PMC9260513 DOI: 10.3389/fmicb.2022.912312] [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: 04/04/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Excessive application of the herbicide chlorimuron-ethyl (CE) severely harms subsequent crops and poses severe risks to environmental health. Therefore, methods for efficiently decreasing and eliminating CE residues are urgently needed. Microbial consortia show potential for bioremediation due to their strong metabolic complementarity and synthesis. In this study, a microbial consortium entitled L1 was enriched from soil contaminated with CE by a “top-down” synthetic biology strategy. The consortium could degrade 98.04% of 100 mg L−1 CE within 6 days. We characterized it from the samples at four time points during the degradation process and a sample without degradation activity via metagenome and 16S rDNA sequencing. The results revealed 39 genera in consortium L1, among which Methyloversatilis (34.31%), Starkeya (28.60%), and Pseudoxanthomonas (7.01%) showed relatively high abundances. Temporal succession and the loss of degradability did not alter the diversity and community composition of L1 but changed the community structure. Taxon-functional contribution analysis predicted that glutathione transferase [EC 2.5.1.18], urease [EC 3.5.1.5], and allophanate hydrolase [EC 3.5.1.54] are relevant for the degradation of CE and that Methyloversatilis, Pseudoxanthomonas, Methylopila, Hyphomicrobium, Stenotrophomonas, and Sphingomonas were the main degrading genera. The degradation pathway of CE by L1 may involve cleavage of the CE carbamide bridge to produce 2-amino-4-chloro-6-methoxypyrimidine and ethyl o-sulfonamide benzoate. The results of network analysis indicated close interactions, cross-feeding, and co-metabolic relationships between strains in the consortium, and most of the above six degrading genera were keystone taxa in the network. Additionally, the degradation of CE by L1 required not only “functional bacteria” with degradation capacity but also “auxiliary bacteria” without degradation capacity but that indirectly facilitate/inhibit the degradation process; however, the abundance of “auxiliary bacteria” should be controlled in an appropriate range. These findings improve the understanding of the synergistic effects of degrading bacterial consortia, which will provide insight for isolating degrading bacterial resources and constructing artificial efficient bacterial consortia. Furthermore, our results provide a new route for pollution control and biodegradation of sulfonylurea herbicides.
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Affiliation(s)
- Xiang Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changming Lu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yumeng Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixiong Yu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wu Gu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Li
- Shenyang Research Institute of Chemical Industry, Shenyang, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xiujuan Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Mingkai Xu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Mingkai Xu
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- *Correspondence: Huiwen Zhang
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Tal O, Bartuv R, Vetcos M, Medina S, Jiang J, Freilich S. NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data. Microorganisms 2021; 9:microorganisms9091838. [PMID: 34576734 PMCID: PMC8468097 DOI: 10.3390/microorganisms9091838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/08/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a high-resolution description of complex microbial communities in their natural environments and support a systematic study of environment-community-function associations. NetCom is a web-tool for predicting metabolic activities of microbial communities based on network-based interpretation of assembled and annotated metagenomics data. The algorithm takes as an input, lists of differentially abundant enzymatic reactions and generates the following outputs: (i) pathway associations of differently abundant enzymes; (ii) prediction of environmental resources that are unique to each treatment, and their pathway associations; (iii) prediction of compounds that are produced by the microbial community, and pathway association of compounds that are treatment-specific; (iv) network visualization of enzymes, environmental resources and produced compounds, that are treatment specific (2 and 3D). The tool is demonstrated on metagenomic data from rhizosphere and bulk soil samples. By predicting root-specific activities, we illustrate the relevance of our framework for forecasting the impact of soil amendments on the corresponding microbial communities. NetCom is available online.
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Affiliation(s)
- Ofir Tal
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Rotem Bartuv
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 7628604, Israel
| | - Maria Vetcos
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Shlomit Medina
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China;
| | - Shiri Freilich
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
- Correspondence:
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3
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Singh AK, Bilal M, Iqbal HMN, Meyer AS, Raj A. Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:145988. [PMID: 33684751 DOI: 10.1016/j.scitotenv.2021.145988] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Anne S Meyer
- Department for Biotechnology and Biomedicine, Technical University of Denmark, Building 221, DK-2800 Lyngby, Denmark.
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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4
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Wu P, Wang YS. Fluorene degradation by Rhodococcus sp. A2-3 isolated from hydrocarbon contaminated sediment of the Pearl River estuary, China. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:929-935. [PMID: 33797662 DOI: 10.1007/s10646-021-02379-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
The pollution of polycyclic aromatic hydrocarbons was serious in sediments of the Pearl River estuary, China. A fluorene-degrading bacterium, strain A2-3, was isolated from hydrocarbon contaminated sediment of this estuary and identified as Rhodococcus sp. based on the analyses of 16S rRNA gene sequence and morphology. Rhodococcus sp. A2-3 can take naphthalene, p-Teropheny, fluorene, pyrene, salicylic acid, citric acid, acetic acid, diethyletheranhydrous, methanol or 4,4'-dibromodiphenyl ether as sole carbon source. 100% of 100 mg/L fluorene or 89% of 400 mg/L fluorene was removed in 7 days by strain A2-3 at 30 °C and pH 7.5. The strain A2-3 showed a high degradation efficiency of fluorene when pH values ranged from 5.5 to 8.5. The proposed pathway of fluorene catabolism by strain A2-3 was initially attacked by 3,4 dioxygenation. Our results suggested Rhodococcus sp. A2-3 can degrade PAHs under aerobic conditions and can function in bioremediation, particularly for weakly acid environment.
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Affiliation(s)
- Peng Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518121, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
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5
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St. Leger RJ, Wang JB. Metarhizium: jack of all trades, master of many. Open Biol 2020; 10:200307. [PMID: 33292103 PMCID: PMC7776561 DOI: 10.1098/rsob.200307] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
The genus Metarhizium and Pochonia chlamydosporia comprise a monophyletic clade of highly abundant globally distributed fungi that can transition between long-term beneficial associations with plants to transitory pathogenic associations with frequently encountered protozoans, nematodes or insects. Some very common 'specialist generalist' species are adapted to particular soil and plant ecologies, but can overpower a wide spectrum of insects with numerous enzymes and toxins that result from extensive gene duplications made possible by loss of meiosis and associated genome defence mechanisms. These species use parasexuality instead of sex to combine beneficial mutations from separate clonal individuals into one genome (Vicar of Bray dynamics). More weakly endophytic species which kill a narrow range of insects retain sexuality to facilitate host-pathogen coevolution (Red Queen dynamics). Metarhizium species can fit into numerous environments because they are very flexible at the genetic, physiological and ecological levels, providing tractable models to address how new mechanisms for econutritional heterogeneity, host switching and virulence are acquired and relate to diverse sexual life histories and speciation. Many new molecules and functions have been discovered that underpin Metarhizium associations, and have furthered our understanding of the crucial ecology of these fungi in multiple habitats.
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Hidalgo KJ, Teramoto EH, Soriano AU, Valoni E, Baessa MP, Richnow HH, Vogt C, Chang HK, Oliveira VM. Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:135152. [PMID: 31812384 DOI: 10.1016/j.scitotenv.2019.135152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (13C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.
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Affiliation(s)
- K J Hidalgo
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, Campinas, SP. ZIP 13083-862, Brazil.
| | - E H Teramoto
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - A U Soriano
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - E Valoni
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - M P Baessa
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - H H Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - C Vogt
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - H K Chang
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - V M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Paulínia, Brazil, Av. Alexandre Cazellato, 999, ZIP 13148-218, Brazil
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Wang C, Chen Y, Zhou H, Li X, Tan Z. Adaptation mechanisms of Rhodococcus sp. CNS16 under different temperature gradients: Physiological and transcriptome. CHEMOSPHERE 2020; 238:124571. [PMID: 31472351 DOI: 10.1016/j.chemosphere.2019.124571] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Rhodococcus exhibits strong adaptability to environmental stressors and plays a crucial role in environmental bioremediation. However, seasonal changes in ambient temperature, especially rapid temperature drops exert an adverse effect on in situ bioremediation. In this paper, we studied the cell morphology and fatty acid composition of an aniline-degrading strain Rhodococcus sp. CNS16 at temperatures of 30 °C, 20 °C, and 10 °C. At suboptimal temperatures, cell morphology of CNS16 changed from short rod-shaped to long rod or irregular shaped, and the proportion of unsaturated fatty acids was upregulated. Transcriptomic technologies were then utilized to gain detailed insights into the adaptive mechanisms of CNS16 subjected to suboptimal temperatures. The results showed that the number of gene responses was significantly higher at 10 °C than that at 20 °C. The inhibition of peptidoglycan synthase expression and up-regulation of Filamentous Temperature Sensitive as well as unsaturated fatty acid synthesis genes at suboptimal temperatures might be closely related to corresponding changes in cell morphology and fatty acids composition. Strain CNS16 showed loss of catalase and superoxide dismutase activity, and utilized thioredoxin-dependent thiol peroxidase to resist oxidative stress. The up-regulation of carotenoid and Vitamin B2 synthesis at 10 °C might also be involved in the resistance to oxidative stress. Amino acid metabolism, coenzyme and vitamin metabolism, ABC transport, and energy metabolism are essential for peptidoglycan synthesis and regulation of cellular metabolism; therefore, synergistically resisting environmental stress. This study provides a mechanistic basis for the regulation of aniline degradation in Rhodococcus sp. CNS16 at low temperatures.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yangwu Chen
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Houzhen Zhou
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Xudong Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Zhouliang Tan
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
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9
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König S, Köhnke MC, Firle AL, Banitz T, Centler F, Frank K, Thullner M. Disturbance Size Can Be Compensated for by Spatial Fragmentation in Soil Microbial Ecosystems. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Liu X, Chen K, Chuang S, Xu X, Jiang J. Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies. Front Microbiol 2019; 10:88. [PMID: 30761118 PMCID: PMC6363660 DOI: 10.3389/fmicb.2019.00088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/16/2019] [Indexed: 02/01/2023] Open
Abstract
Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant-catabolic consortia remain largely unknown. In this study, an original enrichment (AT) capable of degrading atrazine was obtained. And two enrichments - with a better/worse atrazine-degrading efficiency (ATB/ATW) - were derived from the original enrichment AT by continuous sub-enrichment with or without atrazine. Subsequently, an Arthrobacter sp. strain, AT5, that was capable of degrading atrazine was isolated from enrichment AT. The bacterial community structures of these three enrichments were investigated using high-throughput sequencing analysis of the 16S rRNA gene. The atrazine-degrading efficiency improved as the abundance of Arthrobacter species increased in enrichment ATB. The relative abundance of Arthrobacter was positively correlated with those of Hyphomicrobium and Methylophilus, which enhanced atrazine degradation via promoting the growth of Arthrobacter. Furthermore, six genera/families such as Azospirillum and Halomonas showed a significantly negative correlation with atrazine-degrading efficiency, as they suppressed atrazine degradation directly. These results suggested that atrazine-degrading efficiency was affected by not only the degrader but also some non-degraders in the community. The promotion and suppression of atrazine degradation by Methylophilus and Azospirillum/Halomonas, respectively, were experimentally validated in vitro, showing that shifts in both the composition and abundance in consortia can drive the change in the efficiency of catabolic function. This study provides valuable information for designing enhanced bioremediation strategies.
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Affiliation(s)
| | | | | | - Xihui Xu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Lee Y, Jeong SE, Hur M, Ko S, Jeon CO. Construction and Evaluation of a Korean Native Microbial Consortium for the Bioremediation of Diesel Fuel-Contaminated Soil in Korea. Front Microbiol 2018; 9:2594. [PMID: 30425703 PMCID: PMC6218622 DOI: 10.3389/fmicb.2018.02594] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/11/2018] [Indexed: 01/15/2023] Open
Abstract
A native microbial consortium for the bioremediation of soil contaminated with diesel fuel in Korea was constructed and its biodegradation ability was assessed. Microbial strains isolated from Korean terrestrial environments, with the potential to biodegrade aliphatic hydrocarbons, PAHs, and resins, were investigated and among them, eventually seven microbial strains, Acinetobacter oleivorans DR1, Corynebacterium sp. KSS-2, Pseudomonas sp. AS1, Pseudomonas sp. Neph5, Rhodococcus sp. KOS-1, Micrococcus sp. KSS-8, and Yarrowia sp. KSS-1 were selected for the construction of a microbial consortium based on their biodegradation ability, hydrophobicity, and emulsifying activity. Laboratory- and bulk-scale biodegradation tests showed that in diesel fuel-contaminated soil supplemented with nutrients (nitrogen and phosphorus), the microbial consortium clearly improved the biodegradation of total petroleum hydrocarbons, and all microbial strains constituting the microbial consortium, except for Yarrowia survived and grew well, which suggests that the microbial consortium can be used for the bioremediation of diesel fuel-contaminated soil in Korea.
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Affiliation(s)
- Yunho Lee
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Moonsuk Hur
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | | | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, South Korea
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12
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Volke DC, Nikel PI. Getting Bacteria in Shape: Synthetic Morphology Approaches for the Design of Efficient Microbial Cell Factories. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800111] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel C. Volke
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
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13
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Ofaim S, Ofek-Lalzar M, Sela N, Jinag J, Kashi Y, Minz D, Freilich S. Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation. Front Microbiol 2017; 8:1606. [PMID: 28878756 PMCID: PMC5572346 DOI: 10.3389/fmicb.2017.01606] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/07/2017] [Indexed: 12/25/2022] Open
Abstract
Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups. Once a function-taxonomy link is established, prediction of the impact of dominant taxa on the overall community performances is assessed by simulating removal or addition of edges (taxa associated functions). This approach is demonstrated on metagenomic data describing the microbial communities from the root environment of two crop plants – wheat and cucumber. Predictions for environment-dependent effects revealed differences between treatments (root vs. soil), corresponding to documented observations. Metabolism of specific plant exudates (e.g., organic acids, flavonoids) was linked with distinct taxonomic groups in simulated root, but not soil, environments. These dependencies point to the impact of these metabolite families as determinants of community structure. Simulations of the activity of pairwise combinations of taxonomic groups (order level) predicted the possible production of complementary metabolites. Complementation profiles allow formulating a possible metabolic role for observed co-occurrence patterns. For example, production of tryptophan-associated metabolites through complementary interactions is unique to the tryptophan-deficient cucumber root environment. Our approach enables formulation of testable predictions for species contribution to community activity and exploration of the functional outcome of structural shifts in complex bacterial communities. Understanding community-level metabolism is an essential step toward the manipulation and optimization of microbial function. Here, we introduce an analysis framework addressing three key challenges of such data: producing quantified links between taxonomy and function; contextualizing discrete functions into communal networks; and simulating environmental impact on community performances. New technologies will soon provide a high-coverage description of biotic and a-biotic aspects of complex microbial communities such as these found in gut and soil. This framework was designed to allow the integration of high-throughput metabolomic and metagenomic data toward tackling the intricate associations between community structure, community function, and metabolic inputs.
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Affiliation(s)
- Shany Ofaim
- Newe Ya'ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel.,Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Maya Ofek-Lalzar
- Institute of Soil, Water and Environmental Sciences, Agricultural Research OrganizationBeit Dagan, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani CenterBeit Dagan, Israel
| | - Jiandong Jinag
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Yechezkel Kashi
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research OrganizationBeit Dagan, Israel
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
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14
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Williams AK, Bacosa HP, Quigg A. The impact of dissolved inorganic nitrogen and phosphorous on responses of microbial plankton to the Texas City "Y" oil spill in Galveston Bay, Texas (USA). MARINE POLLUTION BULLETIN 2017; 121:32-44. [PMID: 28545863 DOI: 10.1016/j.marpolbul.2017.05.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/26/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
Ongoing bioremediation research seeks to promote naturally occurring microbial polycyclic aromatic hydrocarbon (PAH) degradation during and after oil spill events. However, complex relationships among functionally different microbial groups, nutrients and PAHs remain unconstrained. We conducted a surface water survey and corresponding nutrient amendment bioassays following the Texas City "Y" oil spill in Galveston Bay, Texas. Resident microbial groups, defined as either heterotrophic or autotrophic were enumerated by flow cytometry. Heterotrophic abundance was increased by oil regardless of nutrient concentrations. Contrastingly, autotrophic abundance was inhibited by oil, but this reaction was less severe when nutrient concentrations were higher. Several PAH compounds were reduced in nutrient amended treatments relative to controls suggesting nutrient enhanced microbial PAH processing. These findings provide a first-look at nutrient limitation during microbial oil processing in Galveston Bay, an important step in understanding if nutrient additions would be a useful bioremediation strategy in this and other estuarine systems.
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Affiliation(s)
- Alicia K Williams
- Texas A&M University at Galveston, Department of Marine Biology, 200 Seawolf Parkway, Galveston, TX 77554, USA; Texas A&M University, Department of Oceanography, 797 Lamar Street, College Station, TX 77840, USA.
| | - Hernando P Bacosa
- Texas A&M University at Galveston, Department of Marine Biology, 200 Seawolf Parkway, Galveston, TX 77554, USA; The University of Texas at Austin, Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Antonietta Quigg
- Texas A&M University at Galveston, Department of Marine Biology, 200 Seawolf Parkway, Galveston, TX 77554, USA; Texas A&M University, Department of Oceanography, 797 Lamar Street, College Station, TX 77840, USA
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15
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Sierra-Garcia IN, Dellagnezze BM, Santos VP, Chaves B MR, Capilla R, Santos Neto EV, Gray N, Oliveira VM. Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales. Extremophiles 2016; 21:211-229. [PMID: 27915388 DOI: 10.1007/s00792-016-0897-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
Abstract
Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.
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Affiliation(s)
- Isabel Natalia Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, UNICAMP, Campinas, CEP 13148-218, Brazil. .,School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
| | - Bruna M Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, UNICAMP, Campinas, CEP 13148-218, Brazil
| | - Viviane P Santos
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, UNICAMP, Campinas, CEP 13148-218, Brazil
| | - Michel R Chaves B
- Institute of Chemistry, University of Campinas, Campinas, CEP13083-970, Brazil
| | - Ramsés Capilla
- PETROBRAS/R&D Center, Rio de Janeiro, CEP 21949-900, Brazil
| | | | - Neil Gray
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Valeria M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, UNICAMP, Campinas, CEP 13148-218, Brazil
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16
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Morales M, Sentchilo V, Bertelli C, Komljenovic A, Kryuchkova-Mostacci N, Bourdilloud A, Linke B, Goesmann A, Harshman K, Segers F, Delapierre F, Fiorucci D, Seppey M, Trofimenco E, Berra P, El Taher A, Loiseau C, Roggero D, Sulfiotti M, Etienne A, Ruiz Buendia G, Pillard L, Escoriza A, Moritz R, Schneider C, Alfonso E, Ben Jeddou F, Selmoni O, Resch G, Greub G, Emery O, Dubey M, Pillonel T, Robinson-Rechavi M, van der Meer JR. The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand. PLoS One 2016; 11:e0165850. [PMID: 27812150 PMCID: PMC5094676 DOI: 10.1371/journal.pone.0165850] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene. We obtained a gapless genome sequence of P. veronii 1YdBTEX2 covering three individual replicons with a total size of 8 Mb, two of which are largely unrelated to current known bacterial replicons. One-hour exposure to toluene, both in soil and liquid, triggered massive transcription (up to 208-fold induction) of multiple gene clusters, such as toluene degradation pathway(s), chemotaxis and toluene efflux pumps. This clearly underlines their key role in the adaptive response to toluene. In comparison to liquid medium, cells in soil drastically changed expression of genes involved in membrane functioning (e.g., lipid composition, lipid metabolism, cell fatty acid synthesis), osmotic stress response (e.g., polyamine or trehalose synthesis, uptake of potassium) and putrescine metabolism, highlighting the immediate response mechanisms of P. veronii 1YdBTEX2 for successful establishment in polluted soil.
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Affiliation(s)
- Marian Morales
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Andrea Komljenovic
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Nadezda Kryuchkova-Mostacci
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Audrey Bourdilloud
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Burkhard Linke
- Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Keith Harshman
- Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Francisca Segers
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Fabien Delapierre
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Damien Fiorucci
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Seppey
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Evgeniya Trofimenco
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Pauline Berra
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Athimed El Taher
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Chloé Loiseau
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Dejan Roggero
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Madeleine Sulfiotti
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Angela Etienne
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gustavo Ruiz Buendia
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Loïc Pillard
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Angelique Escoriza
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Roxane Moritz
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Cedric Schneider
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Esteban Alfonso
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Fatma Ben Jeddou
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Oliver Selmoni
- Master in Molecular Life Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gregory Resch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Olivier Emery
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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17
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Li Y, Chen L, Liu Y, Liu F, Fallgren PH, Jin S. Effects of bioaugmentation on sorption and desorption of benzene, 1,3,5-trimethylbenzene and naphthalene in freshly-spiked and historically-contaminated sediments. CHEMOSPHERE 2016; 162:1-7. [PMID: 27474910 DOI: 10.1016/j.chemosphere.2016.07.051] [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: 11/23/2015] [Revised: 07/13/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
This work investigated the frequently observed "rebounds" of contaminants of concern in groundwater systems. Specifically, influences of bioaugmented microorganisms on the sorption and desorption of representative petroleum constituents [benzene, 1,3,5-trimethylbenzene and naphthalene (BTN)] were studied in freshly-spiked and historically-contaminated sediments. Capable microorganisms were enriched and supplemented to contaminated sediments to enhance biodegradation of petroleum hydrocarbons. In freshly-spiked sediments, when petroleum-degrading microorganisms were added, concentrations of dissolved petroleum constituents appeared to increase initially, and 12.4, 14.0 and 20.0 mg/kg of benzene, 1,3,5-trimethylbenzene and naphthalene, respectively desorbed from the sediments into the water phase. In the historically-contaminated sediments, the augmentation of petroleum-degrading microorganisms led to the desorption of 0.023-0.059, 0009-0.016, and 1.731-2.763 mg/L of previously sequestrated BTN into the water phase, and also triggered the desorption of 0.051-0.223, -0.133-2.630, and 2.324-1.200 mg/kg of previously sequestrated BTN as the methanol extraction quantity. The mechanisms of the enhanced desorption at the presence of microbes remain to be determined; however, we presumed that microbially produced constituents such as biosurfactants and cell mass could have attributed to the partition of petroleum compounds from the sediments. Findings from this study may partially explain "rebounds" of certain petroleum constituents into the groundwater during in situ bioremediation practice, although such immediate rebounds sometimes are weak, and the desorbed constituents can be eventually biodegraded under proper biogeochemical conditions.
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Affiliation(s)
- YueHua Li
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin 300072, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, PR China
| | - Liang Chen
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin 300072, PR China; School of Civil Engineering, Tianjin University, Tianjin 300072, PR China.
| | - YuLong Liu
- Research Institute of Safety and Environment Technology, China National Petroleum Corporation, Beijing 102206, PR China
| | - Fei Liu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing 100083, PR China
| | - Paul H Fallgren
- Advanced Environmental Technologies, LLC, Fort Collins, CO 80525, USA
| | - Song Jin
- Advanced Environmental Technologies, LLC, Fort Collins, CO 80525, USA
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18
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Sharma A, Singh SB, Sharma R, Chaudhary P, Pandey AK, Ansari R, Vasudevan V, Arora A, Singh S, Saha S, Nain L. Enhanced biodegradation of PAHs by microbial consortium with different amendment and their fate in in-situ condition. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 181:728-736. [PMID: 27558829 DOI: 10.1016/j.jenvman.2016.08.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Microbial degradation is a useful tool to prevent chemical pollution in soil. In the present study, in-situ bioremediation of polyaromatic hydrocarbons (PAHs) by microbial consortium consisting of Serratia marcescens L-11, Streptomyces rochei PAH-13 and Phanerochaete chrysosporium VV-18 has been reported. In preliminary studies, the consortium degraded nearly 60-70% of PAHs in broth within 7 days under controlled conditions. The same consortium was evaluated for its competence under natural conditions by amending the soil with ammonium sulphate, paddy straw and compost. Highest microbial activity in terms of dehydrogenase, FDA hydrolase and aryl esterase was recorded on the 5(th) day. The degradation rate of PAHs significantly increased up to 56-98% within 7 days under in-situ however almost complete dissipation (83.50-100%) was observed on the 30(th) day. Among all the co-substrates evaluated, faster degradation of PAHs was observed in compost amended soil wherein fluorene, anthracene, phenanthrene and pyrene degraded with half-life of 1.71, 4.70, 2.04 and 6.14 days respectively. Different degradation products formed were also identified by GC-MS. Besides traces of parent PAHs eleven non-polar and five polar products were identified by direct and silylation reaction respectively. Various products formed indicated that consortium was capable to degrade PAHs by oxidation to mineralization.
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Affiliation(s)
- Anamika Sharma
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Shashi Bala Singh
- Division of Agricultural Chemicals, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Richa Sharma
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priyanka Chaudhary
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Alok Kumar Pandey
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Raunaq Ansari
- Division of Agricultural Chemicals, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Venugopal Vasudevan
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Anju Arora
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Surender Singh
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Supradip Saha
- Division of Agricultural Chemicals, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India.
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19
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Jiang S, Huang J, Lu H, Liu J, Yan C. Optimisation for assay of fluorescein diacetate hydrolytic activity as a sensitive tool to evaluate impacts of pollutants and nutrients on microbial activity in coastal sediments. MARINE POLLUTION BULLETIN 2016; 110:424-431. [PMID: 27315754 DOI: 10.1016/j.marpolbul.2016.06.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Fluorescein diacetate (FDA) assay has been widely applied in coastal research to quantify microbial activity in sediments. However, the present FDA assay procedures embodied in sediment studies potentially include operational errors since the protocol was established for studies of terrestrial soil. In the present study, we optimised the procedure of FDA assay using sandy and cohesive sediments to improve experiential sensitivity and reproducibility. The optimised method describes quantitative measurement of the fluorescein produced when 1.0g of fresh sediment is incubated with 50mM phosphate buffer solution (pH: 7.3) and glass beads (2g) at 35°C for 1h under a rotation of 50rpm. The covariation coefficient of the optimised method ranged from 1.9% to 3.8% and the method sensitivity ranged from 0.25 to 1.57. The improved protocol provides a more reliable measurement of the FDA hydrolysis rate over a wide range of sediments compared to the original method.
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Affiliation(s)
- Shan Jiang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, 361005, China
| | - Jing Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, 361005, China
| | - Haoliang Lu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, 361005, China
| | - JingChun Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, 361005, China
| | - Chongling Yan
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, 361005, China.
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20
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Balcom IN, Driscoll H, Vincent J, Leduc M. Metagenomic analysis of an ecological wastewater treatment plant's microbial communities and their potential to metabolize pharmaceuticals. F1000Res 2016; 5:1881. [PMID: 27610223 PMCID: PMC4995686 DOI: 10.12688/f1000research.9157.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 12/29/2022] Open
Abstract
Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm.
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Affiliation(s)
- Ian N Balcom
- Department of Natural Sciences, Lyndon State College, Lyndonville, VT, USA
| | - Heather Driscoll
- Vermont Genetics Network, Department of Biology and Physical Education, Norwich University, Northfield, VT, USA
| | - James Vincent
- Vermont Genetics Network, Department of Biology, University of Vermont, Burlington, VT, USA
| | - Meagan Leduc
- Department of Natural Sciences, Lyndon State College, Lyndonville, VT, USA
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21
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Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress. Appl Environ Microbiol 2016; 82:2227-2237. [PMID: 26850298 DOI: 10.1128/aem.03482-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/29/2016] [Indexed: 11/20/2022] Open
Abstract
Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.
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22
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Moreno-Forero SK, Rojas E, Beggah S, van der Meer JR. Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:91-102. [PMID: 26616826 DOI: 10.1111/1758-2229.12356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 11/15/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Resistance to semi-dry environments has been considered a crucial trait for superior growth and survival of strains used for bioaugmentation in contaminated soils. In order to compare water stress programmes, we analyse differential gene expression among three phylogenetically different strains capable of aromatic compound degradation: Arthrobacter chlorophenolicus A6, Sphingomonas wittichii RW1 and Pseudomonas veronii 1YdBTEX2. Standardized laboratory-induced water stress was imposed by shock exposure of liquid cultures to water potential decrease, induced either by addition of solutes (NaCl, solute stress) or by addition of polyethylene glycol (matric stress), both at absolute similar stress magnitudes and at those causing approximately similar decrease of growth rates. Genome-wide differential gene expression was recorded by micro-array hybridizations. Growth of P. veronii 1YdBTEX2 was the most sensitive to water potential decrease, followed by S. wittichii RW1 and A. chlorophenolicus A6. The number of genes differentially expressed under decreasing water potential was lowest for A. chlorophenolicus A6, increasing with increasing magnitude of the stress, followed by S. wittichii RW1 and P. veronii 1YdBTEX2. Gene inspection and gene ontology analysis under stress conditions causing similar growth rate reduction indicated that common reactions among the three strains included diminished expression of flagellar motility and increased expression of compatible solutes (which were strain-specific). Furthermore, a set of common genes with ill-defined function was found between all strains, including ABC transporters and aldehyde dehydrogenases, which may constitute a core conserved response to water stress. The data further suggest that stronger reduction of growth rate of P. veronii 1YdBTEX2 under water stress may be an indirect result of the response demanding heavy NADPH investment, rather than the presence or absence of a suitable stress defence mechanism per se.
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Affiliation(s)
- Silvia K Moreno-Forero
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Edward Rojas
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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Bacterial PAH degradation in marine and terrestrial habitats. Curr Opin Biotechnol 2015; 33:95-102. [DOI: 10.1016/j.copbio.2015.01.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/15/2014] [Accepted: 01/14/2015] [Indexed: 11/22/2022]
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Babin D, Vogel C, Zühlke S, Schloter M, Pronk GJ, Heister K, Spiteller M, Kögel-Knabner I, Smalla K. Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils. PLoS One 2014; 9:e106865. [PMID: 25222697 PMCID: PMC4164357 DOI: 10.1371/journal.pone.0106865] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/08/2014] [Indexed: 11/30/2022] Open
Abstract
The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.
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Affiliation(s)
- Doreen Babin
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Cordula Vogel
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
| | - Sebastian Zühlke
- Institut für Umweltforschung (INFU), Lehrstuhl für Umweltchemie und Analytische Chemie der Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
| | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Geertje Johanna Pronk
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technische Universität München, Garching, Germany
| | - Katja Heister
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
| | - Michael Spiteller
- Institut für Umweltforschung (INFU), Lehrstuhl für Umweltchemie und Analytische Chemie der Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
| | - Ingrid Kögel-Knabner
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technische Universität München, Garching, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
- * E-mail:
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Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand. ISME JOURNAL 2014; 9:150-65. [PMID: 24936762 PMCID: PMC4274413 DOI: 10.1038/ismej.2014.101] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 05/07/2014] [Accepted: 05/12/2014] [Indexed: 11/08/2022]
Abstract
The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (that is, bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of genome-wide gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated non-sterile sand, compared with regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing dibenzodioxins and dibenzofurans. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well as during growth and stationary phase in sand. Cells during transition show stationary phase characteristics, evidence for stress and for nutrient scavenging, and adjust their primary metabolism if they were not precultured on the same contaminant as found in the soil. Cells growing and surviving in sand degrade dibenzofuran but display a very different transcriptome signature as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous 'soil-specific' expressed genes. Studies focusing on inoculation efficacy should test behaviour under conditions as closely as possible mimicking the intended microbiome conditions.
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Yu FB, Li XD, Ali SW, Shan SD, Luo LP, Guan LB. Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp. ONBA-17 and deduction on its metabolic pathway. Braz J Microbiol 2014; 45:1303-8. [PMID: 25763034 PMCID: PMC4323303 DOI: 10.1590/s1517-83822014000400021] [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: 10/25/2013] [Accepted: 04/17/2014] [Indexed: 11/21/2022] Open
Abstract
A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation.
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Affiliation(s)
- Fang-Bo Yu
- Department of Environmental Sciences Zhejiang Agricultural and Forestry University Linan China Department of Environmental Sciences, Zhejiang Agricultural and Forestry University, Linan, China
| | - Xiao-Dan Li
- Institute of Botany Jiangsu Province and Chinese Academy of Sciences Nanjing China Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Shinawar Waseem Ali
- Institute of Agricultural Sciences University of the Punjab Lahore Pakistan Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Sheng-Dao Shan
- Department of Environmental Sciences Zhejiang Agricultural and Forestry University Linan China Department of Environmental Sciences, Zhejiang Agricultural and Forestry University, Linan, China
| | - Lin-Ping Luo
- Department of Environmental Sciences Zhejiang Agricultural and Forestry University Linan China Department of Environmental Sciences, Zhejiang Agricultural and Forestry University, Linan, China
| | - Li-Bo Guan
- Department of Environmental Sciences Zhejiang Agricultural and Forestry University Linan China Department of Environmental Sciences, Zhejiang Agricultural and Forestry University, Linan, China
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Hydrocarbon biodegradation in intertidal wetland sediments. Curr Opin Biotechnol 2013; 27:46-54. [PMID: 24863896 DOI: 10.1016/j.copbio.2013.10.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 12/23/2022]
Abstract
Intertidal wetlands, primarily salt marsh, mangrove and mudflats, which provide many essential ecosystem services, are under threat on numerous fronts; a situation that is made worse by crude-oil pollution. Microbes are the main vehicle for remediation of such sediments, and new discoveries, such as novel biodegradation pathways, means of accessing oil, multi-species interactions, and community-level responses to oil addition, are helping us to understand, predict and monitor the fate of oil. Despite this, there are many challenges, not least because of the heterogeneity of these ecosystems and the complexity of crude oil. For example, there is growing awareness about the toxicity of the oxygenated products that result from crude-oil weathering, which are difficult to degrade. This review highlights how developments in areas as diverse as systems biology, microbiology, ecology, biogeochemistry and analytical chemistry are enhancing our understanding of hydrocarbon biodegradation and thus bioremediation of oil-polluted intertidal wetlands.
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Agrawal A, Gieg LM. In situ detection of anaerobic alkane metabolites in subsurface environments. Front Microbiol 2013; 4:140. [PMID: 23761789 PMCID: PMC3671572 DOI: 10.3389/fmicb.2013.00140] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/17/2013] [Indexed: 11/13/2022] Open
Abstract
Alkanes comprise a substantial fraction of crude oil and refined fuels. As such, they are prevalent within deep subsurface fossil fuel deposits and in shallow subsurface environments such as aquifers that are contaminated with hydrocarbons. These environments are typically anaerobic, and host diverse microbial communities that can potentially use alkanes as substrates. Anaerobic alkane biodegradation has been reported to occur under nitrate-reducing, sulfate-reducing, and methanogenic conditions. Elucidating the pathways of anaerobic alkane metabolism has been of interest in order to understand how microbes can be used to remediate contaminated sites. Alkane activation primarily occurs by addition to fumarate, yielding alkylsuccinates, unique anaerobic metabolites that can be used to indicate in situ anaerobic alkane metabolism. These metabolites have been detected in hydrocarbon-contaminated shallow aquifers, offering strong evidence for intrinsic anaerobic bioremediation. Recently, studies have also revealed that alkylsuccinates are present in oil and coal seam production waters, indicating that anaerobic microbial communities can utilize alkanes in these deeper subsurface environments. In many crude oil reservoirs, the in situ anaerobic metabolism of hydrocarbons such as alkanes may be contributing to modern-day detrimental effects such as oilfield souring, or may lead to more beneficial technologies such as enhanced energy recovery from mature oilfields. In this review, we briefly describe the key metabolic pathways for anaerobic alkane (including n-alkanes, isoalkanes, and cyclic alkanes) metabolism and highlight several field reports wherein alkylsuccinates have provided evidence for anaerobic in situ alkane metabolism in shallow and deep subsurface environments.
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Affiliation(s)
- Akhil Agrawal
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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