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Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism. Appl Environ Microbiol 2019; 85:AEM.02768-18. [PMID: 30658979 DOI: 10.1128/aem.02768-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/08/2019] [Indexed: 11/20/2022] Open
Abstract
Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader "Candidatus Dichloromethanomonas elyunquensis" strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM's genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase of Dehalococcoides mccartyi strain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase of Dehalobacter sp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.IMPORTANCE Naturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader "Candidatus Dichloromethanomonas elyunquensis" strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacterium Dehalobacterium formicoaceticum and "Candidatus Dichloromethanomonas elyunquensis" strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.
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Türkowsky D, Jehmlich N, Diekert G, Adrian L, von Bergen M, Goris T. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol Ecol 2019; 94:4830072. [PMID: 29390082 DOI: 10.1093/femsec/fiy013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
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Roell GW, Zha J, Carr RR, Koffas MA, Fong SS, Tang YJ. Engineering microbial consortia by division of labor. Microb Cell Fact 2019; 18:35. [PMID: 30736778 PMCID: PMC6368712 DOI: 10.1186/s12934-019-1083-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
During microbial applications, metabolic burdens can lead to a significant drop in cell performance. Novel synthetic biology tools or multi-step bioprocessing (e.g., fermentation followed by chemical conversions) are therefore needed to avoid compromised biochemical productivity from over-burdened cells. A possible solution to address metabolic burden is Division of Labor (DoL) via natural and synthetic microbial consortia. In particular, consolidated bioprocesses and metabolic cooperation for detoxification or cross feeding (e.g., vitamin C fermentation) have shown numerous successes in industrial level applications. However, distributing a metabolic pathway among proper hosts remains an engineering conundrum due to several challenges: complex subpopulation dynamics/interactions with a short time-window for stable production, suboptimal cultivation of microbial communities, proliferation of cheaters or low-producers, intermediate metabolite dilution, transport barriers between species, and breaks in metabolite channeling through biosynthesis pathways. To develop stable consortia, optimization of strain inoculations, nutritional divergence and crossing feeding, evolution of mutualistic growth, cell immobilization, and biosensors may potentially be used to control cell populations. Another opportunity is direct integration of non-bioprocesses (e.g., microbial electrosynthesis) to power cell metabolism and improve carbon efficiency. Additionally, metabolic modeling and 13C-metabolic flux analysis of mixed culture metabolism and cross-feeding offers a computational approach to complement experimental research for improved consortia performance.
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Affiliation(s)
- Garrett W Roell
- Department of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, MO, 63130, USA
| | - Jian Zha
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA
| | - Rhiannon R Carr
- Department of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, MO, 63130, USA
| | - Mattheos A Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA
| | - Stephen S Fong
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, MO, 63130, USA.
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Yu K, Yi S, Li B, Guo F, Peng X, Wang Z, Wu Y, Alvarez-Cohen L, Zhang T. An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community. MICROBIOME 2019; 7:16. [PMID: 30728080 PMCID: PMC6366072 DOI: 10.1186/s40168-019-0634-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/25/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses. RESULTS The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone. CONCLUSION The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.
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Affiliation(s)
- Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China.
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China.
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA.
- Environmental microbiology and bioinformatics Laboratory, Shenzhen Graduate School, Peking University, Nanshan district, Shenzhen, Guangdong, China.
| | - Shan Yi
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA
| | - Bing Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Feng Guo
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Xingxing Peng
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zhiping Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Wu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, USA
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam road, Hong Kong, China.
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55
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Wan J, Chen C, Chen J, Miao Q, Liu Y, Ye J, Chen K, Jin Y, Tang X, Shen C. Acceleration of perchloroethylene dechlorination by extracellular secretions from Microbacterium in a mixed culture containing Desulfitobacterium. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 245:651-657. [PMID: 30481679 DOI: 10.1016/j.envpol.2018.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/23/2018] [Accepted: 10/01/2018] [Indexed: 06/09/2023]
Abstract
The study was conducted to demonstrate the influence of extracellular secretions from Microbacterium on the reductive dechlorination of tetrachloroethene (PCE). A series of mixed cultures were established from a paddy soil sample. In the mixed cultures amended with extracellular secretions from Microbacterium, PCE was rapidly and completely converted into cis-1,2-dichloroethene (cis-DCE) and trans-1,2-dichloroethene (trans-DCE) within 40 days. The unamended mixed cultures showed weak signs of dechlorination after a pronounced lag phase, and trichloroethene (TCE) was accumulated as a major end product. This result means that amendment with extracellular secretions from Microbacterium shortened the lag phase, increased the dechlorination velocity and promoted the production of less-chlorinated chloroethene. The results were corroborated by defined subculture experiments, which proved that microorganisms from unamended mixed cultures could also be stimulated by extracellular secretions from Microbacterium. Desulfitobacterium was identified as the main dechlorinating population in all mixed cultures by direct PCR. Additionally, the 16S rRNA gene copies of Desulfitobacterium increased by one or two orders of magnitude with PCE dechlorination, which provided corroborative evidence for the identification result. The volatile fatty acids were monitored, and most interestingly, a close association between propionate oxidation and dechlorination was found, which has rarely been mentioned before. It was assumed that the oxidation of propionate provided hydrogen for dechlorination, while dechlorination facilitated the shift of the reaction toward propionate oxidation by reducing the partial pressure of hydrogen.
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Affiliation(s)
- Jixing Wan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Chen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Jingwen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Qianyu Miao
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yindong Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Junxiang Ye
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Kezhen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yiying Jin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xianjin Tang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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56
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Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA. An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME JOURNAL 2019; 13:1042-1055. [PMID: 30607026 DOI: 10.1038/s41396-018-0333-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022]
Abstract
Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete set of genes for amino acid biosynthesis yet when grown in isolation requires amino acid supplementation. We reconciled this discrepancy using flux balance analysis considering cofactor availability, enzyme promiscuity, and shared protein expression patterns for several D. restrictus strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of D. restrictus strain PER-K23 cultures were performed to validate the model predictions. The model resolved that the amino acid dependency of D. restrictus resulted from restricted NADPH regeneration and predicted that malate supplementation would replenish intracellular NADPH. Interestingly, we observed unexpected export of pyruvate and glutamate in parallel to malate consumption in strain PER-K23 cultures. Further experimental analysis using the ACT-3 transfer cultures suggested the occurrence of an interspecies malate-pyruvate shuttle reconciling a redox imbalance, reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study suggests that redox imbalance and metabolic complementarity are important driving forces for metabolite exchange in anaerobic microbial communities.
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Affiliation(s)
- Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Han-Chen Ho
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
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57
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Campanaro S, Treu L, Kougias PG, Luo G, Angelidaki I. Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants. WATER RESEARCH 2018; 140:123-134. [PMID: 29704757 DOI: 10.1016/j.watres.2018.04.043] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/22/2018] [Accepted: 04/16/2018] [Indexed: 05/07/2023]
Abstract
The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.
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Affiliation(s)
- Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 200433, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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58
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Ismaeil M, Yoshida N, Katayama A. Bacteroides sedimenti sp. nov., isolated from a chloroethenes-dechlorinating consortium enriched from river sediment. J Microbiol 2018; 56:619-627. [DOI: 10.1007/s12275-018-8187-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/11/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022]
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Chau ATT, Lee M, Adrian L, Manefield MJ. Syntrophic Partners Enhance Growth and Respiratory Dehalogenation of Hexachlorobenzene by Dehalococcoides mccartyi Strain CBDB1. Front Microbiol 2018; 9:1927. [PMID: 30186256 PMCID: PMC6113397 DOI: 10.3389/fmicb.2018.01927] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/30/2018] [Indexed: 11/19/2022] Open
Abstract
This study investigated syntrophic interactions between chlorinated benzene respiring Dehalococcoides mccartyi strain CBDB1 and fermenting partners (Desulfovibrio vulgaris, Syntrophobacter fumaroxidans, and Geobacter lovleyi) during hexachlorobenzene respiration. Dechlorination rates in syntrophic co-cultures were enhanced 2-3 fold compared to H2 fed CBDB1 pure cultures (0.23 ± 0.04 μmol Cl− day−1). Syntrophic partners were also able to supply cobalamins to CBDB1, albeit with 3–10 fold lower resultant dechlorination activity compared to cultures receiving exogenous cyanocobalamin. Strain CBDB1 pure cultures accumulated ~1 μmol of carbon monoxide per 87.5 μmol Cl− released during hexachlorobenzene respiration resulting in decreases in dechlorination activity. The syntrophic partners investigated were shown to consume carbon monoxide generated by CBDB1, thus relieving carbon monoxide autotoxicity. Accumulation of lesser chlorinated chlorobenzene congeners (1,3- and 1,4-dichlorobenzene and 1,3,5-trichlorobenzene) also inhibited dechlorination activity and their removal from the headspace through adsorption to granular activated carbon was shown to restore activity. Proteomic analysis revealed co-culturing strain CBDB1 with Geobacter lovleyi upregulated CBDB1 genes associated with reductive dehalogenases, hydrogenases, formate dehydrogenase, and ribosomal proteins. These data provide insight into CBDB1 ecology and inform strategies for application of CBDB1 in ex situ hexachlorobenzene destruction technologies.
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Affiliation(s)
- Anh T T Chau
- College of Agriculture and Applied Biology, Cantho University, Can Tho, Vietnam.,School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Michael J Manefield
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia.,School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
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60
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Ontiveros-Valencia A, Zhou C, Zhao HP, Krajmalnik-Brown R, Tang Y, Rittmann BE. Managing microbial communities in membrane biofilm reactors. Appl Microbiol Biotechnol 2018; 102:9003-9014. [PMID: 30128582 DOI: 10.1007/s00253-018-9293-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 11/29/2022]
Abstract
Membrane biofilm reactors (MBfRs) deliver gaseous substrates to biofilms that develop on the outside of gas-transfer membranes. When an MBfR delivers electron donors hydrogen (H2) or methane (CH4), a wide range of oxidized contaminants can be reduced as electron acceptors, e.g., nitrate, perchlorate, selenate, and trichloroethene. When O2 is delivered as an electron acceptor, reduced contaminants can be oxidized, e.g., benzene, toluene, and surfactants. The MBfR's biofilm often harbors a complex microbial community; failure to control the growth of undesirable microorganisms can result in poor performance. Fortunately, the community's structure and function can be managed using a set of design and operation features as follows: gas pressure, membrane type, and surface loadings. Proper selection of these features ensures that the best microbial community is selected and sustained. Successful design and operation of an MBfR depends on a holistic understanding of the microbial community's structure and function. This involves integrating performance data with omics results, such as with stoichiometric and kinetic modeling.
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Affiliation(s)
- A Ontiveros-Valencia
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN, 46617, USA. .,Escuela de Ingenieria y Ciencias, Tecnologico de Monterrey, Campus Puebla, Ave. Atlixcáyotl 2301, 72453, Puebla, Pue, Mexico. .,Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001S McAllister Ave, Tempe, AZ, 85287-5701, USA.
| | - C Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001S McAllister Ave, Tempe, AZ, 85287-5701, USA
| | - H-P Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Water Pollution Control & Environmental Safety, Zhejiang University, Hangzhou, Zhejiang, China
| | - R Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001S McAllister Ave, Tempe, AZ, 85287-5701, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Y Tang
- FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, FL, 32310, USA
| | - B E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001S McAllister Ave, Tempe, AZ, 85287-5701, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
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61
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Adam PS, Borrel G, Gribaldo S. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. Proc Natl Acad Sci U S A 2018; 115:E1166-E1173. [PMID: 29358391 PMCID: PMC5819426 DOI: 10.1073/pnas.1716667115] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of uncultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.
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Affiliation(s)
- Panagiotis S Adam
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Guillaume Borrel
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Simonetta Gribaldo
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, 75015 Paris, France;
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Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes. mBio 2017; 8:mBio.02022-17. [PMID: 29259088 PMCID: PMC5736913 DOI: 10.1128/mbio.02022-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi. The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments and provide evidence for a homacetogenic lifestyle of these abundant marine Chloroflexi. Moreover, genome signature and key metabolic genes indicate an evolutionary relationship between these deep-sea sediment microbes and terrestrial, reductively dehalogenating Dehalococcoides.
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Phosphoserine Phosphatase Is Required for Serine and One-Carbon Unit Synthesis in Hydrogenobacter thermophilus. J Bacteriol 2017; 199:JB.00409-17. [PMID: 28784815 DOI: 10.1128/jb.00409-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/31/2017] [Indexed: 01/01/2023] Open
Abstract
Hydrogenobacter thermophilus is an obligate chemolithoautotrophic bacterium of the phylum Aquificae and is capable of fixing carbon dioxide through the reductive tricarboxylic acid (TCA) cycle. The recent discovery of two novel-type phosphoserine phosphatases (PSPs) in H. thermophilus suggests the presence of a phosphorylated serine biosynthesis pathway; however, the physiological role of these novel-type metal-independent PSPs (iPSPs) in H. thermophilus has not been confirmed. In the present study, a mutant strain with a deletion of pspA, the catalytic subunit of iPSPs, was constructed and characterized. The generated mutant was a serine auxotroph, suggesting that the novel-type PSPs and phosphorylated serine synthesis pathway are essential for serine anabolism in H. thermophilus. As an autotrophic medium supplemented with glycine did not support the growth of the mutant, the reversible enzyme serine hydroxymethyltransferase does not appear to synthesize serine from glycine and may therefore generate glycine and 5,10-CH2-tetrahydrofolate (5,10-CH2-THF) from serine. This speculation is supported by the lack of glycine cleavage activity, which is needed to generate 5,10-CH2-THF, in H. thermophilus Determining the mechanism of 5,10-CH2-THF synthesis is important for understanding the fundamental anabolic pathways of organisms, because 5,10-CH2-THF is a major one-carbon donor that is used for the synthesis of various essential compounds, including nucleic and amino acids. The findings from the present experiments using a pspA deletion mutant have confirmed the physiological role of iPSPs as serine producers and show that serine is a major donor of one-carbon units in H. thermophilusIMPORTANCE Serine biosynthesis and catabolism pathways are intimately related to the metabolism of 5,10-CH2-THF, a one-carbon donor that is utilized for the biosynthesis of various essential compounds. For this reason, determining the mechanism of serine synthesis is important for understanding the fundamental anabolic pathways of microorganisms. In the present study, we experimentally confirmed that a novel phosphoserine phosphatase in the obligate chemolithoautotrophic bacterium Hydrogenobacter thermophilus is essential for serine biosynthesis. This finding indicates that serine is synthesized from an intermediate of gluconeogenesis in H. thermophilus In addition, because glycine cleavage system activity and genes encoding an enzyme capable of producing 5,10-CH2-THF were not detected, serine appears to be the major one-carbon donor to tetrahydrofolate (THF) in H. thermophilus.
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Wan N, Sathish A, You L, Tang YJ, Wen Z. Deciphering Clostridium metabolism and its responses to bioreactor mass transfer during syngas fermentation. Sci Rep 2017; 7:10090. [PMID: 28855713 PMCID: PMC5577309 DOI: 10.1038/s41598-017-10312-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 08/07/2017] [Indexed: 12/24/2022] Open
Abstract
This study used 13C tracers and dynamic labeling to reveal metabolic features (nutrients requirements, pathway delineation and metabolite turnover rates) of Clostridium carboxidivorans P7, a model strain for industrial syngas fermentation, and its implication with bioreactor mass transfer. P7 shows poor activity for synthesizing amino acids (e.g., phenylalanine) and thus, needs rich medium for cell growth. The strain has multiple carbon fixation routes (Wood-Ljungdahl pathway, pyruvate:ferredoxin oxidoreductase reaction and anaplerotic pathways) and Re-citrate synthase (Ccar_06155) was a key enzyme in its tricarboxylic acid cycle (TCA) pathway. High fluxes were observed in P7's Wood-Ljungdahl pathway, right branch of TCA cycle, pyruvate synthesis, and sugar phosphate pathways, but the cells anabolic pathways were strikingly slow. In bioreactor culture, when syngas flowrate increased from 1 to 10 mL/min, P7 strain produced same amount of total extracellular products (acids and alcohols) but high flowrate favored alcohol accumulation. This observation was due to the mass transfer limitation influencing energy metabolism (CO/H2 oxidation for cofactor generations) more prominently than carbon fixation. When syngas flowrate increased from 10 of 20 mL/min, the alcohol productivity was not improved and the labeling rate (~0.03 h-1) of key metabolite acetyl-CoA reached to P7 strain's metabolism limitation regime.
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Affiliation(s)
- Ni Wan
- Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, MO, 63130, USA
| | - Ashik Sathish
- Agricultural and Biosystems Engineering Department, Iowa State University, Ames, IA, 50011, USA
| | - Le You
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA.
| | - Zhiyou Wen
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, USA.
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Identification of Multiple Dehalogenase Genes Involved in Tetrachloroethene-to-Ethene Dechlorination in a Dehalococcoides-Dominated Enrichment Culture. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9191086. [PMID: 28894752 PMCID: PMC5574268 DOI: 10.1155/2017/9191086] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/03/2017] [Indexed: 11/17/2022]
Abstract
Chloroethenes (CEs) are widespread groundwater toxicants that are reductively dechlorinated to nontoxic ethene (ETH) by members of Dehalococcoides. This study established a Dehalococcoides-dominated enrichment culture (designated “YN3”) that dechlorinates tetrachloroethene (PCE) to ETH with high dechlorination activity, that is, complete dechlorination of 800 μM PCE to ETH within 14 days in the presence of Dehalococcoides species at 5.7 ± 1.9 × 107 copies of 16S rRNA gene/mL. The metagenome of YN3 harbored 18 rdhA genes (designated YN3rdhA1–18) encoding the catalytic subunit of reductive dehalogenase (RdhA), four of which were suggested to be involved in PCE-to-ETH dechlorination based on significant increases in their transcription in response to CE addition. The predicted proteins for two of these four genes, YN3RdhA8 and YN3RdhA16, showed 94% and 97% of amino acid similarity with PceA and VcrA, which are well known to dechlorinate PCE to trichloroethene (TCE) and TCE to ETH, respectively. The other two rdhAs, YN3rdhA6 and YN3rdhA12, which were never proved as rdhA for CEs, showed particularly high transcription upon addition of vinyl chloride (VC), with 75 ± 38 and 16 ± 8.6 mRNA copies per gene, respectively, suggesting their possible functions as novel VC-reductive dehalogenases. Moreover, metagenome data indicated the presence of three coexisting bacterial species, including novel species of the genus Bacteroides, which might promote CE dechlorination by Dehalococcoides.
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Mortan SH, Martín-González L, Vicent T, Caminal G, Nijenhuis I, Adrian L, Marco-Urrea E. Detoxification of 1,1,2-trichloroethane to ethene in a bioreactor co-culture of Dehalogenimonas and Dehalococcoides mccartyi strains. JOURNAL OF HAZARDOUS MATERIALS 2017; 331:218-225. [PMID: 28273571 DOI: 10.1016/j.jhazmat.2017.02.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/30/2017] [Accepted: 02/23/2017] [Indexed: 06/06/2023]
Abstract
1,1,2-Trichloroethane (1,1,2-TCA) is a non-flammable organic solvent and common environmental contaminant in groundwater. Organohalide-respiring bacteria are key microorganisms to remediate 1,1,2-TCA because they can gain metabolic energy during its dechlorination under anaerobic conditions. However, all current isolates produce hazardous end products such as vinyl chloride, monochloroethane or 1,2-dichloroethane that accumulate in the medium. Here, we constructed a syntrophic co-culture of Dehalogenimonas and Dehalococcoides mccartyi strains to achieve complete detoxification of 1,1,2-TCA to ethene. In this co-culture, Dehalogenimonas transformed 1,1,2-TCA via dihaloelimination to vinyl chloride, whereas Dehalococcoides reduced vinyl chloride via hydrogenolysis to ethene. Molasses, pyruvate, and lactate supported full dechlorination of 1,1,2-TCA in serum bottle co-cultures. Scale up of the cultivation to a 5-L bioreactor operating for 76d in fed-batch mode was successful with pyruvate as substrate. This synthetic combination of bacteria with known complementary metabolic capabilities demonstrates the potential environmental relevance of microbial cooperation to detoxify 1,1,2-TCA.
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Affiliation(s)
- Siti Hatijah Mortan
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Lucía Martín-González
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Gloria Caminal
- Institut de Química Avançada de Catalunya (IQAC) CSIC, Barcelona, Spain
| | - Ivonne Nijenhuis
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain.
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Freedman AJ, Tan B, Thompson JR. Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir. Environ Microbiol 2017; 19:2228-2245. [PMID: 28229521 PMCID: PMC5518199 DOI: 10.1111/1462-2920.13706] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 02/17/2017] [Indexed: 11/30/2022]
Abstract
Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO2 -water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling.
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Affiliation(s)
- Adam J.E. Freedman
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - BoonFei Tan
- Center for Environmental Sensing and ModelingSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Janelle R. Thompson
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Environmental Sensing and ModelingSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
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Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions. Appl Environ Microbiol 2017; 83:AEM.03508-16. [PMID: 28188205 DOI: 10.1128/aem.03508-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/04/2017] [Indexed: 12/21/2022] Open
Abstract
The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions.
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Atashgahi S, Lu Y, Zheng Y, Saccenti E, Suarez-Diez M, Ramiro-Garcia J, Eisenmann H, Elsner M, J.M. Stams A, Springael D, Dejonghe W, Smidt H. Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol. Environ Microbiol 2016; 19:968-981. [DOI: 10.1111/1462-2920.13531] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Yue Lu
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Ying Zheng
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | | | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health; Ingolstädter Landstrasse 1 Neuherberg D-85764 Germany
| | - Alfons J.M. Stams
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Centre of Biological Engineering; University of Minho; Braga Portugal
| | - Dirk Springael
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
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Adrian L, Marco-Urrea E. Isotopes in geobiochemistry: tracing metabolic pathways in microorganisms of environmental relevance with stable isotopes. Curr Opin Biotechnol 2016; 41:19-25. [DOI: 10.1016/j.copbio.2016.03.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/02/2016] [Accepted: 03/18/2016] [Indexed: 11/25/2022]
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Czaplicki LM, Gunsch CK. Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. JOURNAL OF ENVIRONMENTAL ENGINEERING (NEW YORK, N.Y.) 2016; 142:10.1061/(ASCE)EE.1943-7870.0001141. [PMID: 28348455 PMCID: PMC5364726 DOI: 10.1061/(asce)ee.1943-7870.0001141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/31/2016] [Indexed: 05/30/2023]
Abstract
Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application.
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Affiliation(s)
- Lauren M. Czaplicki
- Ph.D. Candidate, Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708-0287 USA
| | - Claudia K. Gunsch
- Associate Professor, Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708-0287 USA
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Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization. Proc Natl Acad Sci U S A 2016; 113:E5802-E5811. [PMID: 27634497 DOI: 10.1073/pnas.1606043113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used 13C-fingerprinting, 13C metabolic flux analysis (13C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO2 release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO2 release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) 13C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH.
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Fullerton H, Moyer CL. Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere. Appl Environ Microbiol 2016; 82:3000-3008. [PMID: 26969693 PMCID: PMC4959059 DOI: 10.1128/aem.00624-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/04/2016] [Indexed: 11/25/2022] Open
Abstract
UNLABELLED Chloroflexi small-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylum Chloroflexi is represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurface Chloroflexi Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurface Chloroflexi single amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nine Chloroflexi SAGs (seven of which are from the order Anaerolineales) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of the Chloroflexi SAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the seven Anaerolineales SAGs contains a distinct reductive dehalogenase homologous (rdhA) gene. IMPORTANCE Through the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, the Chloroflexi These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examined Chloroflexi SAGs, our genomes (several are from the order Anaerolineales) were recovered from a hydrothermally driven system and therefore provide a unique window into the metabolic potential of this type of habitat. In addition, a reductive dehalogenase gene (rdhA) has been directly linked to marine subsurface Chloroflexi, suggesting that reductive dehalogenation is not limited to the class Dehalococcoidia This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group.
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Affiliation(s)
- Heather Fullerton
- Department of Biology, Western Washington University, Bellingham, Washington, USA
| | - Craig L Moyer
- Department of Biology, Western Washington University, Bellingham, Washington, USA
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Impact of Ammonium on Syntrophic Organohalide-Respiring and Fermenting Microbial Communities. mSphere 2016; 1:mSphere00053-16. [PMID: 27303735 PMCID: PMC4894693 DOI: 10.1128/msphere.00053-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/10/2016] [Indexed: 01/27/2023] Open
Abstract
Contamination with ammonium and chlorinated solvents has been reported in numerous subsurface environments, and these chemicals bring significant challenges for in situ bioremediation. Dehalococcoides mccartyi is able to reduce the chlorinated solvent trichloroethene to the nontoxic end product ethene. Fermentative bacteria are of central importance for organohalide respiration and bioremediation to provide D. mccartyi with H2, their electron donor, acetate, their carbon source, and other micronutrients. In this study, we found that high concentrations of ammonium negatively correlated with rates of trichloroethene reductive dehalogenation and fermentation. However, detoxification of trichloroethene to nontoxic ethene occurred even at ammonium concentrations typical of those found in animal waste (up to 2 g liter−1 NH4+-N). To date, hundreds of subsurface environments have been bioremediated through the unique metabolic capability of D. mccartyi. These findings extend our knowledge of D. mccartyi and provide insight for bioremediation of sites contaminated with chlorinated solvents and ammonium. Syntrophic interactions between organohalide-respiring and fermentative microorganisms are critical for effective bioremediation of halogenated compounds. This work investigated the effect of ammonium concentration (up to 4 g liter−1 NH4+-N) on trichloroethene-reducing Dehalococcoides mccartyi and Geobacteraceae in microbial communities fed lactate and methanol. We found that production of ethene by D. mccartyi occurred in mineral medium containing ≤2 g liter−1 NH4+-N and in landfill leachate. For the partial reduction of trichloroethene (TCE) to cis-dichloroethene (cis-DCE) at ≥1 g liter−1 NH4+-N, organohalide-respiring dynamics shifted from D. mccartyi and Geobacteraceae to mainly D. mccartyi. An increasing concentration of ammonium was coupled to lower metabolic rates, longer lag times, and lower gene abundances for all microbial processes studied. The methanol fermentation pathway to acetate and H2 was conserved, regardless of the ammonium concentration provided. However, lactate fermentation shifted from propionic to acetogenic at concentrations of ≥2 g liter−1 NH4+-N. Our study findings strongly support a tolerance of D. mccartyi to high ammonium concentrations, highlighting the feasibility of organohalide respiration in ammonium-contaminated subsurface environments. IMPORTANCE Contamination with ammonium and chlorinated solvents has been reported in numerous subsurface environments, and these chemicals bring significant challenges for in situ bioremediation. Dehalococcoides mccartyi is able to reduce the chlorinated solvent trichloroethene to the nontoxic end product ethene. Fermentative bacteria are of central importance for organohalide respiration and bioremediation to provide D. mccartyi with H2, their electron donor, acetate, their carbon source, and other micronutrients. In this study, we found that high concentrations of ammonium negatively correlated with rates of trichloroethene reductive dehalogenation and fermentation. However, detoxification of trichloroethene to nontoxic ethene occurred even at ammonium concentrations typical of those found in animal waste (up to 2 g liter−1 NH4+-N). To date, hundreds of subsurface environments have been bioremediated through the unique metabolic capability of D. mccartyi. These findings extend our knowledge of D. mccartyi and provide insight for bioremediation of sites contaminated with chlorinated solvents and ammonium.
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Wu SG, Wang Y, Jiang W, Oyetunde T, Yao R, Zhang X, Shimizu K, Tang YJ, Bao FS. Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming. PLoS Comput Biol 2016; 12:e1004838. [PMID: 27092947 PMCID: PMC4836714 DOI: 10.1371/journal.pcbi.1004838] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 03/01/2016] [Indexed: 12/17/2022] Open
Abstract
13C metabolic flux analysis (13C-MFA) has been widely used to measure in vivo enzyme reaction rates (i.e., metabolic flux) in microorganisms. Mining the relationship between environmental and genetic factors and metabolic fluxes hidden in existing fluxomic data will lead to predictive models that can significantly accelerate flux quantification. In this paper, we present a web-based platform MFlux (http://mflux.org) that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. Three machine learning methods, namely Support Vector Machine (SVM), k-Nearest Neighbors (k-NN), and Decision Tree, were employed to study the sophisticated relationship between influential factors and metabolic fluxes. We performed a grid search of the best parameter set for each algorithm and verified their performance through 10-fold cross validations. SVM yields the highest accuracy among all three algorithms. Further, we employed quadratic programming to adjust flux profiles to satisfy stoichiometric constraints. Multiple case studies have shown that MFlux can reasonably predict fluxomes as a function of bacterial species, substrate types, growth rate, oxygen conditions, and cultivation methods. Due to the interest of studying model organism under particular carbon sources, bias of fluxome in the dataset may limit the applicability of machine learning models. This problem can be resolved after more papers on 13C-MFA are published for non-model species.
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Affiliation(s)
- Stephen Gang Wu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Yuxuan Wang
- Department of Computer Science and Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Wu Jiang
- Boxed Wholesale, Edison, New Jersey, United States of America
| | - Tolutola Oyetunde
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, People’s Republic of China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, People’s Republic of China
| | - Kazuyuki Shimizu
- Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yinjie J. Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
- * E-mail: (YJT); (FSB)
| | - Forrest Sheng Bao
- Department of Electrical and Computer Engineering, University of Akron, Akron, Ohio, United States of America
- * E-mail: (YJT); (FSB)
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Antoniewicz MR. Parallel labeling experiments for pathway elucidation and (13)C metabolic flux analysis. Curr Opin Biotechnol 2015; 36:91-7. [PMID: 26322734 DOI: 10.1016/j.copbio.2015.08.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/07/2015] [Accepted: 08/09/2015] [Indexed: 12/21/2022]
Abstract
Metabolic pathway models provide the foundation for quantitative studies of cellular physiology through the measurement of intracellular metabolic fluxes. For model organisms metabolic models are well established, with many manually curated genome-scale model reconstructions, gene knockout studies and stable-isotope tracing studies. However, for non-model organisms a similar level of knowledge is often lacking. Compartmentation of cellular metabolism in eukaryotic systems also presents significant challenges for quantitative (13)C-metabolic flux analysis ((13)C-MFA). Recently, innovative (13)C-MFA approaches have been developed based on parallel labeling experiments, the use of multiple isotopic tracers and integrated data analysis, that allow more rigorous validation of pathway models and improved quantification of metabolic fluxes. Applications of these approaches open new research directions in metabolic engineering, biotechnology and medicine.
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Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA.
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Stenuit B, Agathos SN. Deciphering microbial community robustness through synthetic ecology and molecular systems synecology. Curr Opin Biotechnol 2015; 33:305-17. [PMID: 25880923 DOI: 10.1016/j.copbio.2015.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/16/2015] [Accepted: 03/22/2015] [Indexed: 01/09/2023]
Abstract
Microbial ecosystems exhibit specific robustness attributes arising from the assembly and interaction networks of diverse, heterogeneous communities challenged by fluctuating environmental conditions. Synthetic ecology provides new insights into key biodiversity-stability relationships and robustness determinants of host-associated or environmental microbiomes. Driven by the advances of meta-omics technologies and bioinformatics, community-centered approaches (defined as molecular systems synecology) combined with the development of dynamic and mechanistic mathematical models make it possible to decipher and predict the outcomes of microbial ecosystems under disturbances. Beyond discriminating the normal operating range and natural, intrinsic dynamics of microbial processes from systems-level responses to environmental forcing, predictive modeling is poised to be integrated within prescriptive analytical frameworks and thus provide guidance in decision-making and proactive microbial resource management.
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Affiliation(s)
- Ben Stenuit
- Université catholique de Louvain, Earth & Life Institute, Bioengineering Laboratory, Place Croix du Sud 2, bte. L07.05.19, B-1348 Louvain-la-Neuve, Belgium.
| | - Spiros N Agathos
- Université catholique de Louvain, Earth & Life Institute, Bioengineering Laboratory, Place Croix du Sud 2, bte. L07.05.19, B-1348 Louvain-la-Neuve, Belgium
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Mao X, Stenuit B, Polasko A, Alvarez-Cohen L. Efficient metabolic exchange and electron transfer within a syntrophic trichloroethene-degrading coculture of Dehalococcoides mccartyi 195 and Syntrophomonas wolfei. Appl Environ Microbiol 2015; 81:2015-24. [PMID: 25576615 PMCID: PMC4345365 DOI: 10.1128/aem.03464-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/02/2015] [Indexed: 01/07/2023] Open
Abstract
Dehalococcoides mccartyi 195 (strain 195) and Syntrophomonas wolfei were grown in a sustainable syntrophic coculture using butyrate as an electron donor and carbon source and trichloroethene (TCE) as an electron acceptor. The maximum dechlorination rate (9.9 ± 0.1 μmol day(-1)) and cell yield [(1.1 ± 0.3) × 10(8) cells μmol(-1) Cl(-)] of strain 195 maintained in coculture were, respectively, 2.6 and 1.6 times higher than those measured in the pure culture. The strain 195 cell concentration was about 16 times higher than that of S. wolfei in the coculture. Aqueous H2 concentrations ranged from 24 to 180 nM during dechlorination and increased to 350 ± 20 nM when TCE was depleted, resulting in cessation of butyrate fermentation by S. wolfei with a theoretical Gibbs free energy of -13.7 ± 0.2 kJ mol(-1). Carbon monoxide in the coculture was around 0.06 μmol per bottle, which was lower than that observed for strain 195 in isolation. The minimum H2 threshold value for TCE dechlorination by strain 195 in the coculture was 0.6 ± 0.1 nM. Cell aggregates during syntrophic growth were observed by scanning electron microscopy. The interspecies distances to achieve H2 fluxes required to support the measured dechlorination rates were predicted using Fick's law and demonstrated the need for aggregation. Filamentous appendages and extracellular polymeric substance (EPS)-like structures were present in the intercellular spaces. The transcriptome of strain 195 during exponential growth in the coculture indicated increased ATP-binding cassette transporter activities compared to the pure culture, while the membrane-bound energy metabolism related genes were expressed at stable levels.
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Affiliation(s)
- Xinwei Mao
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Benoit Stenuit
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Alexandra Polasko
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Röling WFM. Maths on microbes: adding microbial ecophysiology to metagenomics. Microb Biotechnol 2014; 8:21-2. [PMID: 25488506 PMCID: PMC4321363 DOI: 10.1111/1751-7915.12233] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/07/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Wilfred F M Röling
- Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands
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