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Mahajan R, Nikitina A, Nozhevnikova A, Goel G. Microbial diversity in an anaerobic digester with biogeographical proximity to geothermally active region. ENVIRONMENTAL TECHNOLOGY 2016; 37:2694-2702. [PMID: 26934210 DOI: 10.1080/09593330.2016.1159733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Anaerobic digestion of agricultural biomass or wastes can offer renewable energy, to help meet the rise in energy demands. The performance of an anaerobic digester considerably depends upon the complex interactions between bacterial and archaeal microbiome, which is greatly influenced by environmental factors. In the present study, we evaluate a microbial community of digester located at two different geographical locations, to understand whether the biogeographical proximity of a digester to a geothermally active region has any influence on microbial composition. The comparative microbial community profiling, highlights coexistence of specific bacterial and archaeal representatives (especially, Prosthecochloris sp., Conexibacter sp., Crenarchaeota isolate (Caldivirga sp.), Metallosphaera sp., Pyrobaculum sp. and Acidianus sp.) in a digester with close proximity to geothermally active region (Site I) and their absence in a digester located far-off from geothermally active region (Site II). A Sörensen's index of similarity of 83.33% and 66.66% for bacterial and archaeal community was observed in both the reactors, respectively.
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Affiliation(s)
- Rishi Mahajan
- a Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Waknaghat, Solan, India
| | - Anna Nikitina
- b Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences , 33,bld. 2, Leninsky ave., Moscow , Russia , 119071
| | - Alla Nozhevnikova
- b Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences , 33,bld. 2, Leninsky ave., Moscow , Russia , 119071
| | - Gunjan Goel
- a Department of Biotechnology and Bioinformatics , Jaypee University of Information Technology , Waknaghat, Solan, India
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152
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De Vrieze J, Raport L, Roume H, Vilchez-Vargas R, Jáuregui R, Pieper DH, Boon N. The full-scale anaerobic digestion microbiome is represented by specific marker populations. WATER RESEARCH 2016; 104:101-110. [PMID: 27522020 DOI: 10.1016/j.watres.2016.08.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 05/20/2023]
Abstract
Anaerobic digestion is a well-established microbial-based technology for the treatment of organic waste streams and subsequent biogas recovery. A robust and versatile microbial community to ensure overall stability of the process is essential. Four full-scale anaerobic digestion plants were followed for one year to link operational characteristics with microbial community composition and structure. Similarities between digesters, community dynamics and co-occurrence between bacteria and archaea within each digester were analysed. Free ammonia concentration (>200 mg N L-1) and conductivity (>30 mS cm-1) hindered acetoclastic methanogenesis by Methanosaetaceae. Thus, methanogenesis was pushed to the hydrogenotrophic pathway carried out by Methanobacteriales and Methanomicrobiales. Firmicutes dominated the overall bacterial community in each of the digesters (>50%), however, principal coordinate analysis of Bray-Curtis indices showed that each of the four digesters hosted a unique microbial community. The uniqueness of this community was related to two phylotypes belonging to the Syntrophomonas genus (Phy32 and Phy34) and to one unclassified bacterium (Phy2), which could both be considered marker populations in the community. A clear differentiation in co-occurrence of methanogens with several bacteria was observed between the different digesters. Our results demonstrated that full-scale anaerobic digestion plants show constant dynamics and co-occurrence patterns in function of time, but are unique in terms of composition, related to the presence of marker populations.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Linde Raport
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium; Innolab, Derbystraat 223, 9051, Sint-Denijs-Westrem, Belgium
| | - Hugo Roume
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium.
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153
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Zhang M, Lin Q, Rui J, Li J, Li X. Ammonium inhibition through the decoupling of acidification process and methanogenesis in anaerobic digester revealed by high throughput sequencing. Biotechnol Lett 2016; 39:247-252. [PMID: 27785595 DOI: 10.1007/s10529-016-2241-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 10/13/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To reveal the shifts of microbial communities along ammonium gradients, and the relationship between microbial community composition and the anaerobic digestion performance using a high throughput sequencing technique. RESULTS Methane production declined with increasing ammonium concentration, and was inhibited above 4 g l-1. The volatile fatty acids, especially acetate, accumulated with elevated ammonium. Prokaryotic populations showed different responses to the ammonium concentration: Clostridium, Tepidimicrobium, Sporanaerobacter, Peptostreptococcus, Sarcina and Peptoniphilus showed good tolerance to ammonium ions. However, Syntrophomonas with poor tolerance to ammonium may be inhibited during anaerobic digestion. During methanogenesis, Methanosarcina was the dominant methanogen. CONCLUSION Excessive ammonium inhibited methane production probably by decoupling the linkage between acidification process and methanogenesis, and finally resulted in different performance in anaerobic digestion.
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Affiliation(s)
- Miao Zhang
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan, 610041, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan, 610041, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Junpeng Rui
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan, 610041, People's Republic of China
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan, 610041, People's Republic of China.
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan, 610041, People's Republic of China
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154
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Wei S. The application of biotechnology on the enhancing of biogas production from lignocellulosic waste. Appl Microbiol Biotechnol 2016; 100:9821-9836. [PMID: 27761635 DOI: 10.1007/s00253-016-7926-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/02/2016] [Accepted: 10/05/2016] [Indexed: 12/11/2022]
Abstract
Anaerobic digestion of lignocellulosic waste is considered to be an efficient way to answer present-day energy crisis and environmental challenges. However, the recalcitrance of lignocellulosic material forms a major obstacle for obtaining maximum biogas production. The use of biological pretreatment and bioaugmentation for enhancing the performance of anaerobic digestion is quite recent and still needs to be investigated. This paper reviews the status and perspectives of recent studies on biotechnology concept and investigates its possible use for enhancing biogas production from lignocellulosic waste with main emphases on biological pretreatment and bioaugmentation techniques.
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Affiliation(s)
- Suzhen Wei
- Department of Resource and Environment, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, 860000, China.
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155
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Purohit HJ, Kapley A, Khardenavis A, Qureshi A, Dafale NA. Insights in Waste Management Bioprocesses Using Genomic Tools. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:121-170. [PMID: 27926430 DOI: 10.1016/bs.aambs.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
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Affiliation(s)
- H J Purohit
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Kapley
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Khardenavis
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - A Qureshi
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
| | - N A Dafale
- National Environmental Engineering Research Institute, CSIR, Nagpur, India
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156
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Xu X, Shao J, Li M, Gao K, Jin J, Zhu L. Reductive Transformation of p-chloronitrobenzene in the upflow anaerobic sludge blanket reactor coupled with microbial electrolysis cell: performance and microbial community. BIORESOURCE TECHNOLOGY 2016; 218:1037-1045. [PMID: 27455127 DOI: 10.1016/j.biortech.2016.07.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/02/2016] [Accepted: 07/09/2016] [Indexed: 06/06/2023]
Abstract
A microbial electrolysis cell (MEC) combined with an upflow anaerobic sludge blanket (UASB) reactor was operated to degrade p-chloronitrobenzenes (p-ClNB) effectively. The results indicated that p-ClNB was transformed to p-chloroaniline (p-ClAn) and then reduced via dechlorination pathways. In the MEC-UASB coupled system, p-ClNB, p-ClAn removal efficiency and dechlorination efficiency reached 99.63±0.37%, 40.39±9.26% and 32.16±8.12%, respectively, which was significantly improved in comparison with the control UASB system. In addition, the coupled system could maintain appropriate pH and promote anaerobic sludge granulation to exert a positive effect on reductive transformation of p-ClNB. PCR-DGGE experiment and 454 pyrophosphate sequencing analysis indicated that applied voltage would significantly influence the succession of microbial community and promote oriented enrichment of the functional bacteria, which could be the underlying reasons for the improved performance. This study demonstrated that MEC-UASB coupled system had a promising application prospect to remove the recalcitrant pollutants effectively.
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Affiliation(s)
- Xiangyang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Junjie Shao
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology University, NJ 07102, United States
| | - Kaituo Gao
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China; Equipment Engineering Company, China United Engineering Corporation, Hangzhou 310052, China
| | - Jie Jin
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Liang Zhu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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157
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Hao L, Bize A, Conteau D, Chapleur O, Courtois S, Kroff P, Desmond-Le Quéméner E, Bouchez T, Mazéas L. New insights into the key microbial phylotypes of anaerobic sludge digesters under different operational conditions. WATER RESEARCH 2016; 102:158-169. [PMID: 27340817 DOI: 10.1016/j.watres.2016.06.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 05/07/2023]
Abstract
Analyses on bacterial, archaeal communities at family level and methane-production metabolism were conducted in thirteen full-scale and pilot-scale anaerobic sludge digesters. These digesters were operated at different conditions regarding solids concentration, sludge retention time, organic loading rate and feedstock composition, seeking to optimize digester capacity. Correlations between process parameters and identified microbial phylotypes were evaluated based on relative abundance of these phylotypes determined by Quantitative PCR and 16S rDNA amplicon sequencing. Results showed that, Total Solids concentration (TS), among the evaluated operational parameters, demonstrated the most positive correlation with chemical parameters (including NH3 and VFAs) and significant impact on the abundance of key microbial phylotypes regardless of other factors. Digesters were grouped into 'Higher-TS' with higher stress (TS > 44 g/L, NH3 > 90 mg/L, VFAs > 300 mg/L) and 'Lower-TS' under easier status (TS ≤ 44 g/L, NH3 < 120 mg/L, VFAs < 525 mg/L) in this study. We identified the key microbial phylotypes, i.e. the most abundant and discriminating populations, in 'Higher-TS' digesters with high biogas production rate, which were the class Clostridia, the family Methanosarcinaceae and the order Methanobacteriales. Thermoanaerobacteraceae and Syntrophomonadaceae were identified as key families of Clostridia. Methane was produced both from acetoclastic and hydrogenotrophic methanogenesis. By contrast, in 'Higher-TS' digesters with low biogas production rate, the classes Alpha-, Beta- and Gamma-proteobacteria were detected in higher percentages, of which Rhodobacteraceae, Comamonadaceae and Xanthomonadaceae were the most abundant families respectively, and Methanomicrobiales was the prevailing methanogen order. Consistently, hydrogenotrophic pathway was predominant for methanogenesis, indicating existence of syntrophic acetate oxidation in such 'high-stress', low biogas production rate digesters. These microbial phylotypes were therefore considered to be associated to 'Higher-TS' operation. In 'Lower-TS' digesters, the abundance of the class Delta-proteobacteria, the families Anaerolineaceae, Rikenellaceae, Candidatus Cloacamonas and Methanosaetaceae was obviously higher compared with those in 'Higher-TS' digesters, which were thus considered to be marker phylotypes of easy status. The influence of TS and NH3 on the microbiome should be considered when a 'TS-increasing' strategy is applied to increase digester capacity.
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Affiliation(s)
- Liping Hao
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France
| | - Ariane Bize
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France
| | - Delphine Conteau
- Suez - CIRSEE, 38 rue du Président Wilson, 78230, Le Pecq, France
| | - Olivier Chapleur
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France
| | - Sophie Courtois
- Suez - CIRSEE, 38 rue du Président Wilson, 78230, Le Pecq, France
| | - Pablo Kroff
- Suez - CIRSEE, 38 rue du Président Wilson, 78230, Le Pecq, France
| | | | - Théodore Bouchez
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France
| | - Laurent Mazéas
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, 92761, Antony, France.
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158
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Lin Q, De Vrieze J, He G, Li X, Li J. Temperature regulates methane production through the function centralization of microbial community in anaerobic digestion. BIORESOURCE TECHNOLOGY 2016; 216:150-8. [PMID: 27236402 DOI: 10.1016/j.biortech.2016.05.046] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 05/20/2023]
Abstract
Temperature is crucial for the performance of anaerobic digestion process. In this study of anaerobic digestion of swine manure, the relationship between the microbial gene expression and methane production at different temperatures (25-55°C) was revealed through metatranscriptomic analysis. Daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. The functional gene expression showed great variation at different temperatures. The function centralization (opposite to alpha-diversity), assessed by the least proportions of functional pathways contributing for at least 50% of total reads positively correlated to methane production. Temperature regulated methane production probably through reducing the diversity of functional pathways, but enhancing central functional pathways, so that most of cellular activities and resource were invested in methanogenesis and related pathways, enhancing the efficiency of conversion of substrates to methane. This research demonstrated the importance of function centralization for efficient system functioning.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jo De Vrieze
- Laboratory of Microbial Ecology and Technology, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Guihua He
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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159
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Fischer MA, Güllert S, Neulinger SC, Streit WR, Schmitz RA. Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs. Front Microbiol 2016; 7:1297. [PMID: 27602022 PMCID: PMC4994424 DOI: 10.3389/fmicb.2016.01297] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/08/2016] [Indexed: 01/23/2023] Open
Abstract
The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis. This finding, previously shown for Bacteria, was as well observed for the archaeal domain.
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Affiliation(s)
- Martin A Fischer
- Department of Biology, Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel Kiel, Germany
| | - Simon Güllert
- Biozentrum Klein Flottbek, Institute of Microbiology & Biotechnology, Universität Hamburg Hamburg, Germany
| | - Sven C Neulinger
- Department of Biology, Institute for General Microbiology, Christian-Albrechts-Universität zu KielKiel, Germany; omics2view.consulting GbRKiel, Germany
| | - Wolfgang R Streit
- Biozentrum Klein Flottbek, Institute of Microbiology & Biotechnology, Universität Hamburg Hamburg, Germany
| | - Ruth A Schmitz
- Department of Biology, Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel Kiel, Germany
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160
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Kinet R, Dzaomuho P, Baert J, Taminiau B, Daube G, Nezer C, Brostaux Y, Nguyen F, Dumont G, Thonart P, Delvigne F. Flow cytometry community fingerprinting and amplicon sequencing for the assessment of landfill leachate cellulolytic bioaugmentation. BIORESOURCE TECHNOLOGY 2016; 214:450-459. [PMID: 27160955 DOI: 10.1016/j.biortech.2016.04.131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 06/05/2023]
Abstract
Flow cytometry (FCM) is a high throughput single cell technology that is actually becoming widely used for studying phenotypic and genotypic diversity among microbial communities. This technology is considered in this work for the assessment of a bioaugmentation treatment in order to enhance cellulolytic potential of landfill leachate. The experimental results reveal the relevant increase of leachate cellulolytic potential due to bioaugmentation. Cytometric monitoring of microbial dynamics along these assays is then realized. The flow FP package is used to establish microbial samples fingerprint from initial 2D cytometry histograms. This procedure allows highlighting microbial communities' variation along the assays. Cytometric and 16S rRNA gene sequencing fingerprinting methods are then compared. The two approaches give same evidence about microbial dynamics throughout digestion assay. There are however a lack of significant correlation between cytometric and amplicon sequencing fingerprint at genus or species level. Same phenotypical profiles of microbiota during assays matched to several 16S rRNA gene sequencing ones. Flow cytometry fingerprinting can thus be considered as a promising routine on-site method suitable for the detection of stability/variation/disturbance of complex microbial communities involved in bioprocesses.
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Affiliation(s)
- R Kinet
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - P Dzaomuho
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - J Baert
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - B Taminiau
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Sart-Tilman, B43b, Liège B-4000, Belgium
| | - G Daube
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Sart-Tilman, B43b, Liège B-4000, Belgium
| | - C Nezer
- Quality Partner S.A., Rue Hayeneux, 62, Herstal, B-4040, Belgium
| | - Y Brostaux
- Computer Science and Modeling, Applied Statistics, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux, B-5030, Belgium
| | - F Nguyen
- University of Liege, Applied Geophysics, Department ArGEnCo, Engineering Faculty, B52, B-4000 Liege, Belgium
| | - G Dumont
- University of Liege, Applied Geophysics, Department ArGEnCo, Engineering Faculty, B52, B-4000 Liege, Belgium
| | - P Thonart
- Artechno S.A., Rue Herman Méganck, 21, Isnes, B-5032, Belgium
| | - F Delvigne
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium.
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161
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Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M, Rapp E, Schlüter A, Sczyrba A, Reichl U. Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:155. [PMID: 27462366 PMCID: PMC4960849 DOI: 10.1186/s13068-016-0572-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/12/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Methane yield and biogas productivity of biogas plants (BGPs) depend on microbial community structure and function, substrate supply, and general biogas process parameters. So far, however, relatively little is known about correlations between microbial community function and process parameters. To close this knowledge gap, microbial communities of 40 samples from 35 different industrial biogas plants were evaluated by a metaproteomics approach in this study. RESULTS Liquid chromatography coupled to tandem mass spectrometry (Orbitrap Elite™ Hybrid Ion Trap-Orbitrap Mass Spectrometer) of all 40 samples as triplicate enabled the identification of 3138 different metaproteins belonging to 162 biological processes and 75 different taxonomic orders. The respective database searches were performed against UniProtKB/Swiss-Prot and seven metagenome databases. Subsequent clustering and principal component analysis of these data allowed for the identification of four main clusters associated with mesophile and thermophile process conditions, the use of upflow anaerobic sludge blanket reactors and BGP feeding with sewage sludge. Observations confirm a previous phylogenetic study of the same BGP samples that was based on 16S rRNA gene sequencing by De Vrieze et al. (Water Res 75:312-323, 2015). In particular, we identified similar microbial key players of biogas processes, namely Bacillales, Enterobacteriales, Bacteriodales, Clostridiales, Rhizobiales and Thermoanaerobacteriales as well as Methanobacteriales, Methanosarcinales and Methanococcales. For the elucidation of the main biomass degradation pathways, the most abundant 1 % of metaproteins was assigned to the KEGG map 1200 representing the central carbon metabolism. Additionally, the effect of the process parameters (i) temperature, (ii) organic loading rate (OLR), (iii) total ammonia nitrogen (TAN), and (iv) sludge retention time (SRT) on these pathways was investigated. For example, high TAN correlated with hydrogenotrophic methanogens and bacterial one-carbon metabolism, indicating syntrophic acetate oxidation. CONCLUSIONS This is the first large-scale metaproteome study of BGPs. Proteotyping of BGPs reveals general correlations between the microbial community structure and its function with process parameters. The monitoring of changes on the level of microbial key functions or even of the microbial community represents a well-directed tool for the identification of process problems and disturbances.Graphical abstractCorrelation between the different orders and process parameter, as well as principle component analysis of all investigated biogas plants based on the identified metaproteins.
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Affiliation(s)
- R. Heyer
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - D. Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - F. Kohrs
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - J. De Vrieze
- Laboratory of Microbial Technology and Ecology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - N. Boon
- Laboratory of Microbial Technology and Ecology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - M. Hoffmann
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - E. Rapp
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Genome Research of Industrial Microorganisms, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology, Computational Metagenomics, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - U. Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
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162
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De Vrieze J, Verstraete W. Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity. Environ Microbiol 2016; 18:2797-809. [DOI: 10.1111/1462-2920.13437] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Gent B-9000 Belgium
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Ghent University; Coupure Links 653 Gent B-9000 Belgium
- Avecom NV, Industrieweg 122P; Wondelgem 9032 Belgium
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163
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Vanwonterghem I, Jensen PD, Rabaey K, Tyson GW. Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environ Microbiol 2016; 18:3144-58. [DOI: 10.1111/1462-2920.13382] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 03/17/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Inka Vanwonterghem
- Advanced Water Management Centre (AWMC), The University of Queensland; QLD 4072 St Lucia Australia
- Australian Centre for Ecogenomics (ACE); The University of Queensland; QLD 4072 St Lucia Australia
| | - Paul D. Jensen
- Advanced Water Management Centre (AWMC), The University of Queensland; QLD 4072 St Lucia Australia
| | - Korneel Rabaey
- Advanced Water Management Centre (AWMC), The University of Queensland; QLD 4072 St Lucia Australia
- Centre for Microbial Ecology and Technology (CMET); Ghent University; Coupure Links 653 Ghent 9000 Belgium
| | - Gene W. Tyson
- Advanced Water Management Centre (AWMC), The University of Queensland; QLD 4072 St Lucia Australia
- Australian Centre for Ecogenomics (ACE); The University of Queensland; QLD 4072 St Lucia Australia
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164
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De Vrieze J, Coma M, Debeuckelaere M, Van der Meeren P, Rabaey K. High salinity in molasses wastewaters shifts anaerobic digestion to carboxylate production. WATER RESEARCH 2016; 98:293-301. [PMID: 27110885 DOI: 10.1016/j.watres.2016.04.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 05/16/2023]
Abstract
Biorefinery wastewaters are often treated by means of anaerobic digestion to produce biogas. Alternatively, these wastewaters can be fermented, leading to the formation of carboxylates. Here, we investigated how lab-scale upflow anaerobic sludge blanket reactors could be shifted to fermentation by changing organic loading rate, hydraulic retention time, pH, and salinity. A strong increase in volatile fatty acid concentration up to 40 g COD L(-1) was achieved through increasing salinity above 30 mS cm(-1), as well as a decrease in methane production by more than 90%, which could not be obtained by adjusting the other parameters, thus, indicating a clear shift from methane to carboxylate production. Microbial community analysis revealed a shift in bacterial community to lower evenness and richness values, following the increased salinity and VFA concentration during the fermentation process. A selective enrichment of the hydrogenotrophic Methanomicrobiales took place upon the shift to fermentation, despite a severe decrease in methane production. Particle size distribution revealed a strong degranulation of the sludge in the reactor, related to the high salinity, which resulted in a wash-out of the biomass. This research shows that salinity is a key parameter enabling a shift from methane to carboxylate production in a stable fermentation process.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Marta Coma
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Matthias Debeuckelaere
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Paul Van der Meeren
- Department of Applied Analytical and Physical Chemistry, Coupure Links 653, B-9000 Gent, Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium; Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland 4072, Australia.
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165
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Niu G, Chater KF, Tian Y, Zhang J, Tan H. Specialised metabolites regulating antibiotic biosynthesis in Streptomyces spp. FEMS Microbiol Rev 2016; 40:554-73. [PMID: 27288284 DOI: 10.1093/femsre/fuw012] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 12/11/2022] Open
Abstract
Streptomyces bacteria are the major source of antibiotics and other secondary metabolites. Various environmental and physiological conditions affect the onset and level of production of each antibiotic by influencing concentrations of the ligands for conserved global regulatory proteins. In addition, as reviewed here, well-known autoregulators such as γ-butyrolactones, themselves products of secondary metabolism, accumulate late in growth to concentrations allowing their effective interaction with cognate binding proteins, in a necessary prelude to antibiotic biosynthesis. Most autoregulator binding proteins target the conserved global regulatory gene adpA, and/or regulatory genes for 'cluster-situated regulators' (CSRs) linked to antibiotic biosynthetic gene clusters. It now appears that some CSRs bind intermediates and end products of antibiotic biosynthesis, with regulatory effects interwoven with those of autoregulators. These ligands can exert cross-pathway effects within producers of more than one antibiotic, and when excreted into the extracellular environment may have population-wide effects on production, and mediate interactions with neighbouring microorganisms in natural communities, influencing speciation. Greater understanding of these autoregulatory and cross-regulatory activities may aid the discovery of new signalling molecules and their use in activating cryptic antibiotic biosynthetic pathways.
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Affiliation(s)
- Guoqing Niu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yuqing Tian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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166
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Jiao J, Lu Q, Forster R, Zhou C, Wang M, Kang J, Tan Z. Age and feeding system (supplemental feeding versus grazing) modulates colonic bacterial succession and host mucosal immune maturation in goats1. J Anim Sci 2016; 94:2506-18. [DOI: 10.2527/jas.2015-0081] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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167
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Zamanzadeh M, Hagen LH, Svensson K, Linjordet R, Horn SJ. Anaerobic digestion of food waste - Effect of recirculation and temperature on performance and microbiology. WATER RESEARCH 2016; 96:246-54. [PMID: 27060528 DOI: 10.1016/j.watres.2016.03.058] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/16/2016] [Accepted: 03/25/2016] [Indexed: 05/07/2023]
Abstract
Recirculation of digestate was investigated as a strategy to dilute the food waste before feeding to anaerobic digesters, and its effects on microbial community structure and performance were studied. Two anaerobic digesters with digestate recirculation were operated at 37 °C (MD + R) and 55 °C (TD + R) and compared to two additional digesters without digestate recirculation operated at the same temperatures (MD and TD). The MD + R digester demonstrated quite stable and similar performance to the MD digester in terms of the methane yield (around 480 mL CH4 per gVSadded). In both MD and MD + R Methanosaeta was the dominant archaea. However, the bacterial community structure was significantly different in the two digesters. Firmicutes dominated in the MD + R, while Chloroflexi was the dominant phylum in the MD. Regarding the thermophilic digesters, the TD + R showed the lowest methane yield (401 mL CH4 per gVSadded) and accumulation of VFAs. In contrast to the mesophilic digesters, the microbial communities in the thermophilic digesters were rather similar, consisting mainly of the phyla Firmicutes, Thermotoga, Synergistetes and the hydrogenotrophic methanogen Methanothermobacter. The impact of ammonia inhibition was different depending on the digesters configurations and operating temperatures.
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Affiliation(s)
- Mirzaman Zamanzadeh
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432 Ås, Norway
| | - Live H Hagen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432 Ås, Norway
| | - Kine Svensson
- NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, N-1431 Ås, Norway
| | - Roar Linjordet
- NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, N-1431 Ås, Norway
| | - Svein J Horn
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432 Ås, Norway.
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168
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Perez-Garcia O, Lear G, Singhal N. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems. Front Microbiol 2016; 7:673. [PMID: 27242701 PMCID: PMC4870247 DOI: 10.3389/fmicb.2016.00673] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022] Open
Abstract
We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations.
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Affiliation(s)
- Octavio Perez-Garcia
- Department of Civil and Environmental Engineering, University of Auckland Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland Auckland, New Zealand
| | - Naresh Singhal
- Department of Civil and Environmental Engineering, University of Auckland Auckland, New Zealand
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169
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Krah D, Ghattas AK, Wick A, Bröder K, Ternes TA. Micropollutant degradation via extracted native enzymes from activated sludge. WATER RESEARCH 2016; 95:348-60. [PMID: 27017196 PMCID: PMC5250800 DOI: 10.1016/j.watres.2016.03.037] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
A procedure was developed to assess the biodegradation of micropollutants in cell-free lysates produced from activated sludge of a municipal wastewater treatment plant (WWTP). This proof-of-principle provides the basis for further investigations of micropollutant biodegradation via native enzymes in a solution of reduced complexity, facilitating downstream protein analysis. Differently produced lysates, containing a variety of native enzymes, showed significant enzymatic activities of acid phosphatase, β-galactosidase and β-glucuronidase in conventional colorimetric enzyme assays, whereas heat-deactivated controls did not. To determine the enzymatic activity towards micropollutants, 20 compounds were spiked to the cell-free lysates under aerobic conditions and were monitored via LC-ESI-MS/MS. The micropollutants were selected to span a wide range of different biodegradabilities in conventional activated sludge treatment via distinct primary degradation reactions. Of the 20 spiked micropollutants, 18 could be degraded by intact sludge under assay conditions, while six showed reproducible degradation in the lysates compared to the heat-deactivated negative controls: acetaminophen, N-acetyl-sulfamethoxazole (acetyl-SMX), atenolol, bezafibrate, erythromycin and 10,11-dihydro-10-hydroxycarbamazepine (10-OH-CBZ). The primary biotransformation of the first four compounds can be attributed to amide hydrolysis. However, the observed biotransformations in the lysates were differently influenced by experimental parameters such as sludge pre-treatment and the addition of ammonium sulfate or peptidase inhibitors, suggesting that different hydrolase enzymes were involved in the primary degradation, among them possibly peptidases. Furthermore, the transformation of 10-OH-CBZ to 9-CA-ADIN was caused by a biologically-mediated oxidation, which indicates that in addition to hydrolases further enzyme classes (probably oxidoreductases) are present in the native lysates. Although the full variety of indigenous enzymatic activity of the activated sludge source material could not be restored, experimental modifications, e.g. different lysate filtration, significantly enhanced specific enzyme activities (e.g. >96% removal of the antibiotic erythromycin). Therefore, the approach presented in this study provides the experimental basis for a further elucidation of the enzymatic processes underlying wastewater treatment on the level of native proteins.
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Affiliation(s)
- Daniel Krah
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Ann-Kathrin Ghattas
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Kathrin Bröder
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany.
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170
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Aydin S. Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure. Appl Microbiol Biotechnol 2016; 100:5313-21. [DOI: 10.1007/s00253-016-7533-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 01/22/2023]
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171
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Li L, He Q, Ma Y, Wang X, Peng X. A mesophilic anaerobic digester for treating food waste: process stability and microbial community analysis using pyrosequencing. Microb Cell Fact 2016; 15:65. [PMID: 27112950 PMCID: PMC4845381 DOI: 10.1186/s12934-016-0466-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/13/2016] [Indexed: 11/30/2022] Open
Abstract
Background Anaerobic digesters become unstable when operated at a high organi c loading rate (OLR). Investigating the microbial community response to OLR disturbance is helpful for achieving efficient and stable process operation. However, previous studies have only focused on community succession during different process stages. How does community succession influence process stability? Is this kind of succession resilient? Are any key microbial indicator closely related to process stability? Such relationships between microbial communities and process stability are poorly understood. Results In this study, a mesophilic anaerobic digester for treating food waste (FW) was operated to study the microbial diversity and dynamicity due to OLR disturbance. Overloading resulted in proliferation of acidogenic bacteria, and the resulting high volatile fatty acid (VFA) yield triggered an abundance of acetogenic bacteria. However, the abundance and metabolic efficiency of hydrogenotrophic methanogens decreased after disturbance, and as a consequence, methanogens and acetogenic bacteria could not efficiently complete the syntrophy. This stress induced the proliferation of homoacetogens as alternative hydrogenotrophs for converting excessive H2 to acetate. However, the susceptible Methanothrix species also failed to degrade the excessive acetate. This metabolic imbalance finally led to process deterioration. After process recovery, the digester gradually returned to its original operational conditions, reached close to its original performance, and the microbial community profile achieved a new steady-state. Interestingly, the abundance of Syntrophomonas and Treponema increased during the deteriorative stage and rebounded after disturbance, suggesting they were resilient groups. Conclusions Acidogenic bacteria showed high functional redundancy, rapidly adapted to the increased OLR, and shaped new microbial community profiles. The genera Syntrophomonas and Treponema were resilient groups. This observation provides insight into the key microbial indicator that are closely related to process stability. Moreover, the succession of methanogens during the disturbance phase was unsuitable for the metabolic function needed at high OLR. This contradiction resulted in process deterioration. Thus, methanogenesis is the main step that interferes with the stable operation of digesters at high OLR. Further studies on identifying and breeding high-efficiency methanogens may be helpful for breaking the technical bottleneck of process instability and achieving stable operation under high OLR.
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Affiliation(s)
- Lei Li
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Qin He
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Yao Ma
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Xiaoming Wang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Xuya Peng
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
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172
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Venkiteshwaran K, Bocher B, Maki J, Zitomer D. Relating Anaerobic Digestion Microbial Community and Process Function. Microbiol Insights 2016; 8:37-44. [PMID: 27127410 PMCID: PMC4841157 DOI: 10.4137/mbi.s33593] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 01/01/2023] Open
Abstract
Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.
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Affiliation(s)
- Kaushik Venkiteshwaran
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
| | | | - James Maki
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Daniel Zitomer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA
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173
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Renslow RS, Lindemann SR, Song HS. A Generalized Spatial Measure for Resilience of Microbial Systems. Front Microbiol 2016; 7:443. [PMID: 27092116 PMCID: PMC4823267 DOI: 10.3389/fmicb.2016.00443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/18/2016] [Indexed: 11/29/2022] Open
Abstract
The emergent property of resilience is the ability of a system to return to an original state after a disturbance. Resilience may be used as an early warning system for significant or irreversible community transition; that is, a community with diminishing or low resilience may be close to catastrophic shift in function or an irreversible collapse. Typically, resilience is quantified using recovery time, which may be difficult or impossible to directly measure in microbial systems. A recent study in the literature showed that under certain conditions, a set of spatial-based metrics termed recovery length, can be correlated to recovery time, and thus may be a reasonable alternative measure of resilience. However, this spatial metric of resilience is limited to use for step-change perturbations. Building upon the concept of recovery length, we propose a more general form of the spatial metric of resilience that can be applied to any shape of perturbation profiles (for example, either sharp or smooth gradients). We termed this new spatial measure “perturbation-adjusted spatial metric of resilience” (PASMORE). We demonstrate the applicability of the proposed metric using a mathematical model of a microbial mat.
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Affiliation(s)
- Ryan S Renslow
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA, USA
| | - Stephen R Lindemann
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA, USA
| | - Hyun-Seob Song
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA, USA
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174
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Cydzik-Kwiatkowska A, Zielińska M. Bacterial communities in full-scale wastewater treatment systems. World J Microbiol Biotechnol 2016; 32:66. [PMID: 26931606 PMCID: PMC4773473 DOI: 10.1007/s11274-016-2012-9] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/13/2016] [Indexed: 01/29/2023]
Abstract
Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.
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Affiliation(s)
- Agnieszka Cydzik-Kwiatkowska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-709, Olsztyn, Poland.
| | - Magdalena Zielińska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-709, Olsztyn, Poland
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175
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Isolation and Cultivation of Anaerobes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:35-53. [DOI: 10.1007/10_2016_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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176
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Thijs S, Sillen W, Rineau F, Weyens N, Vangronsveld J. Towards an Enhanced Understanding of Plant-Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism. Front Microbiol 2016; 7:341. [PMID: 27014254 PMCID: PMC4792885 DOI: 10.3389/fmicb.2016.00341] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/03/2016] [Indexed: 11/23/2022] Open
Abstract
Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant-microbial functions, and facilitate translation to more effective, and predictable phytotechnologies.
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Affiliation(s)
- Sofie Thijs
- Department of Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | | | | | | | - Jaco Vangronsveld
- Department of Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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177
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Oburger E, Schmidt H. New Methods To Unravel Rhizosphere Processes. TRENDS IN PLANT SCIENCE 2016; 21:243-255. [PMID: 26776474 DOI: 10.1016/j.tplants.2015.12.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 12/01/2015] [Accepted: 12/09/2015] [Indexed: 05/19/2023]
Abstract
Root-triggered processes (growth, uptake and release of solutes) vary in space and time, and interact with heterogeneous soil microenvironments that provide habitats for (micro)biota on various scales. Despite tremendous progress in method development in the past decades, finding a suitable experimental set-up to investigate processes occurring at the dynamic conjunction of biosphere, hydrosphere, and pedosphere in the close vicinity of active plant roots still represents a major challenge. We discuss recent methodological developments in rhizosphere research with a focus on imaging techniques. We further review established concepts that have been updated with novel techniques, highlighting the need for combinatorial approaches to disentangle rhizosphere processes on relevant scales.
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Affiliation(s)
- Eva Oburger
- University of Natural Resources and Life Sciences Vienna, Department of Forest and Soil Sciences, Institute of Soil Research, Konrad-Lorenz Strasse 24, 3430 Tulln, Austria.
| | - Hannes Schmidt
- University of Vienna, Research Network 'Chemistry meets Microbiology', Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria.
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178
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Boboescu IZ, Gherman VD, Lakatos G, Pap B, Bíró T, Maróti G. Surpassing the current limitations of biohydrogen production systems: The case for a novel hybrid approach. BIORESOURCE TECHNOLOGY 2016; 204:192-201. [PMID: 26790867 DOI: 10.1016/j.biortech.2015.12.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/22/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
The steadily increase of global energy requirements has brought about a general agreement on the need for novel renewable and environmentally friendly energy sources and carriers. Among the alternatives to a fossil fuel-based economy, hydrogen gas is considered a game-changer. Certain methods of hydrogen production can utilize various low-priced industrial and agricultural wastes as substrate, thus coupling organic waste treatment with renewable energy generation. Among these approaches, different biological strategies have been investigated and successfully implemented in laboratory-scale systems. Although promising, several key aspects need further investigation in order to push these technologies towards large-scale industrial implementation. Some of the major scientific and technical bottlenecks will be discussed, along with possible solutions, including a thorough exploration of novel research combining microbial dark fermentation and algal photoheterotrophic degradation systems, integrated with wastewater treatment and metabolic by-products usage.
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Affiliation(s)
- Iulian Zoltan Boboescu
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania; Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary
| | - Vasile Daniel Gherman
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania
| | - Gergely Lakatos
- Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary
| | - Bernadett Pap
- Seqomics Biotechnology Ltd., Vállalkozók útja 7, 6782 Mórahalom, Hungary
| | - Tibor Bíró
- Szent István University, Faculty of Economics, Agricultural and Health Studies, Szarvas, Hungary
| | - Gergely Maróti
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania; Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary.
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179
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Multiple effects of trace elements on methanogenesis in a two-phase anaerobic membrane bioreactor treating starch wastewater. Appl Microbiol Biotechnol 2016; 100:6631-6642. [DOI: 10.1007/s00253-016-7289-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 10/22/2022]
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180
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Guo J, Peng Y, Fan L, Zhang L, Ni BJ, Kartal B, Feng X, Jetten MSM, Yuan Z. Metagenomic analysis of anammox communities in three different microbial aggregates. Environ Microbiol 2016; 18:2979-93. [DOI: 10.1111/1462-2920.13132] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 11/07/2015] [Accepted: 11/11/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Jianhua Guo
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Yongzhen Peng
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
| | - Lu Fan
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Liang Zhang
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
| | - Bing-Jie Ni
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Boran Kartal
- Microbiology, IWWR; Faculty of Science; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Department of Biochemistry and Microbiology; Laboratory of Microbiology; Gent University; Gent 9000 Belgium
| | - Xin Feng
- Research Department of Microbiology; Beijing Genomics Institute (BGI)-Shenzhen; Shenzhen China
| | - Mike S. M. Jetten
- Microbiology, IWWR; Faculty of Science; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Zhiguo Yuan
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering; Engineering Research Center of Beijing; Beijing University of Technology; Beijing 100124 China
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane QLD 4072 Australia
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181
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Maspolim Y, Guo C, Xiao K, Zhou Y, Ng WJ. Performance and microbial community analysis in alkaline two-stage enhanced anaerobic sludge digestion system. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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182
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De Vrieze J, Regueiro L, Props R, Vilchez-Vargas R, Jáuregui R, Pieper DH, Lema JM, Carballa M. Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:244. [PMID: 27843490 PMCID: PMC5103597 DOI: 10.1186/s13068-016-0652-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/20/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated. RESULTS The application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation. CONCLUSIONS This research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Leticia Regueiro
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ramiro Vilchez-Vargas
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research (HZI), Brunswick, Germany
- AgResearch, Tennent Drive, Palmerston North, 4442 New Zealand
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research (HZI), Brunswick, Germany
| | - Juan M. Lema
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Marta Carballa
- Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gomez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
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183
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Schnürer A. Biogas Production: Microbiology and Technology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:195-234. [PMID: 27432246 DOI: 10.1007/10_2016_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Biogas, containing energy-rich methane, is produced by microbial decomposition of organic material under anaerobic conditions. Under controlled conditions, this process can be used for the production of energy and a nutrient-rich residue suitable for use as a fertilising agent. The biogas can be used for production of heat, electricity or vehicle fuel. Different substrates can be used in the process and, depending on substrate character, various reactor technologies are available. The microbiological process leading to methane production is complex and involves many different types of microorganisms, often operating in close relationships because of the limited amount of energy available for growth. The microbial community structure is shaped by the incoming material, but also by operating parameters such as process temperature. Factors leading to an imbalance in the microbial community can result in process instability or even complete process failure. To ensure stable operation, different key parameters, such as levels of degradation intermediates and gas quality, are often monitored. Despite the fact that the anaerobic digestion process has long been used for industrial production of biogas, many questions need still to be resolved to achieve optimal management and gas yields and to exploit the great energy and nutrient potential available in waste material. This chapter discusses the different aspects that need to be taken into consideration to achieve optimal degradation and gas production, with particular focus on operation management and microbiology.
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Affiliation(s)
- Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Sciences, 7025, 750 07, Uppsala, Sweden.
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184
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Reboleiro-Rivas P, Martín-Pascual J, Morillo JA, Juárez-Jiménez B, Poyatos JM, Rodelas B, González-López J. Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage. WATER RESEARCH 2016; 88:796-807. [PMID: 26599433 DOI: 10.1016/j.watres.2015.10.059] [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: 05/16/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 06/05/2023]
Abstract
Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs.
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Affiliation(s)
- P Reboleiro-Rivas
- Departamento de Microbiología, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain; Instituto del Agua, Universidad de Granada, 18071 Granada, Spain.
| | - J Martín-Pascual
- Departamento de Ingeniería Civil, Universidad de Granada, 18071 Granada, Spain; Instituto del Agua, Universidad de Granada, 18071 Granada, Spain
| | - J A Morillo
- Instituto del Agua, Universidad de Granada, 18071 Granada, Spain
| | - B Juárez-Jiménez
- Departamento de Microbiología, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain; Instituto del Agua, Universidad de Granada, 18071 Granada, Spain
| | - J M Poyatos
- Departamento de Ingeniería Civil, Universidad de Granada, 18071 Granada, Spain; Instituto del Agua, Universidad de Granada, 18071 Granada, Spain
| | - B Rodelas
- Departamento de Microbiología, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain; Instituto del Agua, Universidad de Granada, 18071 Granada, Spain
| | - J González-López
- Departamento de Microbiología, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain; Instituto del Agua, Universidad de Granada, 18071 Granada, Spain
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185
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Beale DJ, Karpe AV, McLeod JD, Gondalia SV, Muster TH, Othman MZ, Palombo EA, Joshi D. An 'omics' approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge. WATER RESEARCH 2016; 88:346-357. [PMID: 26512813 DOI: 10.1016/j.watres.2015.10.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 10/12/2015] [Accepted: 10/17/2015] [Indexed: 06/05/2023]
Abstract
In this study, laboratory scale digesters were operated to simulate potential shocks to the Anaerobic Digestion (AD) process at a 350 ML/day wastewater treatment plant. The shocks included high (42 °C) and low (32 °C) temperature (either side of mesophilic 37 °C) and a 20% loading of fats, oil and grease (FOG; 20% w:v). These variables were explored at two sludge retention times (12 and 20 days) and two organic loading rates (2.0 and 2.5 kgTS/m(3)day OLR). Metagenomic and metabolomic approaches were then used to characterise the impact of operational shocks in regard to temperature and FOG addition, as determined through monitoring of biogas production, the microbial profile and their metabolism. Results showed that AD performance was not greatly affected by temperature shocks, with the biggest impact being a reduction in biogas production at 42 °C that persisted for 32 ± 1 days. The average biogas production across all digesters at the completion of the experiment was 264.1 ± 76.5 mL/day, with FOG addition observed to significantly promote biogas production (+87.8 mL/day). Metagenomic and metabolomic analyses of the digesters indicated that methanogens and methane oxidising bacteria (MOB) were low in relative abundance, and that the ratio of oxidising bacteria (methane, sulphide and sulphate) with respect to sulphate reducing bacteria (SRB) had a noticeable influence on biogas production. Furthermore, increased biogas production correlated with an increase in short chain fatty acids, a product of the addition of 20% FOG. This work demonstrates the application of metagenomics and metabolomics to characterise the microbiota and their metabolism in AD digesters, providing insight to the resilience of crucial microbial populations when exposed to operational shocks.
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Affiliation(s)
- D J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, PO Box 2583, Brisbane, Queensland 4001, Australia.
| | - A V Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, PO Box 2583, Brisbane, Queensland 4001, Australia; Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
| | - J D McLeod
- School of Civil, Environmental and Chemical Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - S V Gondalia
- Centre for Human Psychopharmacology, Faculty of Health, Arts and Design, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
| | - T H Muster
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, PO Box 2583, Brisbane, Queensland 4001, Australia
| | - M Z Othman
- School of Civil, Environmental and Chemical Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - E A Palombo
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
| | - D Joshi
- Melbourne Water, PO Box 4342, Melbourne, Victoria 3001, Australia
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186
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Electrochemical and microbial monitoring of multi-generational electroactive biofilms formed from mangrove sediment. Bioelectrochemistry 2015; 106:125-32. [DOI: 10.1016/j.bioelechem.2015.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/24/2015] [Accepted: 05/04/2015] [Indexed: 12/30/2022]
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187
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Advances in proteomics for production strain analysis. Curr Opin Biotechnol 2015; 35:111-7. [DOI: 10.1016/j.copbio.2015.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/28/2015] [Accepted: 05/12/2015] [Indexed: 11/22/2022]
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188
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Smith BJ, Boothe MA, Fiddler BA, Lozano TM, Rahi RK, Krzmarzick MJ. Enumeration of Organohalide Respirers in Municipal Wastewater Anaerobic Digesters. Microbiol Insights 2015; 8:9-14. [PMID: 26508873 PMCID: PMC4607082 DOI: 10.4137/mbi.s31445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/10/2015] [Accepted: 09/15/2015] [Indexed: 01/01/2023] Open
Abstract
Organohalide contaminants such as triclosan and triclocarban have been well documented in municipal wastewater treatment plants (WWTPs), but the degradation of these contaminants is not well understood. One possible removal mechanism is organohalide respiration by which bacteria reduce the halogenated compound. The purpose of this study was to determine the abundance of organohalide-respiring bacteria in eight WWTP anaerobic digesters. The obligate organohalide respiring Dehalococcoides mccartyi was the most abundant and averaged 3.3 × 107 copies of 16S rRNA genes per gram, while the Dehalobacter was much lower at 2.6 × 104 copies of 16S rRNA genes per gram. The genus Sulfurospirillum spp. was also detected at 1.0 × 107 copies of 16S rRNA genes per gram. No other known or putatively organohalide-respiring strains in the Dehalococcoidaceae family were found to be present nor were the genera Desulfitobacterium or Desulfomonile.
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Affiliation(s)
- Bryan Jk Smith
- School of Civil and Environmental Engineering, College of Engineering, Architecture and Technology, Oklahoma State University, Stillwater, OK, USA
| | - Melissa A Boothe
- School of Civil and Environmental Engineering, College of Engineering, Architecture and Technology, Oklahoma State University, Stillwater, OK, USA
| | - Brice A Fiddler
- School of Civil and Environmental Engineering, College of Engineering, Architecture and Technology, Oklahoma State University, Stillwater, OK, USA
| | - Tania M Lozano
- School of Civil and Environmental Engineering, College of Engineering, Architecture and Technology, Oklahoma State University, Stillwater, OK, USA
| | - Russel K Rahi
- School of Civil and Environmental Engineering, College of Engineering, Architecture and Technology, Oklahoma State University, Stillwater, OK, USA
| | - Mark J Krzmarzick
- School of Civil and Environmental Engineering, College of Engineering, Architecture and Technology, Oklahoma State University, Stillwater, OK, USA
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189
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Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach. Sci Rep 2015; 5:14840. [PMID: 26443302 PMCID: PMC4595844 DOI: 10.1038/srep14840] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/01/2015] [Indexed: 01/28/2023] Open
Abstract
Microorganisms almost always exist as mixed communities in nature. While the significance of microbial community activities is well appreciated, a thorough understanding about how microbial communities respond to environmental perturbations has not yet been achieved. Here we have used a combination of metagenomic, genome binning, and stimulus-induced metatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches existing in a complex microbial biofilm that was producing electrical current via extracellular electron transfer (EET) to a solid electrode surface. Two stimuli were employed: to increase EET and to stop EET. An analysis of cell activity marker genes after stimuli exposure revealed that only two strains within eleven binned genomes had strong transcriptional responses to increased EET rates, with one responding positively and the other responding negatively. Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms. These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions. This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli.
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190
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Bize A, Cardona L, Desmond-Le Quéméner E, Battimelli A, Badalato N, Bureau C, Madigou C, Chevret D, Guillot A, Monnet V, Godon JJ, Bouchez T. Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge. Proteomics 2015; 15:3532-43. [PMID: 26260998 DOI: 10.1002/pmic.201500041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 07/02/2015] [Accepted: 08/05/2015] [Indexed: 01/05/2023]
Abstract
Two parallel anaerobic digestion lines were designed to match a "bovid-like" digestive structure. Each of the lines consisted of two continuous stirred tank reactors placed in series and separated by an acidic treatment step. The first line was inoculated with industrial inocula whereas the second was seeded with cow digestive tract contents. After 3 months of continuous sewage sludge feeding, samples were recovered for shotgun metaproteomic and DNA-based analysis. Strikingly, protein-inferred and 16S ribosomal DNA tags based taxonomic community profiles were not consistent. PCA however revealed a similar clustering pattern of the samples, suggesting that reproducible methodological and/or biological factors underlie this observation. The performances of the two digestion lines did not differ significantly and the cow-derived inocula did not establish in the reactors. A low throughput metagenomic dataset (3.4 × 10(6) reads, 1.1 Gb) was also generated for one of the samples. It allowed a substantial increase of the analysis depth (11 vs. 4% of spectral identification rate for the combined samples). Surprisingly, a high proportion of proteins from members of the "Candidatus Competibacter" group, a key microbial player usually found in activated sludge plants, was retrieved in our anaerobic digester samples. Data are available via ProteomeXchange with identifier PXD002420 (http://proteomecentral.proteomexchange.org/dataset/PXD002420).
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Affiliation(s)
| | | | | | - Audrey Battimelli
- INRA, UR0050 Laboratoire de Biotechnologie de l'Environnement, Narbonne, France
| | | | | | | | | | - Alain Guillot
- INRA, UMR1319 MICALIS, PAPPSO, Jouy-en-Josas, France
| | | | - Jean-Jacques Godon
- INRA, UR0050 Laboratoire de Biotechnologie de l'Environnement, Narbonne, France
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191
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Effect of temperature downshifts on biological nitrogen removal and community structure of a lab-scale aerobic denitrification process. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.05.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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192
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Sun L, Pope PB, Eijsink VGH, Schnürer A. Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure. Microb Biotechnol 2015; 8:815-27. [PMID: 26152665 PMCID: PMC4554469 DOI: 10.1111/1751-7915.12298] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/13/2015] [Indexed: 01/22/2023] Open
Abstract
Responses of bacterial and archaeal communities to the addition of straw during anaerobic digestion of manure at different temperatures (37°C, 44°C and 52°C) were investigated using five laboratory-scale semi-continuous stirred tank reactors. The results revealed that including straw as co-substrate decreased the species richness for bacteria, whereas increasing the operating temperature decreased the species richness for both archaea and bacteria, and also the evenness of the bacteria. Taxonomic classifications of the archaeal community showed that Methanobrevibacter dominated in the manure samples, while Methanosarcina dominated in all digesters regardless of substrate. Increase of the operating temperature to 52°C led to increased relative abundance of Methanoculleus and Methanobacterium. Among the bacteria, the phyla Firmicutes and Bacteroidetes dominated within all samples. Compared with manure itself, digestion of manure resulted in a higher abundance of an uncultured class WWE1 and lower abundance of Bacilli. Adding straw to the digesters increased the level of Bacteroidia, while increasing the operating temperature decreased the level of this class and instead increased the relative abundance of an uncultured genus affiliated to order MBA08 (Clostridia). A considerable fraction of bacterial sequences could not be allocated to genus level, indicating that novel phylotypes are resident in these communities.
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Affiliation(s)
- Li Sun
- Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-750 07, Uppsala, Sweden
| | - Phillip B Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-750 07, Uppsala, Sweden.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
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193
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Hong Y, Liao D, Hu A, Wang H, Chen J, Khan S, Su J, Li H. Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing. Can J Microbiol 2015. [PMID: 26223001 DOI: 10.1139/cjm-2015-0079] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Root-associated microbial communities are very important for biogeochemical cycles in wetland ecosystems and help to elaborate the mechanisms of plant invasions. In the estuary of Jiulong River (China), Spartina alterniflora has widely invaded Kandelia obovata-dominated habitats, offering an opportunity to study the influence of root-associated bacteria. The community structures of endophytic and rhizosphere bacteria associated with selected plant species were investigated using the barcoded Illumina paired-end sequencing technique. The diversity indices of bacteria associated with the roots of S. alterniflora were higher than those of the transition stands and K. obovata monoculture. Using principal coordinate analysis with UniFrac metrics, the comparison of β-diversity showed that all samples could be significantly clustered into 3 major groups, according to the bacteria communities of origin. Four phyla, namely Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, were enriched in the rhizoplane of both salt marsh plants, while they shared higher abundances of Cyanobacteria and Proteobacteria among endophytic bacteria. Members of the phyla Spirochaetes and Chloroflexi were found among the endophytic bacteria of S. alterniflora and K. obovata, respectively. One of the interesting findings was that endophytes were more sensitive in response to plant invasion than were rhizosphere bacteria. With linear discriminate analysis, we found some predominant rhizoplane and endophytic bacteria, including Methylococcales, Pseudoalteromonadacea, Clostridium, Vibrio, and Desulfovibrio, which have the potential to affect the carbon, nitrogen, and sulfur cycles. Thus, the results provide clues to the isolation of functional bacteria and the effects of root-associated microbial groups on S. alterniflora invasions.
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Affiliation(s)
- Youwei Hong
- a Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, People's Republic of China.,b Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Dan Liao
- c Xiamen Huaxia College, Xiamen 361024, People's Republic of China
| | - Anyi Hu
- a Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, People's Republic of China
| | - Han Wang
- d College of Ecology and Resources Engineering, Wuyi University, Wuyishan City 354300, People's Republic of China
| | - Jinsheng Chen
- a Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, People's Republic of China
| | - Sardar Khan
- e Department of Environmental Sciences, University of Peshawar, 25120, Pakistan
| | - Jianqiang Su
- a Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, People's Republic of China
| | - Hu Li
- a Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, People's Republic of China.,f University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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194
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Carballa M, Regueiro L, Lema JM. Microbial management of anaerobic digestion: exploiting the microbiome-functionality nexus. Curr Opin Biotechnol 2015; 33:103-11. [DOI: 10.1016/j.copbio.2015.01.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 01/24/2015] [Accepted: 01/26/2015] [Indexed: 02/04/2023]
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195
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Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome. Appl Microbiol Biotechnol 2015; 99:7791-803. [PMID: 25998656 DOI: 10.1007/s00253-015-6627-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/15/2015] [Accepted: 04/19/2015] [Indexed: 02/03/2023]
Abstract
This study provides a comprehensive, long-term microbiological study of a continuously operated, mesophilic, agricultural biogas plant fed with whole-crop silages of maize and rye, cattle manure and cattle slurry. The microbial community structure was accessed by high-throughput 16S rRNA gene amplicon sequencing. For the characterisation of the microbial dynamics, the community profiling method terminal restriction fragment length polymorphism (TRFLP) in combination with a cloning-sequencing approach as well as a LC-MS/MS approach for protein identification were applied. Our results revealed that the anaerobic digestion is a highly sensitive process: small variations in the process performance induce fluctuations in the microbial community composition and activity. In this context, it could be proven that certain microbial species were better adapted to changing process condition such as temperature (interspecies competition) and that there is a physiological compensation between different microorganisms so that the reactor efficiency was not adversely affected despite of structural and functional changes within the microbial community.
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196
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De Vrieze J, Saunders AM, He Y, Fang J, Nielsen PH, Verstraete W, Boon N. Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome. WATER RESEARCH 2015; 75:312-23. [PMID: 25819618 DOI: 10.1016/j.watres.2015.02.025] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 05/07/2023]
Abstract
Anaerobic digestion is regarded as a key environmental technology in the present and future bio-based economy. The microbial community completing the anaerobic digestion process is considered complex, and several attempts already have been carried out to determine the key microbial populations. However, the key differences in the anaerobic digestion microbiomes, and the environmental/process parameters that drive these differences, remain poorly understood. In this research, we hypothesized that differences in operational parameters lead to a particular composition and organization of microbial communities in full-scale installations. A total of 38 samples were collected from 29 different full-scale anaerobic digestion installations, showing constant biogas production in function of time. Microbial community analysis was carried out by means of amplicon sequencing and real-time PCR. The bacterial community in all samples was dominated by representatives of the Firmicutes, Bacteroidetes and Proteobacteria, covering 86.1 ± 10.7% of the total bacterial community. Acetoclastic methanogenesis was dominated by Methanosaetaceae, yet, only the hydrogenotrophic Methanobacteriales correlated with biogas production, confirming their importance in high-rate anaerobic digestion systems. In-depth analysis of operational and environmental parameters and bacterial community structure indicated the presence of three potential clusters in anaerobic digestion. These clusters were determined by total ammonia concentration, free ammonia concentration and temperature, and characterized by an increased relative abundance of Bacteroidales, Clostridiales and Lactobacillales, respectively. None of the methanogenic populations, however, could be significantly attributed to any of the three clusters. Nonetheless, further experimental research will be required to validate the existence of these different clusters, and to which extent the presence of these clusters relates to stable or sub-optimal anaerobic digestion.
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Affiliation(s)
- Jo De Vrieze
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Aaron Marc Saunders
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngårdsholmsvej 49, 9000 Aalborg, Denmark
| | - Ying He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Fang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Per Halkjaer Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngårdsholmsvej 49, 9000 Aalborg, Denmark
| | - Willy Verstraete
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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197
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Abstract
A host's microbiota may increase, diminish, or have no effect at all on cancer susceptibility. Assigning causal roles in cancer to specific microbes and microbiotas, unraveling host-microbiota interactions with environmental factors in carcinogenesis, and exploiting such knowledge for cancer diagnosis and treatment are areas of intensive interest. This Review considers how microbes and the microbiota may amplify or mitigate carcinogenesis, responsiveness to cancer therapeutics, and cancer-associated complications.
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Affiliation(s)
- Wendy S Garrett
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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198
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Ju F, Zhang T. 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions. Appl Microbiol Biotechnol 2015; 99:4119-29. [PMID: 25808518 DOI: 10.1007/s00253-015-6536-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/24/2022]
Abstract
The ubiquitous occurrence of microorganisms gives rise to continuous public concerns regarding their pathogenicity and threats to human environment, as well as potential engineering benefits in biotechnology. The development and wide application of environmental biotechnology, for example in bioenergy production, wastewater treatment, bioremediation, and drinking water disinfection, have been bringing us with both environmental and economic benefits. Strikingly, extensive applications of microscopic and molecular techniques since 1990s have allowed engineers to peep into the microbiology in "black box" of engineered microbial communities in biotechnological processes, providing guidelines for process design and optimization. Recently, revolutionary advances in DNA sequencing technologies and rapidly decreasing costs are altering conventional ways of microbiology and ecology research, as it launches an era of next-generation sequencing (NGS). The principal research burdens are now transforming from traditional labor-intensive wet-lab experiments to dealing with analysis of huge and informative NGS data, which is computationally expensive and bioinformatically challenging. This study discusses state-of-the-art bioinformatics and statistical analyses of 16S ribosomal RNA (rRNA) gene high-throughput sequencing (HTS) data from prevalent NGS platforms to promote its applications in exploring microbial diversity of functional and pathogenic microorganisms, as well as their interactions in biotechnological processes.
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Affiliation(s)
- Feng Ju
- Environmental Biotechnology Lab, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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199
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Guo J, Peng Y, Ni BJ, Han X, Fan L, Yuan Z. Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing. Microb Cell Fact 2015; 14:33. [PMID: 25880314 PMCID: PMC4381419 DOI: 10.1186/s12934-015-0218-4] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anaerobic digestion has been widely applied to treat the waste activated sludge from biological wastewater treatment and produce methane for biofuel, which has been one of the most efficient solutions to both energy crisis and environmental pollution challenges. Anaerobic digestion sludge contains highly complex microbial communities, which play crucial roles in sludge treatment. However, traditional approaches based on 16S rRNA amplification or fluorescent in situ hybridization cannot completely reveal the whole microbial community structure due to the extremely high complexity of the involved communities. In this sense, the next-generation high-throughput sequencing provides a powerful tool for dissecting microbial community structure and methane-producing pathways in anaerobic digestion. RESULTS In this work, the metagenomic sequencing was used to characterize microbial community structure of the anaerobic digestion sludge from a full-scale municipal wastewater treatment plant. Over 3.0 gigabases of metagenomic sequence data were generated with the Illumina HiSeq 2000 platform. Taxonomic analysis by MG-RAST server indicated that overall bacteria were dominant (~93%) whereas a considerable abundance of archaea (~6%) were also detected in the anaerobic digestion sludge. The most abundant bacterial populations were found to be Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Key microorganisms and related pathways involved in methanogenesis were further revealed. The dominant proliferation of Methanosaeta and Methanosarcina, together with the functional affiliation of enzymes-encoding genes (acetate kinase (AckA), phosphate acetyltransferase (PTA), and acetyl-CoA synthetase (ACSS)), suggested that the acetoclastic methanogenesis is the dominant methanogenesis pathway in the full-scale anaerobic digester. CONCLUSIONS In short, the metagenomic sequencing study of this work successfully dissected the detail microbial community structure and the dominated methane-producing pathways of a full-scale anaerobic digester. The knowledge garnered would facilitate to develop more efficient full-scale anaerobic digestion systems to achieve high-rate waste sludge treatment and methane production.
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Affiliation(s)
- Jianhua Guo
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Yongzhen Peng
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
| | - Bing-Jie Ni
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Xiaoyu Han
- Key Laboratory of Beijing for Water Quality Science and Water Environmental Recovery Engineering, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, 100124, Peoples' Republic of China.
- Beijing Drainage Group Co., Ltd, Beijing, 100022, Peoples' Republic of China.
| | - Lu Fan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
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200
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Vanwonterghem I, Jensen PD, Rabaey K, Tyson GW. Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters. Sci Rep 2015; 5:8496. [PMID: 25683239 PMCID: PMC4329568 DOI: 10.1038/srep08496] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/21/2015] [Indexed: 11/09/2022] Open
Abstract
Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C; 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.
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Affiliation(s)
- Inka Vanwonterghem
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, QLD 4072, Australia
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul D. Jensen
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, QLD 4072, Australia
| | - Korneel Rabaey
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, QLD 4072, Australia
- Laboratory for Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Gene W. Tyson
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, QLD 4072, Australia
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
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