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Tan ZQ, Leow HY, Lee DCW, Karisnan K, Song AAL, Mai CW, Yap WS, Lim SHE, Lai KS. Co-Culture Systems for the Production of Secondary Metabolites: Current and Future Prospects. ACTA ACUST UNITED AC 2019. [DOI: 10.2174/1874070701913010018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Microorganisms are the great sources of Natural Products (NPs); these are imperative to their survival apart from conferring competitiveness amongst each other within their environmental niches. Primary and secondary metabolites are the two major classes of NPs that help in cell development, where antimicrobial activity is closely linked with secondary metabolites. To capitalize on the effects of secondary metabolites, co-culture methods have been often used to develop an artificial microbial community that promotes the action of these metabolites. Different analytical techniques will subsequently be employed based on the metabolite specificity and sensitivity to further enhance the metabolite induction. Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas Chromatography (GC)-MS are commonly used for metabolite separation while Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS) have been used as tools to elucidate the structure of compounds. This review intends to discuss current systems in use for co-culture in addition to its advantages, with discourse into the investigation of specific techniques in use for the detailed study of secondary metabolites. Further advancements and focus on co-culture technologies are required to fully realize the massive potential in synthetic biological systems.
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Carrillo-Barragan P, Bowler B, Dolfing J, Sallis P, Gray ND. Enrichment and Characterisation of a Mixed-Source Ethanologenic Community Degrading the Organic Fraction of Municipal Solid Waste Under Minimal Environmental Control. Front Microbiol 2019; 10:722. [PMID: 31024500 PMCID: PMC6465759 DOI: 10.3389/fmicb.2019.00722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/21/2019] [Indexed: 01/08/2023] Open
Abstract
The utilisation of the organic fraction of municipal solid waste as feedstock for bioethanol production could reduce the need for disposal of the ever-increasing amounts of municipal solid waste, especially in developing countries, and fits with the integrated goals of climate change mitigation and transport energy security. Mixed culture fermentation represents a suitable approach to handle the complexity and variability of such waste, avoiding expensive and vulnerable closed-control operational conditions. It is widely accepted that the control of pH in these systems can direct the fermentation process toward a desired fermentation product, however, little empirical evidence has been provided in respect of lignocellulosic waste substrates and different environmental inocula sources. We evaluated ethanol production from the organic fraction of municipal solid waste using five different inocula sources where lignocellulose degradation putatively occurs, namely, compost, woodland soil, rumen, cow faeces and anaerobic granular sludge, when incubated in batch microcosms at either initially neutral or acidic pH and under initially aerobic or anaerobic conditions. Although ethanol was produced by all the inocula tested, their performance was different in response to the imposed experimental conditions. Rumen and anaerobic granular sludge produced significantly the highest ethanol concentrations (∼30 mM) under initially neutral and acidic pH, respectively. A mixed-source community formed by mixing rumen and sludge (R + S) was then tested over a range of initial pH. In contrast to the differences observed for the individual inocula, the maximal ethanol production of the mixed community was not significantly different at initial pH of 5.5 and 7. Consistent with this broader functionality, the microbial community analyses confirmed the R + S community enriched comprised bacterial taxa representative of both original inocula. It was demonstrated that the interaction of initial pH and inocula source dictated ethanologenic activity from the organic fraction of municipal solid waste. Furthermore, the ethanologenic mixed-source community enriched, was comprised of taxa belonging to the two original inocula sources (rumen and sludge) and had a broader functionality. This information is relevant when diverse inocula sources are combined for mix culture fermentation studies as it experimentally demonstrates the benefits of diversity and function assembled from different inocula.
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Affiliation(s)
| | - Bernard Bowler
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jan Dolfing
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paul Sallis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Neil Duncan Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Cui J, Mai G, Wang Z, Liu Q, Zhou Y, Ma Y, Liu C. Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation. Front Microbiol 2019; 10:618. [PMID: 30984144 PMCID: PMC6447707 DOI: 10.3389/fmicb.2019.00618] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/11/2019] [Indexed: 11/22/2022] Open
Abstract
Background Cellulose is the most abundant organic polymer mainly produced by plants in nature. It is insoluble and highly resistant to enzymatic hydrolysis. Cellulolytic microorganisms that are capable of producing a battery of related enzymes play an important role in recycling cellulose-rich plant biomass. Effective cellulose degradation by multiple synergic microorganisms has been observed within a defined microbial consortium in the lab culture. Metagenomic analysis may enable us to understand how microbes cooperate in cellulose degradation in a more complex microbial free-living ecosystem in nature. Results Here we investigated a typical cellulose-rich and alkaline niche where constituent microbes survive through inter-genera cooperation in cellulose utilization. The niche has been generated in an ancient paper-making plant, which has served as an isolated habitat for over 7 centuries. Combined amplicon-based sequencing of 16S rRNA genes and metagenomic sequencing, our analyses showed a microbial composition with 6 dominant genera including Cloacibacterium, Paludibacter, Exiguobacterium, Acetivibrio, Tolumonas, and Clostridium in this cellulose-rich niche; the composition is distinct from other cellulose-rich niches including a modern paper mill, bamboo soil, wild giant panda guts, and termite hindguts. In total, 11,676 genes of 96 glucoside hydrolase (GH) families, as well as 1,744 genes of carbohydrate transporters were identified, and modeling analysis of two representative genes suggested that these glucoside hydrolases likely evolved to adapt to alkaline environments. Further reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction between the dominant microbes regarding the cellulolytic process in the niche, with Paludibacter and Clostridium acting as helpers that produce endoglucanases, and Cloacibacterium, Exiguobacterium, Acetivibrio, and Tolumonas being beneficiaries that cross-feed on the cellodextrins by oligosaccharide uptake. Conclusion The analysis of the key genes involved in cellulose degradation and reconstruction of the microbial draft genomes by binning the assembled contigs predicted a mutualistic interaction based on public goods regarding the cellulolytic process in the niche, suggesting that in the studied microbial consortium, free-living bacteria likely survive on each other by acquisition and exchange of metabolites. Knowledge gained from this study will facilitate the design of complex microbial communities with a better performance in industrial bioprocesses.
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Affiliation(s)
- Jinming Cui
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Guoqin Mai
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zuowei Wang
- Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Quan Liu
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yan Zhou
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingfei Ma
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chenli Liu
- Institute of Synthetic Biology - Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Bohra V, Dafale NA, Hathi Z, Purohit HJ. Genomic annotation and validation of bacterial consortium NDMC-1 for enhanced degradation of sugarcane bagasse. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01462-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Liu X, Chen K, Chuang S, Xu X, Jiang J. Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies. Front Microbiol 2019; 10:88. [PMID: 30761118 PMCID: PMC6363660 DOI: 10.3389/fmicb.2019.00088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/16/2019] [Indexed: 02/01/2023] Open
Abstract
Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant-catabolic consortia remain largely unknown. In this study, an original enrichment (AT) capable of degrading atrazine was obtained. And two enrichments - with a better/worse atrazine-degrading efficiency (ATB/ATW) - were derived from the original enrichment AT by continuous sub-enrichment with or without atrazine. Subsequently, an Arthrobacter sp. strain, AT5, that was capable of degrading atrazine was isolated from enrichment AT. The bacterial community structures of these three enrichments were investigated using high-throughput sequencing analysis of the 16S rRNA gene. The atrazine-degrading efficiency improved as the abundance of Arthrobacter species increased in enrichment ATB. The relative abundance of Arthrobacter was positively correlated with those of Hyphomicrobium and Methylophilus, which enhanced atrazine degradation via promoting the growth of Arthrobacter. Furthermore, six genera/families such as Azospirillum and Halomonas showed a significantly negative correlation with atrazine-degrading efficiency, as they suppressed atrazine degradation directly. These results suggested that atrazine-degrading efficiency was affected by not only the degrader but also some non-degraders in the community. The promotion and suppression of atrazine degradation by Methylophilus and Azospirillum/Halomonas, respectively, were experimentally validated in vitro, showing that shifts in both the composition and abundance in consortia can drive the change in the efficiency of catabolic function. This study provides valuable information for designing enhanced bioremediation strategies.
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Affiliation(s)
| | | | | | - Xihui Xu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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56
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Haruta S, Yamamoto K. Model Microbial Consortia as Tools for Understanding Complex Microbial Communities. Curr Genomics 2018; 19:723-733. [PMID: 30532651 PMCID: PMC6225455 DOI: 10.2174/1389202919666180911131206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/19/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023] Open
Abstract
A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.
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Affiliation(s)
- Shin Haruta
- Address correspondence to this author at the Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; Tel: +81-42-677-2580; Fax: +81-42-677-2559; E-mail:
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Wang F, Chen S, Wang Y, Zhang Y, Hu C, Liu B. Long-Term Nitrogen Fertilization Elevates the Activity and Abundance of Nitrifying and Denitrifying Microbial Communities in an Upland Soil: Implications for Nitrogen Loss From Intensive Agricultural Systems. Front Microbiol 2018; 9:2424. [PMID: 30405543 PMCID: PMC6206047 DOI: 10.3389/fmicb.2018.02424] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/21/2018] [Indexed: 12/18/2022] Open
Abstract
The continuous use of nitrogen (N) fertilizers to increase soil fertility and crop productivity often results in unexpected environmental effects and N losses through biological processes, such as nitrification and denitrification. In this study, multidisciplinary approaches were employed to assess the effects of N fertilization in a long-term (~20 years) field experiment in which a fertilizer gradient (0, 200, 400, and 600 kg N ha−1 yr−1) was applied in a winter wheat-summer maize rotation cropping system in the North China Plain, one of the most intensive agricultural regions in China. The potential nitrification/denitrification rates, bacterial community structure, and abundances of functional microbial communities involved in key processes of the N cycle were assessed during both the summer maize (SM) and winter wheat (WW) seasons. Long-term N fertilization resulted in a decrease in soil pH and an increase in soil organic matter (OM), total N and total carbon concentrations. Potential nitrification/denitrification and the abundances of corresponding functional N cycling genes were positively correlated with the fertilization intensity. High-throughput sequencing of the 16S rRNA gene revealed that the increased fertilization intensity caused a significant decrease of bacterial diversity in SM season, while changed the microbial community composition such as increasing the Bacteroidetes abundance and decreasing Acidobacteria abundance in both SM and WW seasons. The alteration of soil properties markedly correlated with the variation in microbial structure, as soil pH and OM were the most predominant factors affecting the microbial structure in the SM and WW seasons, respectively. Furthermore, consistently with the results of functional gene quantification, functional prediction of microbial communities based on 16S rRNA sequence data also revealed that the abundances of the key nitrificaiton/denitrification groups were elevated by long-term N inputs. Taken together, our results suggested that soil microbial community shifted consistently in both SM and WW seasons toward a higher proportion of N-cycle microbes and exhibited higher N turnover activities in response to long-term elevated N fertilizer. These findings provided new insights into the molecular mechanisms responsible for N loss in intensively N fertilized agricultural ecosystems.
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Affiliation(s)
- Fenghua Wang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Shuaimin Chen
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China.,University of Chinese Academy of Sciences Beijing, China
| | - Yuying Wang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Yuming Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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Xu X, Zarecki R, Medina S, Ofaim S, Liu X, Chen C, Hu S, Brom D, Gat D, Porob S, Eizenberg H, Ronen Z, Jiang J, Freilich S. Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions. ISME JOURNAL 2018; 13:494-508. [PMID: 30291327 DOI: 10.1038/s41396-018-0288-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 12/26/2022]
Abstract
Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine-a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances. Genome-scale metabolic models were constructed for Arthrobacter, the atrazine degrader, and four other non-atrazine degrading species whose relative abundance in soil was changed following exposure to the herbicide. By modeling community function we show that consortia including the direct degrader and non-degrader differentially abundant species perform better than Arthrobacter alone. Simulations predict that growth/degradation enhancement is derived by metabolic exchanges between community members. Based on simulations we designed endogenous consortia optimized for enhanced degradation whose performances were validated in vitro and biostimulation strategies that were tested in pot experiments. Overall, our analysis demonstrates that understanding community function in its wider context, beyond the single direct degrader perspective, promotes the design of biostimulation strategies.
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Affiliation(s)
- Xihui Xu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.,Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Raphy Zarecki
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Shlomit Medina
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Shany Ofaim
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel.,Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Xiaowei Liu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Chen
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shunli Hu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dan Brom
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Daniella Gat
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Seema Porob
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Hanan Eizenberg
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Zeev Ronen
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel.
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Schmid CAO, Schröder P, Armbruster M, Schloter M. Organic Amendments in a Long-term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis. MICROBIAL ECOLOGY 2018; 76:226-239. [PMID: 29188301 DOI: 10.1007/s00248-017-1110-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/13/2017] [Indexed: 05/09/2023]
Abstract
This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.
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Affiliation(s)
- Christoph A O Schmid
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Peter Schröder
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | | | - Michael Schloter
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
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Xu XH, Liu XM, Zhang L, Mu Y, Zhu XY, Fang JY, Li SP, Jiang JD. Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community. JOURNAL OF HAZARDOUS MATERIALS 2018; 351:240-249. [PMID: 29550558 DOI: 10.1016/j.jhazmat.2018.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/02/2018] [Accepted: 03/03/2018] [Indexed: 05/24/2023]
Abstract
Although bioaugmentation of pollutant-contaminated sites is a great concern, there are few reports on the relationships among indigenous microbial consortia, exogenous inocula, and pollutants in a bioaugmentation process. In this study, bioaugmentation with Pseudochrobactrum sp. BSQ1 and Massilia sp. BLM18, which can hydrolytically and reductively dehalogenate chlorothalonil (TPN), respectively, was studied for its ability to remove TPN from soil; the alteration of the soil microbial community during the bioaugmentation process was investigated. The results showed that TPN (50 mg/kg) was completely removed in both bioaugmentation treatments within 35 days with half-lives of 6.8 and 9.8 days for strains BSQ1 and BLM18 respectively. In high concentration of TPN-treated soils (100 mg/kg), the bioaugmentation with strains BSQ1 and BLM18 respectively reduced 76.7% and 62.0% of TPN within 35 days. The TPN treatment significantly decreased bacterial richness and diversity and improved the growth of bacteria related to the elimination of chlorinated organic pollutants. However, little influence on soil microbial community was observed for each inoculation treatment (without TPN treatment), showing that TPN treatment is the main force for the shift in indigenous consortia. This study provides insights into the effects of halogenated fungicide application and bioaugmentation on indigenous soil microbiomes.
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Affiliation(s)
- Xi-Hui Xu
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiao-Mei Liu
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China; College of Food Science and Engineering, Inner Mongolia Agricultural University, 010018, Hohhot, China
| | - Long Zhang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yang Mu
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xu-Yuan Zhu
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jing-Ya Fang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shun-Peng Li
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China; Jiangsu Key Lab for Solid Organic Waste Utilization, 210095, Nanjing, China.
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61
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Chaijarasphong T, Savage DF. Sequestered: Design and Construction of Synthetic Organelles. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Thawatchai Chaijarasphong
- Mahidol University; Faculty of Science, Department of Biotechnology; Rama VI Rd. Bangkok 10400 Thailand
| | - David F. Savage
- University of California; Department of Molecular and Cell Biology; 2151 Berkeley Way, Berkeley CA 94720 USA
- University of California; Department of Chemistry; 2151 Berkeley Way, Berkeley CA 94720 USA
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Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms. Appl Microbiol Biotechnol 2018; 102:1639-1650. [PMID: 29362825 DOI: 10.1007/s00253-018-8777-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/07/2018] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
Abstract
Mushrooms are an important food crop for many millions of people worldwide. The most important edible mushroom is the button mushroom (Agaricus bisporus), an excellent example of sustainable food production which is cultivated on a selective compost produced from recycled agricultural waste products. A diverse population of bacteria and fungi are involved throughout the production of Agaricus. A range of successional taxa convert the wheat straw into compost in the thermophilic composting process. These initially break down readily accessible compounds and release ammonia, and then assimilate cellulose and hemicellulose into compost microbial biomass that forms the primary source of nutrition for the Agaricus mycelium. This key process in composting is performed by a microbial consortium consisting of the thermophilic fungus Mycothermus thermophilus (Scytalidium thermophilum) and a range of thermophilic proteobacteria and actinobacteria, many of which have only recently been identified. Certain bacterial taxa have been shown to promote elongation of the Agaricus hyphae, and bacterial activity is required to induce production of the mushroom fruiting bodies during cropping. Attempts to isolate mushroom growth-promoting bacteria for commercial mushroom production have not yet been successful. Compost bacteria and fungi also cause economically important losses in the cropping process, causing a range of destructive diseases of mushroom hyphae and fruiting bodies. Recent advances in our understanding of the key bacteria and fungi in mushroom compost provide the potential to improve productivity of mushroom compost and to reduce the impact of crop disease.
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Dolinšek J, Goldschmidt F, Johnson DR. Synthetic microbial ecology and the dynamic interplay between microbial genotypes. FEMS Microbiol Rev 2018; 40:961-979. [PMID: 28201744 DOI: 10.1093/femsre/fuw024] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/27/2016] [Accepted: 07/04/2016] [Indexed: 01/27/2023] Open
Abstract
Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.
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Affiliation(s)
- Jan Dolinšek
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Felix Goldschmidt
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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64
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Microbial community response and SDS-PAGE reveal possible mechanism of waste activated sludge acidification enhanced by microaeration coupled thermophilic pretreatment. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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65
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Wongwilaiwalin S, Mhuantong W, Champreda V, Tangphatsornruang S, Panichnumsin P, Ratanakhanokchai K, Tachaapaikoon C. Structural and metabolic adaptation of cellulolytic microcosm in co-digested Napier grass-swine manure and its application in enhancing thermophilic biogas production. RSC Adv 2018; 8:29806-29815. [PMID: 35547297 PMCID: PMC9085282 DOI: 10.1039/c8ra05616a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 08/09/2018] [Indexed: 11/21/2022] Open
Abstract
Biogas production from cellulosic wastes has received increasing attention. However, its efficiency is limited by the recalcitrant nature of plant cell wall materials. In this study, an active and structurally stable lignocellulolytic microcosm (PLMC) was isolated from seed culture in sugarcane bagasse compost by successive enrichment on Napier grass supplemented with swine manure, which is a mixture of highly fibrous co-digested waste under septic conditions. Tagged 16S rRNA gene sequencing on an Ion PGM platform revealed the adaptive merging of microorganisms in the co-digested substrates resulting in a stable symbiotic consortium comprising anaerobic cellulolytic clostridia stably co-existing with facultative (hemi)cellulolytic bacteria in the background of native microflora in the substrates. Ethanoligenens, Tepidimicrobium, Clostridium, Coprococcus, and Ruminococcus were the most predominant taxonomic groups comprising 72.82% of the total community. The remarkable enrichment of catabolic genes encoding for endo-cellulases and hemicellulases, both of which are key accessory enzymes in PLMC, was predicted by PICRUSt. PLMC was capable of degrading 43.6% g VS and 36.8% g VSS of the co-digested substrates within 7 days at 55 °C. Inoculation of the microcosm to batch thermophilic anaerobic digestion containing both substrates led to a 36.6% increase in methane yield along with an increase in cellulose removal efficiency. This study demonstrated structural and metabolic adaptation of the cellulolytic microcosms isolated in the background of native microflora from the co-digested wastes and its potent application in the enhancement of anaerobic digestion efficiency. Structurally and functionally stable symbiotic cellulolytic consortium was established for enhancing the methane production from Napier grass co-digested with swine manure.![]()
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Affiliation(s)
- Sarunyou Wongwilaiwalin
- The Joint Graduate School of Energy and Environment
- King Mongkut's University of Technology Thonburi
- Bangkok 10140
- Thailand
- Enzyme Technology Laboratory and BIOTEC-JGSEE Integrative Biorefinery Laboratory
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory and BIOTEC-JGSEE Integrative Biorefinery Laboratory
- National Center for Genetic Engineering and Biotechnology
- Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory and BIOTEC-JGSEE Integrative Biorefinery Laboratory
- National Center for Genetic Engineering and Biotechnology
- Thailand
| | | | - Pornpan Panichnumsin
- Excellent Center of Waste Utilization and Management
- National Center for Genetic Engineering and Biotechnology at King Mongkut's University of Technology Thonburi
- Bangkok 10150
- Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources Technology
- King Mongkut's University of Technology Thonburi
- Bangkok 10150
- Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources Technology
- King Mongkut's University of Technology Thonburi
- Bangkok 10150
- Thailand
- Pilot Plant Development and Training Institute
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66
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Kanokratana P, Wongwilaiwalin S, Mhuantong W, Tangphatsornruang S, Eurwilaichitr L, Champreda V. Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches. J Biosci Bioeng 2017; 125:439-447. [PMID: 29169786 DOI: 10.1016/j.jbiosc.2017.10.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 09/11/2017] [Accepted: 10/25/2017] [Indexed: 11/17/2022]
Abstract
Energy grass is a promising substrate for production of biogas by anaerobic digestion. However, the conversion efficiency is limited by the enzymatically recalcitrant nature of cellulosic wastes. In this study, an active, structurally stable mesophilic lignocellulolytic degrading microbial consortium (Np-LMC) was constructed from forest compost soil microbiota by successive subcultivation on Napier grass under facultative anoxic conditions. According to tagged 16S rRNA gene amplicon sequencing, increasing abundance of facultative Proteobacteria was found in the middle of batch cycle which was then subsequently replaced by the cellulose degraders Firmicutes and Bacteroidetes along with decreasing CMCase, xylanase, and β-glucanase activity profiles in the supernatant after 5 days of incubation. Anaerobic/facultative bacteria Dysgonomonas and Sedimentibacter and aerobic bacteria Comamonas were the major genera found in Np-LMC. The consortium was active on degradation of the native and delignified grass. Direct shotgun sequencing of the consortium metagenome revealed relatively high abundance of genes encoding for various lignocellulose degrading enzymes in 23 glycosyl hydrolase (GH) families compared to previously reported cellulolytic microbial communities in mammalian digestive tracts. Enzymes attacking cellulose and hemicellulose were dominated by GH2, 3, 5, 9, 10, 26, 28 and 43 in addition to a variety of carbohydrate esterases (CE) and auxiliary activities (AA), reflecting adaptation of the enzyme systems to the native herbaceous substrate. The consortium identified here represents the microcosm specifically bred on energy grass, with potential for enhancing degradation of fibrous substrates in bioenergy industry.
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Affiliation(s)
- Pattanop Kanokratana
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand.
| | - Sarunyou Wongwilaiwalin
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- Genomic Research Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Lily Eurwilaichitr
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pahonyothin Road, Klong Luang, Pathum Thani 12120, Thailand
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67
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Deng YJ, Wang SY. Complex carbohydrates reduce the frequency of antagonistic interactions among bacteria degrading cellulose and xylan. FEMS Microbiol Lett 2017; 364:fnx019. [PMID: 28130369 DOI: 10.1093/femsle/fnx019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/24/2017] [Indexed: 11/14/2022] Open
Abstract
Bacterial competition for resources is common in nature but positive interactions among bacteria are also evident. We speculate that the structural complexity of substrate might play a role in mediating bacterial interactions. We tested the hypothesis that the frequency of antagonistic interactions among lignocellulolytic bacteria is reduced when complex polysaccharide is the main carbon source compared to when a simple sugar such as glucose is available. Results using all possible pairwise interactions among 35 bacteria isolated from salt marsh detritus showed that the frequency of antagonistic interactions was significantly lower on carboxymethyl cellulose (CMC)-xylan medium (7.8%) than on glucose medium (15.5%). The two interaction networks were also different in their structures. Although 75 antagonistic interactions occurred on both media, there were 115 that occurred only on glucose and 20 only on CMC-xylan, indicating that some antagonistic interactions were substrate specific. We also found that the frequency of antagonism differed among phylogenetic groups. Gammaproteobacteria and Bacillus sp. were the most antagonistic and they tended to antagonize Bacteroidetes and Actinobacteria, the most susceptible groups. Results from the study suggest that substrate complexity affects how bacteria interact and that bacterial interactions in a community are dynamic as nutrient conditions change.
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68
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Pagaling E, Vassileva K, Mills CG, Bush T, Blythe RA, Schwarz-Linek J, Strathdee F, Allen RJ, Free A. Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states. Environ Microbiol 2017; 19:3374-3386. [PMID: 28677203 DOI: 10.1111/1462-2920.13849] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 12/23/2022]
Abstract
We studied in detail the reproducibility of community development in replicate nutrient-cycling microbial microcosms that were set up identically and allowed to develop under the same environmental conditions. Multiple replicate closed microcosms were constructed using pond sediment and water, enriched with cellulose and sulphate, and allowed to develop over several months under constant environmental conditions, after which their microbial communities were characterized using 16S rRNA gene sequencing. Our results show that initially similar microbial communities can follow alternative - yet stable - trajectories, diverging in time in a system size-dependent manner. The divergence between replicate communities increased in time and decreased with larger system size. In particular, notable differences emerged in the heterotrophic degrader communities in our microcosms; one group of steady state communities was enriched with Firmicutes, while the other was enriched with Bacteroidetes. The communities dominated by these two phyla also contained distinct populations of sulphate-reducing bacteria. This biomodality in community composition appeared to arise during recovery from a low-diversity state that followed initial cellulose degradation and sulphate reduction.
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Affiliation(s)
- Eulyn Pagaling
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Kristin Vassileva
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Catherine G Mills
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Timothy Bush
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Richard A Blythe
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | | | - Fiona Strathdee
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rosalind J Allen
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Andrew Free
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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69
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Analysis of stable 1,2-dichlorobenzene-degrading enrichments and two newly isolated degrading strains, Acidovorax sp. sk40 and Ralstonia sp. sk41. Appl Microbiol Biotechnol 2017; 101:6821-6828. [DOI: 10.1007/s00253-017-8406-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/22/2017] [Accepted: 06/25/2017] [Indexed: 10/19/2022]
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70
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Lusk BG, Colin A, Parameswaran P, Rittmann BE, Torres CI. Simultaneous fermentation of cellulose and current production with an enriched mixed culture of thermophilic bacteria in a microbial electrolysis cell. Microb Biotechnol 2017; 11:63-73. [PMID: 28557303 PMCID: PMC5743814 DOI: 10.1111/1751-7915.12733] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022] Open
Abstract
An enriched mixed culture of thermophilic (60°C) bacteria was assembled for the purpose of using cellulose to produce current in thermophilic microbial electrolysis cells (MECs). Cellulose was fermented into sugars and acids before being consumed by anode‐respiring bacteria (ARB) for current production. Current densities (j) were sustained at 6.5 ± 0.2 A m−2 in duplicate reactors with a coulombic efficiency (CE) of 84 ± 0.3%, a coulombic recovery (CR) of 54 ± 11% and without production of CH4. Low‐scan rate cyclic voltammetry (LSCV) revealed a mid‐point potential (Eka) of −0.17 V versus SHE. Pyrosequencing analysis of the V4 hypervariable region of 16S rDNA and scanning electron microscopy present an enriched thermophilic microbial community consisting mainly of the phylum Firmicutes with the Thermoanaerobacter (46 ± 13%) and Thermincola (28 ± 14%) genera occupying the biofilm anode in high relative abundance and Tepidmicrobium (38 ± 6%) and Moorella (11 ± 8%) genera present in high relative abundance in the bulk medium. The Thermoanaerobacter (15 ± 16%) and Brevibacillus (21 ± 30%) genera were also present in the bulk medium; however, their relative abundance varied by reactor. This study indicates that thermophilic consortia can obtain high CE and CR, while sustaining high current densities from cellulose in MECs.
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Affiliation(s)
- Bradley G Lusk
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ, 85287-5701, USA.,#ScienceTheEarth, Mesa, AZ, 85201, USA
| | - Alexandra Colin
- Ecole Normale Superieure, 45, rue d'Ulm, 75230, Paris Cedex 05, France
| | - Prathap Parameswaran
- Department of Civil Engineering, Kansas State University, 2123 Fiedler Hall, Manhattan, KS, 66502, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ, 85287-5701, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Cesar I Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ, 85287-5701, USA.,School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
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71
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Momeni B, Xie L, Shou W. Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions. eLife 2017; 6. [PMID: 28350295 PMCID: PMC5469619 DOI: 10.7554/elife.25051] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/18/2017] [Indexed: 01/01/2023] Open
Abstract
Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics.
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Affiliation(s)
- Babak Momeni
- Department of Biology, Boston College, Chestnut Hill, United States.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Li Xie
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Wenying Shou
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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72
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Van Wyk N, Navarro D, Blaise M, Berrin JG, Henrissat B, Drancourt M, Kremer L. Characterization of a mycobacterial cellulase and its impact on biofilm- and drug-induced cellulose production. Glycobiology 2017; 27:392-399. [DOI: 10.1093/glycob/cwx014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/01/2017] [Indexed: 12/20/2022] Open
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73
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Hero JS, Pisa JH, Perotti NI, Romero CM, Martínez MA. Endoglucanase and xylanase production by Bacillus sp. AR03 in co-culture. Prep Biochem Biotechnol 2017; 47:589-596. [PMID: 28106512 DOI: 10.1080/10826068.2017.1280826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The behavior of three isolates retrieved from different cellulolytic consortia, Bacillus sp. AR03, Paenibacillus sp. AR247 and Achromobacter sp. AR476-2, were examined individually and as co-cultures in order to evaluate their ability to produce extracellular cellulases and xylanases. Utilizing a peptone-based medium supplemented with carboxymethyl cellulose (CMC), an increase estimation of 1.30 and 1.50 times was obtained by the co-culture containing the strains AR03 and AR247, with respect to enzyme titles registered by their individual cultivation. On the contrary, the extracellular enzymatic production decreased during the co-cultivation of strain AR03 with the non-cellulolytic Achromobacter sp. AR476-2. The synergistic behavior observed through the combined cultivation of the strains AR03 and AR247 might be a consequence of the consumption by Paenibacillus sp. AR247 of the products of the CMC hydrolysis (i.e., cellobiose and/or cello-oligosaccharides), which were mostly generated by the cellulase producer Bacillus sp. AR03. The effect observed could be driven by the requirement to fulfill the nutritional supply from both strains on the substrate evaluated. These results would contribute to a better description of the degradation of the cellulose fraction of the plant cell walls in nature, expected to an efficient utilization of renewable sources.
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Affiliation(s)
- Johan S Hero
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina
| | - José H Pisa
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina
| | - Nora I Perotti
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina.,b Facultad de Ciencias Exactas y Tecnología , Universidad Nacional de Tucumán , Tucumán , Argentina
| | - Cintia M Romero
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina.,c Facultad de Bioquímica, Química y Farmacia , Universidad Nacional de Tucumán , Tucumán , Argentina
| | - María A Martínez
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina.,b Facultad de Ciencias Exactas y Tecnología , Universidad Nacional de Tucumán , Tucumán , Argentina
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74
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Wang Y, Zhao C, Zhang D, Zhao M, Zheng D, Lyu Y, Cheng W, Guo P, Cui Z. Effective degradation of aflatoxin B 1 using a novel thermophilic microbial consortium TADC7. BIORESOURCE TECHNOLOGY 2017; 224:166-173. [PMID: 27866802 DOI: 10.1016/j.biortech.2016.11.033] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
We constructed a novel thermophilic microbial consortium, TADC7, with stable and efficient aflatoxin B1 (AFB1) degradation activity. The microbial consortium degraded more than 95% of the toxin within 72h when cultured with AFB1, and the optimum temperature was 55-60°C. TADC7 tolerated high doses of AFB1, with no inhibitory effects up to 5000μgL-1 AFB1; moreover, the degradation kinetics fit well with the Monod model. The proteins or enzymes in the TADC7 cell-free supernatant played a major role in AFB1 degradation. AFB1 degradation by the cell-free supernatant was stable up to 90°C, with an optimal pH of 8-10. We performed 16S rRNA sequencing to determine TADC7 community structure dynamics; the results indicated that Geobacillus and Tepidimicrobium played major roles in AFB1 degradation.
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Affiliation(s)
- Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; College of Biology and Pharmacy, Three Gorges University, Yichang 443002, China
| | - Chunxia Zhao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; College of Biology and Pharmacy, Three Gorges University, Yichang 443002, China
| | - Dongdong Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Mingming Zhao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Dan Zheng
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yucai Lyu
- College of Biology and Pharmacy, Three Gorges University, Yichang 443002, China
| | - Wei Cheng
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Zongjun Cui
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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75
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Alvarez A, Saez JM, Davila Costa JS, Colin VL, Fuentes MS, Cuozzo SA, Benimeli CS, Polti MA, Amoroso MJ. Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals. CHEMOSPHERE 2017; 166:41-62. [PMID: 27684437 DOI: 10.1016/j.chemosphere.2016.09.070] [Citation(s) in RCA: 269] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 05/03/2023]
Abstract
Actinobacteria exhibit cosmopolitan distribution since their members are widely distributed in aquatic and terrestrial ecosystems. In the environment they play relevant ecological roles including recycling of substances, degradation of complex polymers, and production of bioactive molecules. Biotechnological potential of actinobacteria in the environment was demonstrated by their ability to remove organic and inorganic pollutants. This ability is the reason why actinobacteria have received special attention as candidates for bioremediation, which has gained importance because of the widespread release of contaminants into the environment. Among organic contaminants, pesticides are widely used for pest control, although the negative impact of these chemicals in the environmental balance is increasingly becoming apparent. Similarly, the extensive application of heavy metals in industrial processes lead to highly contaminated areas worldwide. Several studies focused in the use of actinobacteria for cleaning up the environment were performed in the last 15 years. Strategies such as bioaugmentation, biostimulation, cell immobilization, production of biosurfactants, design of defined mixed cultures and the use of plant-microbe systems were developed to enhance the capabilities of actinobacteria in bioremediation. In this review, we compiled and discussed works focused in the study of different bioremediation strategies using actinobacteria and how they contributed to the improvement of the already existing strategies. In addition, we discuss the importance of omic studies to elucidate mechanisms and regulations that bacteria use to cope with pollutant toxicity, since they are still little known in actinobacteria. A brief account of sources and harmful effects of pesticides and heavy metals is also given.
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Affiliation(s)
- Analia Alvarez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, Tucumán 4000, Argentina.
| | - Juliana Maria Saez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - José Sebastian Davila Costa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - Veronica Leticia Colin
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - María Soledad Fuentes
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - Sergio Antonio Cuozzo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, Tucumán 4000, Argentina.
| | - Claudia Susana Benimeli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - Marta Alejandra Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, Tucumán 4000, Argentina.
| | - María Julia Amoroso
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
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76
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Montalvo S, Ojeda F, Huiliñir C, Guerrero L, Borja R, Castillo A. Performance evaluation of micro-aerobic hydrolysis of mixed sludge: Optimum aeration and effect on its biochemical methane potential. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2016; 51:1269-1277. [PMID: 27532802 DOI: 10.1080/10934529.2016.1215195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This study evaluated the performance of a micro-aerobic hydrolysis of mixed sludge and its influence as a pretreatment of this waste for its subsequent anaerobic digestion. Three experimental series were carried out to evaluate the optimum micro-aeration levels in the range from 0.1 to 0.5 air volume/min.reactor volume (vvm) and operation times within the range of 24-60 h. The maximum methane yield [35 mL CH4/g volatile suspended solids (VSS) added] was obtained for an aeration level of 0.35 vvm. This methane yield value increased 114% with respect to that obtained with the non-aerated sludge. In the micro-aeration process carried out at an aeration level of 0.35 vvm, increases in soluble proteins and total sugars concentrations of 185% and 192% with respect to their initial values were found, respectively, after 48 h of aeration. At the above micro-aerobic conditions, soluble chemical oxygen demand (CODS) augmented 150%, whereas VSS content decreased until 40% of their initial respective values. Higher COD increases and VSS decreases were found at 60 h of micro-aeration, but the above parameters did not vary significantly with respect to the values found at 48 h.
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Affiliation(s)
- Silvio Montalvo
- a Department of Chemical Engineering , Universidad de Santiago de Chile , Santiago de Chile , Chile
| | - Felipe Ojeda
- a Department of Chemical Engineering , Universidad de Santiago de Chile , Santiago de Chile , Chile
| | - César Huiliñir
- a Department of Chemical Engineering , Universidad de Santiago de Chile , Santiago de Chile , Chile
| | - Lorna Guerrero
- b Department of Chemical and Environmental Engineering , Universidad Federico Santa María , Valparaíso , Chile
| | - Rafael Borja
- c Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide , Sevilla , Spain
| | - Alejandra Castillo
- a Department of Chemical Engineering , Universidad de Santiago de Chile , Santiago de Chile , Chile
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77
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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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78
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van Wyk N, Drancourt M, Henrissat B, Kremer L. Current perspectives on the families of glycoside hydrolases ofMycobacterium tuberculosis: their importance and prospects for assigning function to unknowns. Glycobiology 2016; 27:112-122. [DOI: 10.1093/glycob/cww099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 08/28/2016] [Accepted: 09/26/2016] [Indexed: 11/14/2022] Open
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79
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Kumar V, Baweja M, Singh PK, Shukla P. Recent Developments in Systems Biology and Metabolic Engineering of Plant-Microbe Interactions. FRONTIERS IN PLANT SCIENCE 2016; 7:1421. [PMID: 27725824 PMCID: PMC5035732 DOI: 10.3389/fpls.2016.01421] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/06/2016] [Indexed: 05/07/2023]
Abstract
Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant-microbe interactions using gene editing and system biology tools toward the comprehension in improvement of plant traits. Further, system biology tools like FBA (flux balance analysis), OptKnock, and constraint-based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g., single nucleotide polymorphism detection, RNA-seq, proteomics) and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.
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Affiliation(s)
| | | | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
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80
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Hua B, Dai J, Liu B, Zhang H, Yuan X, Wang X, Cui Z. Pretreatment of non-sterile, rotted silage maize straw by the microbial community MC1 increases biogas production. BIORESOURCE TECHNOLOGY 2016; 216:699-705. [PMID: 27289062 DOI: 10.1016/j.biortech.2016.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 06/06/2023]
Abstract
Using microbial community MC1 to pretreat lignocellulosic materials increased the yield of biogas production, and the substrate did not need to be sterilized, lowering the cost. Rotted silage maize straw carries many microbes. To determine whether such contamination affects MC1, rotted silage maize straw was pretreated with MC1 prior to biogas production. The decreases in the weights of unsterilized and sterilized rotted silage maize straw were similar, as were their carboxymethyl cellulase activities. After 5d pretreatment, denaturing gradient gel electrophoresis and quantitative polymerase chain reaction results indicated that the proportions of five key strains in MC1 were the same in the unsterilized and sterilized groups; thus, MC1 was resistant to microbial contamination. However, its resistance to contamination decreased as the degradation time increased. Following pretreatment, volatile fatty acids, especially acetic acid, were detected, and MC1 enhanced biogas yields by 74.7% compared with the untreated group.
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Affiliation(s)
- Binbin Hua
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Jiali Dai
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Bin Liu
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Huan Zhang
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Xufeng Yuan
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
| | - Xiaofen Wang
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China.
| | - Zongjun Cui
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
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81
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Yuan X, Ma L, Wen B, Zhou D, Kuang M, Yang W, Cui Z. Enhancing anaerobic digestion of cotton stalk by pretreatment with a microbial consortium (MC1). BIORESOURCE TECHNOLOGY 2016; 207:293-301. [PMID: 26896713 DOI: 10.1016/j.biortech.2016.02.037] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/06/2016] [Accepted: 02/09/2016] [Indexed: 05/25/2023]
Abstract
Microbial pretreatment is beneficial in some anaerobic digestion systems, but the consortia used to date have not been able to effectively increase methane production from cotton stalk. In this study, a thermophilic microbial consortium (MC1) was used for pretreatment in order to enhance biogas and methane production yields. The results indicated that the concentrations of soluble chemical oxygen demand and volatile organic products increased significantly in the early stages of pretreatment. Ethanol, acetic acid, propionic acid, and butyric acid were the predominant volatile organic products in the MC1 hydrolysate. Biogas and methane production yields from cotton stalk were significantly increased following MC1 pretreatment. In addition, the methane production rate from the treated cotton stalk was greater than that from the untreated sample.
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Affiliation(s)
- Xufeng Yuan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lei Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Boting Wen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Dayun Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Meng Kuang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Weihua Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Zongjun Cui
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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82
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Predicting microbial interactions through computational approaches. Methods 2016; 102:12-9. [PMID: 27025964 DOI: 10.1016/j.ymeth.2016.02.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/15/2016] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
Microorganisms play a vital role in various ecosystems and characterizing interactions between them is an essential step towards understanding the organization and function of microbial communities. Computational prediction has recently become a widely used approach to investigate microbial interactions. We provide a thorough review of emerging computational methods organized by the type of data they employ. We highlight three major challenges in inferring interactions using metagenomic survey data and discuss the underlying assumptions and mathematics of interaction inference algorithms. In addition, we review interaction prediction methods relying on metabolic pathways, which are increasingly used to reveal mechanisms of interactions. Furthermore, we also emphasize the importance of mining the scientific literature for microbial interactions - a largely overlooked data source for experimentally validated interactions.
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83
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Poszytek K, Ciezkowska M, Sklodowska A, Drewniak L. Microbial Consortium with High Cellulolytic Activity (MCHCA) for Enhanced Biogas Production. Front Microbiol 2016; 7:324. [PMID: 27014244 PMCID: PMC4791528 DOI: 10.3389/fmicb.2016.00324] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/29/2016] [Indexed: 11/26/2022] Open
Abstract
The use of lignocellulosic biomass as a substrate in agricultural biogas plants is very popular and yields good results. However, the efficiency of anaerobic digestion, and thus biogas production, is not always satisfactory due to the slow or incomplete degradation (hydrolysis) of plant matter. To enhance the solubilization of the lignocellulosic biomass various physical, chemical and biological pretreatment methods are used. The aim of this study was to select and characterize cellulose-degrading bacteria, and to construct a microbial consortium, dedicated for degradation of maize silage and enhancing biogas production from this substrate. Over 100 strains of cellulose-degrading bacteria were isolated from: sewage sludge, hydrolyzer from an agricultural biogas plant, cattle slurry and manure. After physiological characterization of the isolates, 16 strains (representatives of Bacillus, Providencia, and Ochrobactrum genera) were chosen for the construction of a Microbial Consortium with High Cellulolytic Activity, called MCHCA. The selected strains had a high endoglucanase activity (exceeding 0.21 IU/mL CMCase activity) and a wide range of tolerance to various physical and chemical conditions. Lab-scale simulation of biogas production using the selected strains for degradation of maize silage was carried out in a two-bioreactor system, similar to those used in agricultural biogas plants. The obtained results showed that the constructed MCHCA consortium is capable of efficient hydrolysis of maize silage, and increases biogas production by even 38%, depending on the inoculum used for methane fermentation. The results in this work indicate that the mesophilic MCHCA has a great potential for application on industrial scale in agricultural biogas plants.
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Affiliation(s)
- Krzysztof Poszytek
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Martyna Ciezkowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Aleksandra Sklodowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
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84
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Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach. ISME JOURNAL 2016; 10:1656-68. [PMID: 26859770 DOI: 10.1038/ismej.2015.236] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/12/2015] [Accepted: 11/10/2015] [Indexed: 12/28/2022]
Abstract
The intricacies of cooperation and competition between microorganisms are poorly investigated for particular components of the gut microbiota. In order to obtain insights into the manner by which different bifidobacterial species coexist in the mammalian gut, we investigated possible interactions between four human gut commensals, Bifidobacterium bifidum PRL2010, Bifidobacterium adolescentis 22L, Bifidobacterium breve 12L and Bifidobacterium longum subsp. infantis ATCC15697, in the intestine of conventional mice. The generated information revealed various ecological/metabolic strategies, including glycan-harvesting, glycan-breakdown and cross-feeding behavior, adopted by bifidobacteria in the highly competitive environment of the mammalian intestine. Introduction of two or multiple bifidobacterial strains caused a clear shift in the microbiota composition of the murine cecum. Whole-genome transcription profiling coupled with metagenomic analyses of single, dual or multiple associations of bifidobacterial strains revealed an expansion of the murine gut glycobiome toward enzymatic degradation of plant-derived carbohydrates, such as xylan, arabinoxylan, starch and host-derived glycan substrates. Furthermore, these bifidobacterial communities evoked major changes in the metabolomic profile of the microbiota as observed by shifts in short chain fatty acid production and carbohydrate availability in the murine cecum. Overall, these data support an ecological role of bifidobacteria acting directly or through cross-feeding activities in shaping the gut murine microbiome to instigate an enrichment of saccharolytic microbiota.
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85
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Brzoska RM, Bollmann A. The long-term effect of uranium and pH on the community composition of an artificial consortium. FEMS Microbiol Ecol 2015; 92:fiv158. [DOI: 10.1093/femsec/fiv158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2015] [Indexed: 11/12/2022] Open
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86
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Fuentes MS, Colin VL, Amoroso MJ, Benimeli CS. Selection of an actinobacteria mixed culture for chlordane remediation. Pesticide effects on microbial morphology and bioemulsifier production. J Basic Microbiol 2015; 56:127-37. [DOI: 10.1002/jobm.201500514] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022]
Affiliation(s)
- María S. Fuentes
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET); Avenida Belgrano y Pasaje Caseros; Tucumán Argentina
| | - Verónica L. Colin
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET); Avenida Belgrano y Pasaje Caseros; Tucumán Argentina
- Universidad de San Pablo-Tucumán; Argentina
| | - María J. Amoroso
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET); Avenida Belgrano y Pasaje Caseros; Tucumán Argentina
- Universidad del Norte Santo Tomás de Aquino; Tucumán Argentina
- Facultad de Bioquímica; Química y Farmacia; Universidad Nacional de Tucumán; Tucumán Argentina
| | - Claudia S. Benimeli
- Universidad del Norte Santo Tomás de Aquino; Tucumán Argentina
- Unidad de Administración Territorial; Centro Científico Tecnológico; CONICET-Tucumán; Tucumán Argentina
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87
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Hanajima D, Aoyagi T, Hori T. Survival of free-living Acholeplasma in aerated pig manure slurry revealed by (13)C-labeled bacterial biomass probing. Front Microbiol 2015; 6:1206. [PMID: 26583009 PMCID: PMC4628116 DOI: 10.3389/fmicb.2015.01206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/16/2015] [Indexed: 12/02/2022] Open
Abstract
Many studies have been performed on microbial community succession and/or predominant taxa during the composting process; however, the ecophysiological roles of microorganisms are not well understood because microbial community structures are highly diverse and dynamic. Bacteria are the most important contributors to the organic-waste decomposition process, while decayed bacterial cells can serve as readily digested substrates for other microbial populations. In this study, we investigated the active bacterial species responsible for the assimilation of dead bacterial cells and their components in aerated pig manure slurry by using 13C-labeled bacterial biomass probing. After 3 days of forced aeration, 13C-labeled and unlabeled dead Escherichia coli cell suspensions were added to the slurry. The suspensions contained 13C-labeled and unlabeled bacterial cell components, possibly including the cell wall and membrane, as well as intracellular materials. RNA extracted from each slurry sample 2 h after addition of E. coli suspension was density-resolved by isopycnic centrifugation and analyzed by terminal restriction fragment length polymorphism, followed by cloning and sequencing of bacterial 16S rRNA genes. In the heavy isotopically labeled RNA fraction, the predominant 13C-assimilating population was identified as belonging to the genus Acholeplasma, which was not detected in control heavy RNA. Acholeplasma spp. have limited biosynthetic capabilities and possess a wide variety of transporters, resulting in their metabolic dependence on external carbon and energy sources. The prevalence of Acholeplasma spp. was further confirmed in aerated pig manure slurry from four different pig farms by pyrosequencing of 16S rRNA genes; their relative abundance was ∼4.4%. Free-living Acholeplasma spp. had a competitive advantage for utilizing dead bacterial cells and their components more rapidly relative to other microbial populations, thus allowing the survival and prevalence of Acholeplasma spp. in pig manure slurry.
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Affiliation(s)
- Dai Hanajima
- Dairy Research Division, Hokkaido Agricultural Research Center, National Agricultural and Food Research Organization Sapporo, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
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88
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Aziz FAA, Suzuki K, Ohtaki A, Sagegami K, Hirai H, Seno J, Mizuno N, Inuzuka Y, Saito Y, Tashiro Y, Hiraishi A, Futamata H. Interspecies interactions are an integral determinant of microbial community dynamics. Front Microbiol 2015; 6:1148. [PMID: 26539177 PMCID: PMC4611161 DOI: 10.3389/fmicb.2015.01148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/05/2015] [Indexed: 11/26/2022] Open
Abstract
This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem.
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Affiliation(s)
- Fatma A A Aziz
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia Serdang, Malaysia ; Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Kenshi Suzuki
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Akihiro Ohtaki
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Keita Sagegami
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Hidetaka Hirai
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Jun Seno
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Naoko Mizuno
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Yuma Inuzuka
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Yasuhisa Saito
- Department of Mathematics, Shimane University Matsue, Japan
| | - Yosuke Tashiro
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
| | - Akira Hiraishi
- Department of Environmental and Life Sciences, Toyohashi University of Technology Toyohashi, Japan
| | - Hiroyuki Futamata
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Hamamatsu, Japan
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89
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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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90
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Ponomarova O, Patil KR. Metabolic interactions in microbial communities: untangling the Gordian knot. Curr Opin Microbiol 2015. [DOI: 10.1016/j.mib.2015.06.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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91
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Abstract
In this work, we present a novel approach for performing (13)C metabolic flux analysis ((13)C-MFA) of co-culture systems. We demonstrate for the first time that it is possible to determine metabolic flux distributions in multiple species simultaneously without the need for physical separation of cells or proteins, or overexpression of species-specific products. Instead, metabolic fluxes for each species in a co-culture are estimated directly from isotopic labeling of total biomass obtained using conventional mass spectrometry approaches such as GC-MS. In addition to determining metabolic fluxes, this approach estimates the relative population size of each species in a mixed culture and inter-species metabolite exchange. As such, it enables detailed studies of microbial communities including species dynamics and interactions between community members. The methodology is experimentally validated here using a co-culture of two E. coli knockout strains. Taken together, this work greatly extends the scope of (13)C-MFA to a large number of multi-cellular systems that are of significant importance in biotechnology and medicine.
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Affiliation(s)
- Nikodimos A Gebreselassie
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA.
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92
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Escalante AE, Rebolleda-Gómez M, Benítez M, Travisano M. Ecological perspectives on synthetic biology: insights from microbial population biology. Front Microbiol 2015; 6:143. [PMID: 25767468 PMCID: PMC4341553 DOI: 10.3389/fmicb.2015.00143] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/07/2015] [Indexed: 11/13/2022] Open
Abstract
The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems.
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Affiliation(s)
- Ana E. Escalante
- Department of Ecology, Evolution and Behavior, University of MinnesotaSt. Paul, MN, USA
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Departamento de Ecología de la Biodiversidad Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | - María Rebolleda-Gómez
- Department of Ecology, Evolution and Behavior, University of MinnesotaSt. Paul, MN, USA
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Departamento de Ecología de la Biodiversidad Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of MinnesotaSt. Paul, MN, USA
- BioTechnology Institute, University of MinnesotaSt. Paul, MN, USA
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Du R, Yan J, Li S, Zhang L, Zhang S, Li J, Zhao G, Qi P. Cellulosic ethanol production by natural bacterial consortia is enhanced by Pseudoxanthomonas taiwanensis. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:10. [PMID: 25648981 PMCID: PMC4308921 DOI: 10.1186/s13068-014-0186-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/15/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND Natural bacterial consortia are considered a promising solution for one-step production of ethanol from lignocellulose because of their adaptation to a wide range of natural lignocellulosic substrates and their capacity for efficient cellulose degradation. However, their low ethanol conversion efficiency has greatly limited the development and application of natural bacterial consortia. RESULTS In the present study, we analyzed 16 different natural bacterial consortia from a variety of habitats in China and found that the HP consortium exhibited relatively high ethanol production (2.06 g/L ethanol titer from 7 g/L α-cellulose at 55°C in 6 days). Further studies showed that Pseudoxanthomonas taiwanensis played an important role in the high ethanol productivity of HP and that this strain effectively boosted the ethanol production of various other natural bacterial consortia. Finally, we developed a new consortium, termed HPP, by optimizing the proportion of P. taiwanensis in the HP consortium to achieve the highest ethanol production reported for natural consortia. The ethanol conversion ratio reached 78%, with ethanol titers up to 2.5 g/L. CONCLUSIONS In the present study, we found a natural bacterial consortium with outstanding ethanol production performance, and revealed an efficient method with potentially broad applicability for further improving the ethanol production of natural bacterial consortia.
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Affiliation(s)
- Ran Du
- />Institute of New Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Jianbin Yan
- />The Tsinghua University-Peking University Center for Life Sciences, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- />Institute of New Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Lei Zhang
- />Institute of New Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Sandra Zhang
- />Institute of New Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Jihong Li
- />Institute of New Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Gang Zhao
- />Institute of New Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Panlu Qi
- />Research Institute of Petroleum Processing, Beijing, 100000 China
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94
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Goers L, Freemont P, Polizzi KM. Co-culture systems and technologies: taking synthetic biology to the next level. J R Soc Interface 2014; 11:rsif.2014.0065. [PMID: 24829281 DOI: 10.1098/rsif.2014.0065] [Citation(s) in RCA: 350] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions.
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Affiliation(s)
- Lisa Goers
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Paul Freemont
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Karen M Polizzi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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95
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Microbial community structure and disposal issues of table olive wastewaters generated from the fermentation of the olive cultivar ‘Kalamon’. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-013-0791-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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96
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Kato S, Yoshida R, Yamaguchi T, Sato T, Yumoto I, Kamagata Y. The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium. Front Microbiol 2014; 5:575. [PMID: 25400628 PMCID: PMC4214200 DOI: 10.3389/fmicb.2014.00575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/13/2014] [Indexed: 11/13/2022] Open
Abstract
Investigation of microbial interspecies interactions is essential for elucidating the function and stability of microbial ecosystems. However, community-based analyses including molecular-fingerprinting methods have limitations for precise understanding of interspecies interactions. Construction of model microbial consortia consisting of defined mixed cultures of isolated microorganisms is an excellent method for research on interspecies interactions. In this study, a model microbial consortium consisting of microorganisms that convert acetate into methane directly (Methanosaeta thermophila) and syntrophically (Thermacetogenium phaeum and Methanothermobacter thermautotrophicus) was constructed and the effects of elevated CO2 concentrations on intermicrobial competition were investigated. Analyses on the community dynamics by quantitative RT-PCR and fluorescent in situ hybridization targeting their 16S rRNAs revealed that high concentrations of CO2 have suppressive effects on the syntrophic microorganisms, but not on the aceticlastic methanogen. The pathways were further characterized by determining the Gibbs free energy changes (ΔG) of the metabolic reactions conducted by each microorganism under different CO2 concentrations. The ΔG value of the acetate oxidation reaction (T. phaeum) under high CO2 conditions became significantly higher than -20 kJ per mol of acetate, which is the borderline level for sustaining microbial growth. These results suggest that high concentrations of CO2 undermine energy acquisition of T. phaeum, resulting in dominance of the aceticlastic methanogen. This study demonstrates that investigation on model microbial consortia is useful for untangling microbial interspecies interactions, including competition among microorganisms occupying the same trophic niche in complex microbial ecosystems.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
- Research Center for Advanced Science and Technology, The University of TokyoTokyo, Japan
| | - Rina Yoshida
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Tomoyuki Sato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
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97
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Dynamic changes in the composite microbial system MC1 during and following its rapid degradation of lignocellulose. Appl Biochem Biotechnol 2014; 172:951-62. [PMID: 24122707 DOI: 10.1007/s12010-013-0566-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/29/2013] [Indexed: 10/26/2022]
Abstract
To monitor the dynamics of the composite microbial system MC1 during its degradation of lignocellulose and to improve our understanding of the microbial communities involved in this biomass conversion, MC1 was characterized at eight time points over an 18-day, thermophilic, aerobic, static cultivation. We found the microbial communities to be dynamic, rhythmic consortia capable of changing in response to lignocellulose degradation. The growth curve over 18 days was M-shaped. Based on the quantitative changes in five major components of MC1 (Clostridium straminisolvens CSK-1, Clostridium sp. FG4, Pseudoxanthomonas sp. M1-3, Brevibacillus sp. M1-5, and Bordetella sp. M1-6), reduction in rice straw weight, cellulase (CMCase) activity, xylanase activity, and changes in medium pH, we found that the process comprised two identifiable phases. Rapid degradation occurred from day 0 to day 9, while the post-rapid degradation phase included days 10 to 18. Day 3 and day 12 were two key time points in the rapid degradation phase and post-rapid degradation phase, respectively. Two anaerobes, C. straminisolvens CSK-1 and Clostridium sp. FG4, dominated the MC1 system from day 0 to day 18.
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98
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Mori T, Kamei I, Hirai H, Kondo R. Identification of novel glycosyl hydrolases with cellulolytic activity against crystalline cellulose from metagenomic libraries constructed from bacterial enrichment cultures. SPRINGERPLUS 2014; 3:365. [PMID: 25077068 PMCID: PMC4112031 DOI: 10.1186/2193-1801-3-365] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/08/2014] [Indexed: 11/11/2022]
Abstract
To obtain cellulases that are capable of degrading crystalline cellulose and cedar wood, metagenomic libraries were constructed from raw soil sample which was covered to pile of cedar wood sawdust or from its enrichment cultures. The efficiency of screening of metagenomic library was improved more than 3 times by repeating enrichment cultivation using crystalline cellulose as a carbon source, compared with the library constructed from raw soil. Four cellulase genes were obtained from the metagenomic libraries that were constructed from the total genome extracted from an enrichment culture that used crystalline cellulose as a carbon source. A cellulase gene and a xylanase gene were obtained from the enrichment culture that used unbleached kraft pulp as a carbon source. The culture supernatants of Escherichia coli expressing three clones that were derived from the enrichment culture that used crystalline cellulose showed activity against crystalline cellulose. In addition, these three enzyme solutions generated a reducing sugar from cedar wood powder. From these results, the construction of a metagenomic library from cultures that were repetition enriched using crystalline cellulose demonstrated that this technique is a powerful tool for obtaining cellulases that have activity toward crystalline cellulose.
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Affiliation(s)
- Toshio Mori
- />Department of Agro-environmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Ichiro Kamei
- />Department of Forest and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192 Japan
| | - Hirofumi Hirai
- />Department of Applied Biological Chemistry, Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529 Japan
| | - Ryuichiro Kondo
- />Department of Agro-environmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
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99
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Zhou Y, Pope PB, Li S, Wen B, Tan F, Cheng S, Chen J, Yang J, Liu F, Lei X, Su Q, Zhou C, Zhao J, Dong X, Jin T, Zhou X, Yang S, Zhang G, Yang H, Wang J, Yang R, Eijsink VGH, Wang J. Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community. Sci Rep 2014; 4:5288. [PMID: 24924356 PMCID: PMC5381534 DOI: 10.1038/srep05288] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/23/2014] [Indexed: 01/10/2023] Open
Abstract
Reaching a comprehensive understanding of how nature solves the problem of degrading recalcitrant biomass may eventually allow development of more efficient biorefining processes. Here we interpret genomic and proteomic information generated from a cellulolytic microbial consortium (termed F1RT) enriched from soil. Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes. Support for cellulolytic inter-species cooperation came from the discovery of F1RT microbes that encode and express complimentary enzymatic inventories that include both extracellular cellulosomes and secreted free-enzyme systems. Metabolic reconstruction of the seven F1RT phylotypes predicted a wider genomic rationale as to how this particular community functions as well as possible reasons as to why biomass conversion in nature relies on a structured and cooperative microbial community.
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Affiliation(s)
- Yizhuang Zhou
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA [3]
| | - Phillip B Pope
- 1] Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432 NORWAY [2]
| | - Shaochun Li
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Bo Wen
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Fengji Tan
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Shu Cheng
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Jing Chen
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Jinlong Yang
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Feng Liu
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Xuejing Lei
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Qingqing Su
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Chengran Zhou
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Jiao Zhao
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, The Institute of Microbiology, Chinese Academy of Sciences. Beijing 100101, CHINA
| | - Tao Jin
- BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Xin Zhou
- BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Shuang Yang
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | | | - Huangming Yang
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Jian Wang
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA
| | - Ruifu Yang
- 1] Shenzhen Key laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, CHINA [2] BGI-Shenzhen, Shenzhen 518083, CHINA [3] State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, CHINA
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432 NORWAY
| | - Jun Wang
- 1] BGI-Shenzhen, Shenzhen 518083, CHINA [2] Department of Biology, University of Copenhagen, Copenhagen, DENMARK [3] King Abdulaziz University, Jeddah, SAUDI ARABIA [4] Macau University of Science and Technology, Macau, CHINA
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100
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Maki M, Iskhakova S, Zhang T, Qin W. Bacterial consortia constructed for the decomposition of Agave biomass. Bioengineered 2014; 5:165-72. [PMID: 24637707 DOI: 10.4161/bioe.28431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Research has shown that a greater variety of enzymes, as well as variety of microorganisms producing enzymes, can have an overall synergistic effect on the decomposition of lignocellulosic biomass for the production of value-added bio-products. Here, 8 cellulase-degrading bacterial isolates were selected to develop co-, tri-, and tetra-cultures for the decomposition of lignocellulosic biomass. Glucose and xylose equivalents released from imitation biomass media containing 0.5% (w/v) beechwood xylan and 0.5% (w/v) Avicel was measured using di-nitrosalicylic acid for all consortia, along with cell growth and survival. Thereafter, 6 co- and 2 tri-cultures with greatest decomposition were examined for ability to degrade Agave americana fiber. Interestingly, when strains were paired up in co-culture, four pairs: G+5, G+A, C+A1, and G+A1 produced high reducing sugars in 24 h: 6 µM, 8 µM, 8 µM, and finally, 6 µM, respectively. From 4 co-cultures with highest reducing sugar equivalents, tri- and tetra-cultures were produced. The bacterial consortia which had the highest reducing sugars detected were 2 tri-cultures: G + A1 + A4 and G + A1 + 5, displaying levels as high as 9 µM and 5 µM in day 1, respectively. All co- and tri-cultures maintained high cell survival for 14 days with 0.5 g ground Agave. Upon evaluating Agave dry weight after treatment, it was evident that almost half the biomass could be decomposed in 14 days. Scanning electron microscopy of treated Agave supported decomposition when compared with the control. These bacterial consortia have potential for further study of value-added by-product production during metabolism of lignocellulosic biomasses.
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Affiliation(s)
- Miranda Maki
- Department of Biology; Lakehead University; Thunder Bay, ON Canada
| | | | - Tingzhou Zhang
- Department of Environmental Engineering; Zhejiang Gongshang University; Hangzhou, China
| | - Wensheng Qin
- Department of Biology; Lakehead University; Thunder Bay, ON Canada
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