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Zhang X, Miao Q, Tang B, Mijakovic I, Ji XJ, Qu L, Wei Y. Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:182. [PMID: 38012750 PMCID: PMC10683242 DOI: 10.1186/s13068-023-02435-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 ℃ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 ℃. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.
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Affiliation(s)
- Xiaoling Zhang
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Qin Miao
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Bingling Tang
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 41296, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Lingbo Qu
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China.
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2
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Liu H, Jiang S, Ou J, Tang J, Lu Y, Wei Y. Investigation of soil microbiota reveals variable dominant species at different land areas in China. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2071634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Hai Liu
- Criminal technology corps of Henan Provincial Public Security Bureau, Zhengzhou, Henan Province, China
| | - Shan Jiang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, PR China
| | - Jintao Ou
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Jinfeng Tang
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Key Laboratory for Water Quality and Conservation of Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Linköping University – Guangzhou University Research Center on Urban Sustainable Development, Guangzhou, People’s Republic of China
| | - Yang Lu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Yongjun Wei
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
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3
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Characterization of Novel Pectinolytic Enzymes Derived from the Efficient Lignocellulose Degradation Microbiota. Biomolecules 2022; 12:biom12101388. [PMID: 36291597 PMCID: PMC9599418 DOI: 10.3390/biom12101388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 01/20/2023] Open
Abstract
Diverse pectinolytic enzymes are widely applied in the food, papermaking, and other industries, and they account for more than 25% of the global industrial enzyme demands. Efficient lignocellulose degradation microbiota are reservoirs of pectinolytic enzymes and other lignocellulose-degrading genes. Metagenomics has been widely used to discover new pectinolytic enzymes. Here, we used a metagenomic strategy to characterize pectinolytic genes from one efficient lignocellulose-degrading microbiota derived from pulp and paper wastewater treatment microbiota. A total of 23 predicted full-length GH28 and PL1 family pectinolytic genes were selectively cloned and expressed in Escherichia coli, and 5 of the expressed proteins had pectinolytic activities. Among them, the characterization of one pectinolytic enzyme, PW-pGH28-3, which has a 58.4% identity with an exo-polygalacturonase gene of Aquipluma nitroreducens, was further investigated. The optimal pH and optimal temperature of PW-pGH28-3 were 8.0 and 40 °C, respectively, and its pectinolytic activity at the optimal condition was 13.5 ± 1.1 U/mg protein. Bioinformatics analyses and structural modeling suggest that PW-pGH28-3 is a novel secretory exo-polygalacturonase, which is confirmed by its hydrolysates of polygalacturonic acid. The detection of PW-pGH28-3 and other pectinolytic genes showed that efficient lignocellulose degradation microbiota could provide potential efficient pectinolytic enzymes for industrial application. In the future, improving metagenomic screening efficiency would discover efficient lignocellulose-degrading enzymes and lead to the sustainable and green utilization of lignocellulose.
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Mai W, Chen J, Liu H, Liang J, Tang J, Wei Y. Advances in Studies on Microbiota Involved in Nitrogen Removal Processes and Their Applications in Wastewater Treatment. Front Microbiol 2021; 12:746293. [PMID: 34733260 PMCID: PMC8560000 DOI: 10.3389/fmicb.2021.746293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
The discharge of excess nitrogenous pollutants in rivers or other water bodies often leads to serious ecological problems and results in the collapse of aquatic ecosystems. Nitrogenous pollutants are often derived from the inefficient treatment of industrial wastewater. The biological treatment of industrial wastewater for the removal of nitrogen pollution is a green and efficient strategy. In the initial stage of the nitrogen removal process, the nitrogenous pollutants are converted to ammonia. Traditionally, nitrification and denitrification processes have been used for nitrogen removal in industrial wastewater; while currently, more efficient processes, such as simultaneous nitrification-denitrification, partial nitrification-anammox, and partial denitrification-anammox processes, are used. The microorganisms participating in nitrogen pollutant removal processes are diverse, but information about them is limited. In this review, we summarize the microbiota participating in nitrogen removal processes, their pathways, and associated functional genes. We have also discussed the design of efficient industrial wastewater treatment processes for the removal of nitrogenous pollutants and the application of microbiome engineering technology and synthetic biology strategies in the modulation of the nitrogen removal process. This review thus provides insights that would help in improving the efficiency of nitrogen pollutant removal from industrial wastewater.
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Affiliation(s)
- Wenning Mai
- School of Ecology and Environment, Zhengzhou University, Zhengzhou, China.,College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jiamin Chen
- School of Ecology and Environment, Zhengzhou University, Zhengzhou, China.,Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
| | - Hai Liu
- Henan Public Security Bureau, Zhengzhou, China
| | - Jiawei Liang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jinfeng Tang
- Key Laboratory for Water Quality and Conservation of Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Linköping University - Guangzhou University Research Center on Urban Sustainable Development, Guangzhou University, Guangzhou, China
| | - Yongjun Wei
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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5
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Wang J, Liang J, Li Y, Tian L, Wei Y. Characterization of efficient xylanases from industrial-scale pulp and paper wastewater treatment microbiota. AMB Express 2021; 11:19. [PMID: 33464408 PMCID: PMC7815853 DOI: 10.1186/s13568-020-01178-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 02/08/2023] Open
Abstract
Xylanases are widely used enzymes in the food, textile, and paper industries. Most efficient xylanases have been identified from lignocellulose-degrading microbiota, such as the microbiota of the cow rumen and the termite hindgut. Xylanase genes from efficient pulp and paper wastewater treatment (PPWT) microbiota have been previously recovered by metagenomics, assigning most of the xylanase genes to the GH10 family. In this study, a total of 40 GH10 family xylanase genes derived from a certain PPWT microbiota were cloned and expressed in Escherichia coli BL21 (DE3). Among these xylanase genes, 14 showed xylanase activity on beechwood substrate. Two of these, PW-xyl9 and PW-xyl37, showed high activities, and were purified to evaluate their xylanase properties. Values of optimal pH and temperature for PW-xyl9 were pH 7 and 60 ℃, respectively, while those for PW-xyl37 were pH 7 and 55 ℃, respectively; their specific xylanase activities under optimal conditions were 470.1 U/mg protein and 113.7 U/mg protein, respectively. Furthermore, the Km values of PW-xyl9 and PW-xyl37 were determined as 8.02 and 18.8 g/L, respectively. The characterization of these two xylanases paves the way for potential application in future pulp and paper production and other industries, indicating that PPWT microbiota has been an undiscovered reservoir of efficient lignocellulase genes. This study demonstrates that a metagenomic approach has the potential to screen efficient xylanases of uncultured microorganisms from lignocellulose-degrading microbiota. In a similar way, other efficient lignocellulase genes might be identified from PPWT treatment microbiota in the future.
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Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil. mBio 2021; 12:mBio.03099-20. [PMID: 33402535 PMCID: PMC8545098 DOI: 10.1128/mbio.03099-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.
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Dadwal A, Sharma S, Satyanarayana T. Progress in Ameliorating Beneficial Characteristics of Microbial Cellulases by Genetic Engineering Approaches for Cellulose Saccharification. Front Microbiol 2020; 11:1387. [PMID: 32670240 PMCID: PMC7327088 DOI: 10.3389/fmicb.2020.01387] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/29/2020] [Indexed: 12/15/2022] Open
Abstract
Lignocellulosic biomass is a renewable and sustainable energy source. Cellulases are the enzymes that cleave β-1, 4-glycosidic linkages in cellulose to liberate sugars that can be fermented to ethanol, butanol, and other products. Low enzyme activity and yield, and thermostability are, however, some of the limitations posing hurdles in saccharification of lignocellulosic residues. Recent advancements in synthetic and systems biology have generated immense interest in metabolic and genetic engineering that has led to the development of sustainable technology for saccharification of lignocellulosics in the last couple of decades. There have been several attempts in applying genetic engineering in the production of a repertoire of cellulases at a low cost with a high biomass saccharification. A diverse range of cellulases are produced by different microbes, some of which are being engineered to evolve robust cellulases. This review summarizes various successful genetic engineering strategies employed for improving cellulase kinetics and cellulolytic efficiency.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
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8
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Becker D, Popp D, Harms H, Centler F. A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion. Microorganisms 2020; 8:microorganisms8050669. [PMID: 32380653 PMCID: PMC7284732 DOI: 10.3390/microorganisms8050669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 11/21/2022] Open
Abstract
Metagenomics analysis revealing the composition and functional repertoire of complex microbial communities typically relies on large amounts of sequence data. Numerous analysis strategies and computational tools are available for their analysis. Fully integrated automated analysis pipelines such as MG-RAST or MEGAN6 are user-friendly but not designed for integrating specific knowledge on the biological system under study. In order to facilitate the consideration of such knowledge, we introduce a modular, adaptable analysis pipeline combining existing tools. We applied the novel pipeline to simulated mock data sets focusing on anaerobic digestion microbiomes and compare results to those obtained with established automated analysis pipelines. We find that the analysis strategy and choice of tools and parameters have a strong effect on the inferred taxonomic community composition, but not on the inferred functional profile. By including prior knowledge, computational costs can be decreased while improving result accuracy. While automated off-the-shelf analysis pipelines are easy to apply and require no knowledge on the microbial system under study, custom-made pipelines require more preparation time and bioinformatics expertise. This extra effort is minimized by our modular, flexible, custom-made pipeline, which can be adapted to different scenarios and can take available knowledge on the microbial system under study into account.
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Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source. Microorganisms 2018; 6:microorganisms6030080. [PMID: 30081593 PMCID: PMC6163493 DOI: 10.3390/microorganisms6030080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/31/2022] Open
Abstract
This study investigated whether biogas reactor performance, including microbial community development, in response to a change in substrate composition is influenced by initial inoculum source. For the study, reactors previously operated with the same grass–manure mixture for more than 120 days and started with two different inocula were used. These reactors initially showed great differences depending on inoculum source, but eventually showed similar performance and overall microbial community structure. At the start of the present experiment, the substrate was complemented with milled feed wheat, added all at once or divided into two portions. The starting hypothesis was that process performance depends on initial inoculum source and microbial diversity, and thus that reactor performance is influenced by the feeding regime. In response to the substrate change, all reactors showed increases and decreases in volumetric and specific methane production, respectively. However, specific methane yield and development of the microbial community showed differences related to the initial inoculum source, confirming the hypothesis. However, the different feeding regimes had only minor effects on process performance and overall community structure, but still induced differences in the cellulose-degrading community and in cellulose degradation.
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Liu T, Sun L, Müller B, Schnürer A. Importance of inoculum source and initial community structure for biogas production from agricultural substrates. BIORESOURCE TECHNOLOGY 2017; 245:768-777. [PMID: 28926908 DOI: 10.1016/j.biortech.2017.08.213] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
This study evaluated the importance of inoculum source for start-up and operation of biogas processes. Three different inocula with different community structure were used to initiate six laboratory continuous stirred tank reactor (CSTR) processes operated with a grass manure mixture as substrate. The processes were evaluated by chemical and microbiological analysis, by targeting the overall bacterial community and potential cellulose-degrading bacteria. As expected, the results showed a large difference in community structure in the inocula and in process performance during the first hydraulic retention time (HRT). However, the performance and overall microbial community structure became similar in the reactors over time. An inoculum from a high-ammonia process, characterized by low diversity and low degradation efficiency, took the longest time to reach stability and final methane yield. The overall bacterial community was mainly shaped by the operating conditions but, interestingly, potential cellulose-degrading bacteria seemed mainly to originate from the substrate.
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Affiliation(s)
- Tong Liu
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-75007 Uppsala, Sweden
| | - Li Sun
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-75007 Uppsala, Sweden
| | - Bettina Müller
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-75007 Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-75007 Uppsala, Sweden.
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Cho K, Shin SG, Kim W, Lee J, Lee C, Hwang S. Microbial community shifts in a farm-scale anaerobic digester treating swine waste: Correlations between bacteria communities associated with hydrogenotrophic methanogens and environmental conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 601-602:167-176. [PMID: 28551535 DOI: 10.1016/j.scitotenv.2017.05.188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/19/2017] [Accepted: 05/20/2017] [Indexed: 06/07/2023]
Abstract
Microbial community structure in a farm-scale anaerobic digester treating swine manure was investigated during three process events: 1) prolonged starvation, and changes of 2) operating temperature (between meso- and thermophilic) and 3) hydraulic retention time (HRT). Except during the initial period, the digester was dominated by hydrogenotrophic methanogens (HMs). The bacterial community structure significantly shifted with operating temperature and HRT but not with long-term starvation. Clostridiales (26.5-54.4%) and Bacteroidales (2.5-13.7%) became dominant orders in the digester during the period of HM dominance. Abundance of diverse meso- and thermophilic bacteria increased during the same period; many of these species may be H2 producers, and/or syntrophic acetate oxidizers. Some of these species showed positive correlations with [NH4+-N] (p<0.1); this relationship suggests that ammonia was a significant parameter for bacterial selection. The bacterial niche information reported in this study can be useful to understand the ecophysiology of anaerobic digesters treating swine manure that contains high ammonia content.
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Affiliation(s)
- Kyungjin Cho
- Center for Water Resource Cycle Research, Korea Institute of Science and Technology, 39-1 Hawolgok-Dong, Seongbuk-Gu, Seoul 136-791, Republic of Korea
| | - Seung Gu Shin
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea.
| | - Woong Kim
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Joonyeob Lee
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Seokhwan Hwang
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea.
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12
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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13
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Bozan M, Akyol Ç, Ince O, Aydin S, Ince B. Application of next-generation sequencing methods for microbial monitoring of anaerobic digestion of lignocellulosic biomass. Appl Microbiol Biotechnol 2017; 101:6849-6864. [PMID: 28779289 DOI: 10.1007/s00253-017-8438-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
The anaerobic digestion of lignocellulosic wastes is considered an efficient method for managing the world's energy shortages and resolving contemporary environmental problems. However, the recalcitrance of lignocellulosic biomass represents a barrier to maximizing biogas production. The purpose of this review is to examine the extent to which sequencing methods can be employed to monitor such biofuel conversion processes. From a microbial perspective, we present a detailed insight into anaerobic digesters that utilize lignocellulosic biomass and discuss some benefits and disadvantages associated with the microbial sequencing techniques that are typically applied. We further evaluate the extent to which a hybrid approach incorporating a variation of existing methods can be utilized to develop a more in-depth understanding of microbial communities. It is hoped that this deeper knowledge will enhance the reliability and extent of research findings with the end objective of improving the stability of anaerobic digesters that manage lignocellulosic biomass.
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Affiliation(s)
- Mahir Bozan
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
| | - Çağrı Akyol
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
| | - Orhan Ince
- Department of Environmental Engineering, Istanbul Technical University, Maslak, 34469, Istanbul, Turkey
| | - Sevcan Aydin
- Department of Genetics and Bioengineering, Nişantaşı University, Maslak, 34469, Istanbul, Turkey.
| | - Bahar Ince
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
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14
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da Silva RR, Pedezzi R, Souto TB. Exploring the bioprospecting and biotechnological potential of white-rot and anaerobic Neocallimastigomycota fungi: peptidases, esterases, and lignocellulolytic enzymes. Appl Microbiol Biotechnol 2017; 101:3089-3101. [PMID: 28314873 DOI: 10.1007/s00253-017-8225-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 02/26/2017] [Accepted: 03/04/2017] [Indexed: 11/28/2022]
Abstract
Fungi constitute an invaluable natural resource for scientific research, owing to their diversity; they offer a promising alternative for bioprospecting, thus contributing to biotechnological advances. For a long time, extensive information has been exploited and fungal products have been tested as a source of natural compounds. In this context, enzyme production remains a field of interest, since it offers an efficient alternative to the hazardous processes of chemical transformations. Owing to their vast biodiversity and peculiar biochemical characteristics, two fungal categories, white-rot and anaerobic Neocallimastigomycota, have gathered considerable attention for biotechnological applications. These fungi are known for their ability to depolymerize complex molecular structures and are used in degradation of lignocellulosic biomass, improvement of animal feed digestibility, biogas and bioethanol production, and various other applications. However, there are only limited reports that describe proteolytic enzymes and esterases in these fungi and their synergistic action with lignocellulolytic enzymes on degradation of complex polymers. Thus, in this minireview, we focus on the importance of these organisms in enzyme technology, their bioprospecting, possibility of integration of their enzyme repertoire, and their prospects for future biotechnological innovation.
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Affiliation(s)
- Ronivaldo Rodrigues da Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n Campus Universitário da USP, Ribeirão Preto, São Paulo, 14040-903, Brazil.
| | - Rafael Pedezzi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n Campus Universitário da USP, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Tatiane Beltramini Souto
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo (IFES), Nova Venécia, ES, Brazil
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15
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Wilkens C, Busk PK, Pilgaard B, Zhang WJ, Nielsen KL, Nielsen PH, Lange L. Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:158. [PMID: 28649277 PMCID: PMC5480151 DOI: 10.1186/s13068-017-0840-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Improved carbohydrate-active enzymes (CAZymes) are needed to fulfill the goal of producing food, feed, fuel, chemicals, and materials from biomass. Little is known about how the diverse microbial communities in anaerobic digesters (ADs) metabolize carbohydrates or which CAZymes that are present, making the ADs a unique niche to look for CAZymes that can potentiate the enzyme blends currently used in industry. RESULTS Enzymatic assays showed that functional CAZymes were secreted into the AD environments in four full-scale mesophilic Danish ADs fed with primary and surplus sludge from municipal wastewater treatment plants. Metagenomes from the ADs were mined for CAZymes with Homology to Peptide Patterns (HotPep). 19,335 CAZymes were identified of which 30% showed 50% or lower identity to known proteins demonstrating that ADs make up a promising pool for discovery of novel CAZymes. A function was assigned to 54% of all CAZymes identified by HotPep. Many different α-glucan-acting CAZymes were identified in the four metagenomes, and the most abundant family was glycoside hydrolase family 13, which contains α-glucan-acting CAZymes. Cellulytic and xylanolytic CAZymes were also abundant in the four metagenomes. The cellulytic enzymes were limited almost to endoglucanases and β-glucosidases, which reflect the large amount of partly degraded cellulose in the sludge. No dockerin domains were identified suggesting that the cellulytic enzymes in the ADs studied operate independently. Of xylanolytic CAZymes, especially xylanases and β-xylosidase, but also a battery of accessory enzymes, were present in the four ADs. CONCLUSIONS Our findings suggest that the ADs are a good place to look for novel plant biomass degrading and modifying enzymes that can potentiate biological processes and provide basis for production of a range of added-value products from biorefineries.
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Affiliation(s)
- Casper Wilkens
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kongens Lyngby, Denmark
| | - Peter Kamp Busk
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kongens Lyngby, Denmark
| | - Bo Pilgaard
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kongens Lyngby, Denmark
| | - Wen-Jing Zhang
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University, A. C. Meyers Vænge 15, 2450 Copenhagen, Denmark
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Kåre L. Nielsen
- Center for Microbial Communities, Section for Biotechnology, Department of Chemistry and Bioscience, Aalborg University, Frederiks Bajer Vej 7, 9220 Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Section for Biotechnology, Department of Chemistry and Bioscience, Aalborg University, Frederiks Bajer Vej 7, 9220 Aalborg, Denmark
| | - Lene Lange
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kongens Lyngby, Denmark
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A Metagenomic Advance for the Cloning and Characterization of a Cellulase from Red Rice Crop Residues. Molecules 2016; 21:molecules21070831. [PMID: 27347917 PMCID: PMC6274478 DOI: 10.3390/molecules21070831] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 01/28/2023] Open
Abstract
Many naturally-occurring cellulolytic microorganisms are not readily cultivable, demanding a culture-independent approach in order to study their cellulolytic genes. Metagenomics involves the isolation of DNA from environmental sources and can be used to identify enzymes with biotechnological potential from uncultured microbes. In this study, a gene encoding an endoglucanase was cloned from red rice crop residues using a metagenomic strategy. The amino acid identity between this gene and its closest published counterparts is lower than 70%. The endoglucanase was named EglaRR01 and was biochemically characterized. This recombinant protein showed activity on carboxymethylcellulose, indicating that EglaRR01 is an endoactive lytic enzyme. The enzymatic activity was optimal at a pH of 6.8 and at a temperature of 30 °C. Ethanol production from this recombinant enzyme was also analyzed on EglaRR01 crop residues, and resulted in conversion of cellulose from red rice into simple sugars which were further fermented by Saccharomyces cerevisiae to produce ethanol after seven days. Ethanol yield in this study was approximately 8 g/L. The gene found herein shows strong potential for use in ethanol production from cellulosic biomass (second generation ethanol).
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Dollhofer V, Callaghan TM, Dorn-In S, Bauer J, Lebuhn M. Development of three specific PCR-based tools to determine quantity, cellulolytic transcriptional activity and phylogeny of anaerobic fungi. J Microbiol Methods 2016; 127:28-40. [PMID: 27220661 DOI: 10.1016/j.mimet.2016.05.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 11/27/2022]
Abstract
Anaerobic fungi (AF) decompose plant material with their rhizoid and multiple cellulolytic enzymes. They disintegrate the complex structure of lignocellulosic substrates, making them more accessible and suitable for further microbial degradation. There is also much interest in their use as biocatalysts for biotechnological applications. Here, three novel polymerase chain reaction (PCR)-based methods for detecting AF and their transcriptional activity in in vitro cultures and environmental samples were developed. Two real-time quantitative PCR (qPCR)-based methods targeting AF were developed: AF-SSU, was designed to quantify the 18S rRNA genes of AF. AF-Endo, measuring transcripts of an endoglucanase gene from the glycoside hydrolase family 5 (GH5), was developed to quantify their transcriptional cellulolytic activity. The third PCR based approach was designed for phylogenetical analysis. It targets the 28S rRNA gene (LSU) of AF revealing their phylogenetic affiliation. The in silico-designed primer/probe combinations were successfully tested for the specific amplification of AF from animal and biogas plant derived samples. In combination, these three methods represent useful tools for the analysis of AF transcriptional cellulolytic activity, their abundance and their phylogenetic placement.
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Affiliation(s)
- Veronika Dollhofer
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany.
| | - Tony Martin Callaghan
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany.
| | - Samart Dorn-In
- Chair of Animal Hygiene, WZW, TUM, Weihenstephaner Berg 3, 85354 Freising, Germany.
| | - Johann Bauer
- Chair of Animal Hygiene, WZW, TUM, Weihenstephaner Berg 3, 85354 Freising, Germany.
| | - Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany.
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18
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Sun L, Liu T, Müller B, Schnürer A. The microbial community structure in industrial biogas plants influences the degradation rate of straw and cellulose in batch tests. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:128. [PMID: 27330562 PMCID: PMC4912747 DOI: 10.1186/s13068-016-0543-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/02/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Materials rich in lignocellulose, such as straw, are abundant, cheap and highly interesting for biogas production. However, the complex structure of lignocellulose is difficult for microbial cellulolytic enzymes to access, limiting degradation. The rate of degradation depends on the activity of members of the microbial community, but the knowledge of this community in the biogas process is rather limited. This study, therefore, investigated the degradation rate of cellulose and straw in batch cultivation test initiated with inoculums from four co-digestion biogas plants (CD) and six wastewater treatment plants (WWTP). The results were correlated to the bacterial community by 454-pyrosequencing targeting 16S rRNA gene and by T-RFLP analysis targeting genes of glycoside hydrolase families 5 (cel5) and 48 (cel48), combined with construction of clone libraries. RESULTS UniFrac principal coordinate analysis of 16S rRNA gene amplicons revealed a clustering of WWTPs, while the CDs were more separated from each other. Bacteroidetes and Firmicutes dominated the community with a comparably higher abundance of the latter in the processes operating at high ammonia levels. Sequences obtained from the cel5 and cel 48 clone libraries were also mainly related to the phyla Firmicutes and Bacteroidetes and here ammonia was a parameter with a strong impact on the cel5 community. The results from the batch cultivation showed similar degradation pattern for eight of the biogas plants, while two characterised by high ammonia level and low bacterial diversity, showed a clear lower degradation rate. Interestingly, two T-RFs from the cel5 community were positively correlated to high degradation rates of both straw and cellulose. One of the respective partial cel5 sequences shared 100 % identity to Clostridium cellulolyticum. CONCLUSION The degradation rate of cellulose and straw varied in the batch tests dependent on the origin of the inoculum and was negatively correlated with the ammonia level. The cellulose-degrading community, targeted by analysis of the glycoside hydrolase families 5 (cel5) and 48 (cel48), showed a dominance of bacteria belonging the Firmicutes and Bacteriodetes, and a positive correlation was found between the cellulose degradation rate of wheat straw with the level of C. cellulolyticum.
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Affiliation(s)
- Li Sun
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Tong Liu
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Bettina Müller
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Anna Schnürer
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Science, 1432 Ås, Norway
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Zheng S, Zhang H, Li Y, Zhang H, Wang O, Zhang J, Liu F. Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Front Microbiol 2015; 6:941. [PMID: 26441876 PMCID: PMC4562271 DOI: 10.3389/fmicb.2015.00941] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 08/24/2015] [Indexed: 01/06/2023] Open
Abstract
Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET) in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III)-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III)-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates.
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Affiliation(s)
- Shiling Zheng
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Hongxia Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; University of Chinese Academy of Sciences Beijing, China
| | - Ying Li
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; University of Chinese Academy of Sciences Beijing, China
| | - Hua Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Oumei Wang
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University Yantai, China
| | - Jun Zhang
- The College of Life Sciences, Northwest University Xi'an, China
| | - Fanghua Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
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