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Ji J, Escobar M, Cui S, Zhang W, Bao C, Su X, Wang G, Zhang S, Chen H, Chen G. Isolation and Characterization of a Low-Temperature, Cellulose-Degrading Microbial Consortium from Northeastern China. Microorganisms 2024; 12:1059. [PMID: 38930441 DOI: 10.3390/microorganisms12061059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The lack of efficient ways to dispose of lignocellulosic agricultural residues is a serious environmental issue. Low temperatures greatly impact the ability of organisms to degrade these wastes and convert them into nutrients. Here, we report the isolation and genomic characterization of a microbial consortium capable of degrading corn straw at low temperatures. The microorganisms isolated showed fast cellulose-degrading capabilities, as confirmed by scanning electron microscopy and the weight loss in corn straw. Bacteria in the consortium behaved as three diverse and functionally distinct populations, while fungi behaved as a single population in both diversity and functions overtime. The bacterial genus Pseudomonas and the fungal genus Thermoascus had prominent roles in the microbial consortium, showing significant lignocellulose waste-degrading functions. Bacteria and fungi present in the consortium contained high relative abundance of genes for membrane components, with amino acid breakdown and carbohydrate degradation being the most important metabolic pathways for bacteria, while fungi contained more genes involved in energy use, carbohydrate degradation, lipid and fatty acid decomposition, and biosynthesis.
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Affiliation(s)
- Jiaoyang Ji
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Maia Escobar
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Shijia Cui
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Wei Zhang
- Jilin Province Hydraulic Research Institute, Changchun 130022, China
| | - Changjie Bao
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Xuhan Su
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Gang Wang
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Sitong Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Huan Chen
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Guang Chen
- College of Life Science, Jilin Agricultural University, Changchun 130022, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
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Burkhardt C, Baruth L, Neele Meyer-Heydecke, Klippel B, Margaryan A, Paloyan A, Panosyan HH, Antranikian G. Mining thermophiles for biotechnologically relevant enzymes: evaluating the potential of European and Caucasian hot springs. Extremophiles 2023; 28:5. [PMID: 37991546 PMCID: PMC10665251 DOI: 10.1007/s00792-023-01321-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/06/2023] [Indexed: 11/23/2023]
Abstract
The development of sustainable and environmentally friendly industrial processes is becoming very crucial and demanding for the rapid implementation of innovative bio-based technologies. Natural extreme environments harbor the potential for discovering and utilizing highly specific and efficient biocatalysts that are adapted to harsh conditions. This review focuses on extremophilic microorganisms and their enzymes (extremozymes) from various hot springs, shallow marine vents, and other geothermal habitats in Europe and the Caucasus region. These hot environments have been partially investigated and analyzed for microbial diversity and enzymology. Hotspots like Iceland, Italy, and the Azores harbor unique microorganisms, including bacteria and archaea. The latest results demonstrate a great potential for the discovery of new microbial species and unique enzymes that can be explored for the development of Circular Bioeconomy.Different screening approaches have been used to discover enzymes that are active at extremes of temperature (up 120 °C), pH (0.1 to 11), high salt concentration (up to 30%) as well as activity in the presence of solvents (up to 99%). The majority of published enzymes were revealed from bacterial or archaeal isolates by traditional activity-based screening techniques. However, the latest developments in molecular biology, bioinformatics, and genomics have revolutionized life science technologies. Post-genomic era has contributed to the discovery of millions of sequences coding for a huge number of biocatalysts. Both strategies, activity- and sequence-based screening approaches, are complementary and contribute to the discovery of unique enzymes that have not been extensively utilized so far.
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Affiliation(s)
- Christin Burkhardt
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Leon Baruth
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Neele Meyer-Heydecke
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Barbara Klippel
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Armine Margaryan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
- Research Institute of Biology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Ani Paloyan
- Scientific and Production Center, "Armbiotechnology" NAS RA, 14 Gyurjyan Str. 0056, Yerevan, Armenia
| | - Hovik H Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
- Research Institute of Biology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Garabed Antranikian
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany.
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Ali NS, Huang F, Qin W, Yang TC. A high throughput screening process and quick isolation of novel lignin-degrading microbes from large number of natural biomasses. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2023; 39:e00809. [PMID: 37583477 PMCID: PMC10423689 DOI: 10.1016/j.btre.2023.e00809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/14/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
High throughput screening approaches can significantly speed up the identification of novel enzymes from natural microbial consortiums. A two-step high throughput screening process was proposed and explored to screen lignin-degrading microorganisms. By employing this modified culture enrichment method and screening based on enzyme activity, a total of 82 bacterial and 46 fungal strains were isolated from fifty decayed wood samples (100 liquid cultures) collected from the banks of the Ottawa River in Canada. Among them, ten bacterial and five fungal strains were selected and identified based on their high laccase activities by 16S rDNA and ITS gene sequencing, respectively. The study identified bacterial strains from various genera including Serratia, Enterobacter, Raoultella, and Bacillus, along with fungal counterparts including Mucor, Trametes, Conifera and Aspergillus. Moreover, Aspergillus sydowii (AORF21), Mucor sp. (AORF43), Trametes versicolor (AORF3) and Enterobacter sp. (AORB55) exhibited xylanase and β- glucanase activities in addition to laccase production. The proposed approach allowed for the quick identification of promising consortia and enhanced the chance of isolating desired strains based on desired enzyme activities. This method is not limited to lignocellulose and lignin-degrading microorganisms but can be applied to identify novel microbial strains and enzymes from different natural samples.
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Affiliation(s)
- Nadia Sufdar Ali
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
- Aquatic and Crop Resource Development Research Centre, National Research Council, Ottawa, ON, Canada
| | - Fang Huang
- Aquatic and Crop Resource Development Research Centre, National Research Council, Ottawa, ON, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Trent Chunzhong Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council, Ottawa, ON, Canada
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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5
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Jeilu O, Simachew A, Alexandersson E, Johansson E, Gessesse A. Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics. Front Microbiol 2022; 13:1059061. [PMID: 36569080 PMCID: PMC9768486 DOI: 10.3389/fmicb.2022.1059061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.
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Affiliation(s)
- Oliyad Jeilu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden,*Correspondence: Oliyad Jeilu,
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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Sartaj K, Patel A, Matsakas L, Prasad R. Unravelling Metagenomics Approach for Microbial Biofuel Production. Genes (Basel) 2022; 13:1942. [PMID: 36360179 PMCID: PMC9689425 DOI: 10.3390/genes13111942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
Renewable biofuels, such as biodiesel, bioethanol, and biobutanol, serve as long-term solutions to fossil fuel depletion. A sustainable approach feedstock for their production is plant biomass, which is degraded to sugars with the aid of microbes-derived enzymes, followed by microbial conversion of those sugars to biofuels. Considering their global demand, additional efforts have been made for their large-scale production, which is ultimately leading breakthrough research in biomass energy. Metagenomics is a powerful tool allowing for functional gene analysis and new enzyme discovery. Thus, the present article summarizes the revolutionary advances of metagenomics in the biofuel industry and enlightens the importance of unexplored habitats for novel gene or enzyme mining. Moreover, it also accentuates metagenomics potentials to explore uncultivable microbiomes as well as enzymes associated with them.
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Affiliation(s)
- Km Sartaj
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Alok Patel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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Xu J, Zhang K, Lin Y, Li M, Wang X, Yu Q, Sun H, Cheng Q, Xie Y, Wang C, Li P, Chen C, Yang F, Zheng Y. Effect of cellulase and lactic acid bacteria on the fermentation quality, carbohydrate conversion, and microbial community of ensiling oat with different moisture contents. Front Microbiol 2022; 13:1013258. [PMID: 36274697 PMCID: PMC9581316 DOI: 10.3389/fmicb.2022.1013258] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Oat (Avena sativa L.) is one of the most widely cultivated crops used as forage. The aim of this study was to evaluate the effects of cellulase and Lactobacillus plantarum interactions with different moisture contents on oat ensiling. Oats with three moisture contents were treated with nothing (C), cellulase (CE), lactic acid bacteria (LP), or CE+LP and ensiled for 30 and 60 days. Compared with the control, LP and CE treatments increased crude protein and lactic acid concentrations and reduced the pH and ammonia nitrogen/total nitrogen (NH3-N/TN) ratios of silages. The addition of CE improved lignocellulosic degradation, compared with approximately 67% (LD) and 81% moisture content (HD) ensiling, CE (CE, CE+LP) ensiling in the approximately 75% moisture content (MD) group retained higher water-soluble carbohydrate, glucose, sucrose and fructose concents. The LP and CE inoculations significantly reduced the microbial community diversity, and lower values for the observed species, ACE, Chao1, and Shannon indices compared with CK-treated samples. Additives inhibited the growth of unfavorable bacteria (such as Clostridium) and increased the abundances of lactic acid bacteria (LAB); the maximum increases in the Lactiplantibacillus abundance were obtained in the LP- and CE+LP-treated samples, improving the microbial community structure in silage. In summary, adding LP and CE effectively improved the oat fermentation quality, and better performances in ensiling oat and lignocellulose degradation were obtained with LP and CE combinations, especially for the MD group of silages that were ensiled for 60 days. The addition of CE and LP at the appropriate moisture content might be helpful for producing high-quality oat silage, and also provide a simple and feasible method to enhance the effects of bacteria and enzymes.
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Affiliation(s)
- Jinyi Xu
- College of Animal Science, Guizhou University, Guiyang, China
| | - Keyi Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yufan Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Mengxin Li
- College of Animal Science, Guizhou University, Guiyang, China
| | - Xuekai Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Qiang Yu
- College of Animal Science, Guizhou University, Guiyang, China
| | - Hong Sun
- College of Animal Science, Guizhou University, Guiyang, China
| | - Qiming Cheng
- College of Animal Science, Guizhou University, Guiyang, China
| | - Yixiao Xie
- College of Animal Science, Guizhou University, Guiyang, China
| | - Chunmei Wang
- College of Animal Science, Guizhou University, Guiyang, China
| | - Ping Li
- College of Animal Science, Guizhou University, Guiyang, China
| | - Chao Chen
- College of Animal Science, Guizhou University, Guiyang, China
| | - Fuyu Yang
- College of Animal Science, Guizhou University, Guiyang, China
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yulong Zheng
- College of Animal Science, Guizhou University, Guiyang, China
- *Correspondence: Yulong Zheng,
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Wani AK, Akhtar N, Singh R, Chopra C, Kakade P, Borde M, Al-Khayri JM, Suprasanna P, Zimare SB. Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response. Mol Biol Rep 2022; 49:12165-12179. [PMID: 36169892 DOI: 10.1007/s11033-022-07936-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/19/2022] [Accepted: 09/08/2022] [Indexed: 12/01/2022]
Abstract
Microorganisms dwell in diverse plant niches as non-axenic biotic components that are beneficial as well pathogenic for the host. They improve nutrients-uptake, stress tolerance, phytohormone synthesis, and strengthening the defense system through phyllosphere, rhizosphere, and endosphere. The negative consequences of the microbial communities are largely in the form of diseases characterized by certain symptoms such as gall, cankers, rots etc. Uncultivable and unspecified nature of different phytomicrobiomes communities is a challenge in the management of plant disease, a leading cause for the loss of the plant products. Metagenomics has opened a new gateway for the exploration of microorganisms that are hitherto unknown, enables investigation of the functional aspect of microbial gene products through metatranscriptomics and metabolomics. Metagenomics offers advantages of characterizing previously unknown microorganisms from extreme environments like hot springs, glaciers, deep seas, animal gut etc. besides bioprospecting gene products such as Taq polymerase, bor encoded indolotryptoline, hydrolases, and polyketides. This review provides a detailed account of the phytomicrobiome networks and highlights the importance and limitations of metagenomics and other meta-omics approaches for the understanding of plant microbial diversity with special focus on the disease control and its management.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Prachi Kakade
- Department of Botany, Amdar Shashikant Shinde Mahavidyalay, 415012, Medha, Satara, India
| | - Mahesh Borde
- Department of Botany, Savitribai Phule Pune University, 411007, Pune, India
| | - Jameel M Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, 31982, Al- Ahsa, Saudi Arabia
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, 400094, Mumbai, India
| | - Saurabha B Zimare
- Department of Botany, Amdar Shashikant Shinde Mahavidyalay, 415012, Medha, Satara, India. .,Department of Botany, D. P. Bhosale College, Koregaon, , Satara, 415501, Maharashtra, India.
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9
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Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D. Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. Front Microbiol 2022; 13:708335. [PMID: 35655999 PMCID: PMC9152772 DOI: 10.3389/fmicb.2022.708335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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10
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Singh N, Singh V, Singh MP. Microbial degradation of lignocellulosic biomass for bioenergy production: A metagenomic-based approach. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2056451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nidhi Singh
- Centre of Bioinformatics, University of Allahabad, Allahabad, India
- School of Biochemical Engineering, IIT (BHU), Varanasi, India
| | - Veer Singh
- Centre of Biotechnology, University of Allahabad, Allahabad, India
| | - Mohan P. Singh
- Centre of Biotechnology, University of Allahabad, Allahabad, India
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11
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Borjigin Q, Zhang B, Yu X, Gao J, Zhang X, Qu J, Ma D, Hu S, Han S. Metagenomics study to compare the taxonomic composition and metabolism of a lignocellulolytic microbial consortium cultured in different carbon conditions. World J Microbiol Biotechnol 2022; 38:78. [PMID: 35325312 DOI: 10.1007/s11274-022-03260-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
Abstract
A lignocellulolytic microbial consortium holds promise for the in situ biodegradation of crop straw and the comprehensive and effective utilization of agricultural waste. In this study, we applied metagenomics technology to comprehensively explore the metabolic functional potential and taxonomic diversity of the microbial consortia CS (cultured on corn stover) and FP (cultured on filter paper). Analyses of the data on metagenomics taxonomic affiliations revealed considerable differences in the taxonomic composition and carbohydrate-active enzymes profile of the microbial consortia CS and FP. Pseudomonas, Dysgonomonas and Sphingobacterium in CS and Cellvibrio and Pseudomonas in FP had a much wider distribution of lignocellulose degradative ability. The genes for more lignocellulose degradative enzymes were detected when the relatively simple substrate filter paper was used as the carbon source. Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses revealed considerable levels of similarity, and carbohydrate metabolic and amino acid metabolic pathways were the most enriched in CS and FP, respectively. The mechanism used by the two microbial consortia to degrade lignocellulose was similar, but the annotation of quantity of genes indicated that they are diverse and vary greatly. These data underlie the interactions between microorganisms and the synergism of enzymes during the degradative process of lignocellulose under different substrates and suggest the development of potential microbial resources.
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Affiliation(s)
- Qinggeer Borjigin
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Bizhou Zhang
- Special Crops Institute, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, No.22, ZhaoJun Road, Hohhot, 010031, China
| | - Xiaofang Yu
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China. .,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.
| | - Julin Gao
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China. .,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.
| | - Xin Zhang
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Jiawei Qu
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Daling Ma
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Shuping Hu
- Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.,Vocational and Technical College, Inner Mongolia Agricultural University, Altan street, Baotou, 014109, China
| | - Shengcai Han
- Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.,Hortlculture and Plant Protection College, Inner Mongolia Agricultural University, No. 29, Eerduosi East Street, Hohhot, 010019, China
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12
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Ndata K, Nevondo W, Cekuse B, van Zyl LJ, Trindade M. Characterization of a highly xylose tolerant β-xylosidase isolated from high temperature horse manure compost. BMC Biotechnol 2021; 21:61. [PMID: 34689773 PMCID: PMC8543862 DOI: 10.1186/s12896-021-00722-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a continued need for improved enzymes for industry. β-xylosidases are enzymes employed in a variety of industries and although many wild-type and engineered variants have been described, enzymes that are highly tolerant of the products produced by catalysis are not readily available and the fundamental mechanisms of tolerance are not well understood. RESULTS Screening of a metagenomic library constructed of mDNA isolated from horse manure compost for β-xylosidase activity identified 26 positive hits. The fosmid clones were sequenced and bioinformatic analysis performed to identity putative β-xylosidases. Based on the novelty of its amino acid sequence and potential thermostability one enzyme (XylP81) was selected for expression and further characterization. XylP81 belongs to the family 39 β-xylosidases, a comparatively rarely found and characterized GH family. The enzyme displayed biochemical characteristics (KM-5.3 mM; Vmax-122 U/mg; kcat-107; Topt-50 °C; pHopt-6) comparable to previously characterized glycoside hydrolase family 39 (GH39) β-xylosidases and despite nucleotide identity to thermophilic species, the enzyme displayed only moderate thermostability with a half-life of 32 min at 60 °C. Apart from acting on substrates predicted for β-xylosidase (xylobiose and 4-nitrophenyl-β-D-xylopyranoside) the enzyme also displayed measurable α-L-arabainofuranosidase, β-galactosidase and β-glucosidase activity. A remarkable feature of this enzyme is its ability to tolerate high concentrations of xylose with a Ki of 1.33 M, a feature that is highly desirable for commercial applications. CONCLUSIONS Here we describe a novel β-xylosidase from a poorly studied glycosyl hydrolase family (GH39) which despite having overall kinetic properties similar to other bacterial GH39 β-xylosidases, displays unusually high product tolerance. This trait is shared with only one other member of the GH39 family, the recently described β-xylosidases from Dictyoglomus thermophilum. This feature should allow its use as starting material for engineering of an enzyme that may prove useful to industry and should assist in the fundamental understanding of the mechanism by which glycosyl hydrolases evolve product tolerance.
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Affiliation(s)
- Kanyisa Ndata
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Walter Nevondo
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa.,Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Bongi Cekuse
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
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13
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Effect of culture conditions on the performance of lignocellulose-degrading synthetic microbial consortia. Appl Microbiol Biotechnol 2021; 105:7981-7995. [PMID: 34596724 PMCID: PMC8502130 DOI: 10.1007/s00253-021-11591-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 11/05/2022]
Abstract
In this study, we examined a synthetic microbial consortium, composed of two selected bacteria, i.e., Citrobacter freundii so4 and Sphingobacterium multivorum w15, next to the fungus Coniochaeta sp. 2T2.1, with respect to their fate and roles in the degradation of wheat straw (WS). A special focus was placed on the effects of pH (7.2, 6.2, or 5.2), temperature (25 versus 28 °C), and shaking speed (60 versus 180 rpm). Coniochaeta sp. 2T2.1 consistently had a key role in the degradation process, with the two bacteria having additional roles. Whereas temperature exerted only minor effects on the degradation, pH and shaking speed were key determinants of both organismal growth and WS degradation levels. In detail, the three-partner degrader consortium showed significantly higher WS degradation values at pH 6.2 and 5.2 than at pH 7.2. Moreover, the two bacteria revealed up to tenfold enhanced final cell densities (ranging from log8.0 to log9.0 colony forming unit (CFU)/mL) in the presence of Coniochaeta sp. 2T2.1 than when growing alone or in a bacterial bi-culture, regardless of pH range or shaking speed. Conversely, at 180 rpm, fungal growth was clearly suppressed by the presence of the bacteria at pH 5.2 and pH 6.2, but not at pH 7.2. In contrast, at 60 rpm, the presence of the bacteria fostered fungal growth. In these latter cultures, oxygen levels were significantly lowered as compared to the maximal levels found at 180 rpm (about 5.67 mg/L, ~ 62% of saturation). Conspicuous effects on biomass appearance pointed to a fungal biofilm–modulating role of the bacteria. Key points • Coniochaeta sp. 2T2.1 has a key role in wheat straw (WS) degradation. • Bacterial impact shifts when conditions change. • pH and shaking speed are key drivers of the growth dynamics and WS degradation.
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14
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Du R, Li C, Pan P, Sze Ki Lin C, Yan J. Characterization and evaluation of a natural derived bacterial consortium for efficient lignocellulosic biomass valorization. BIORESOURCE TECHNOLOGY 2021; 329:124909. [PMID: 33684842 DOI: 10.1016/j.biortech.2021.124909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 05/26/2023]
Abstract
A consortium (HPP) with improved ability in biomass conversion was achieved by adjusting the proportion of Pseudoxanthomonas taiwanensis in a natural consortium (HP), but the mechanism behind was unknown. Herein, the diversities of microbial community structure and gene functions of the consortia were analyzed first, and found that HPP had a more balanced microbial structure with enriched gene pathways related to cellular processes, environmental information processing and metabolism. Then, key genes responsible for biomass conversion were further analyzed, finding that their abundance and distribution contributed to HPP's efficient biomass conversion. Finally, consolidated bioprocessing of agricultural wastes by HPP was carried out to verify its enhanced ability, and ethanol with the highest yield that was ever reported was achieved at 0.28 g/g. This is the first study which reported the underlying mechanisms for synergistic effects of microbial consortia, and will guide the artificial construction of complex microbial consortium for specific purpose.
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Affiliation(s)
- Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peipei Pan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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15
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Two-step functional screen on multiple proteinaceous substrates reveals temperature-robust proteases with a broad-substrate range. Appl Microbiol Biotechnol 2021; 105:3195-3209. [PMID: 33770243 PMCID: PMC8053189 DOI: 10.1007/s00253-021-11235-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 02/15/2021] [Accepted: 03/14/2021] [Indexed: 01/21/2023]
Abstract
Abstract To support the bio-based industry in development of environment-friendly processes and products, an optimal toolbox of biocatalysts is key. Although functional screen of (meta)genomic libraries may potentially contribute to identifying new enzymes, the discovery of new enzymes meeting industry compliance demands is still challenging. This is particularly noticeable in the case of proteases, for which the reports of metagenome-derived proteases with industrial applicability are surprisingly limited. Indeed, proteolytic clones have been typically assessed by its sole activity on casein or skim milk and limited to mild screening conditions. Here, we demonstrate the use of six industry-relevant animal and plant by-products, namely bone, feather, blood meals, gelatin, gluten, and zein, as complementary substrates in functional screens and show the utility of temperature as a screening parameter to potentially discover new broad-substrate range and robust proteases for the biorefinery industry. By targeting 340,000 clones from two libraries of pooled isolates of mesophilic and thermophilic marine bacteria and two libraries of microbial communities inhabiting marine environments, we identified proteases in four of eleven selected clones that showed activity against all substrates herein tested after prolonged incubation at 55 °C. Following sequencing, in silico analysis and recombinant expression in Escherichia coli, one functional protease, 58% identical at sequence level to previously reported homologs, was found to readily hydrolyze highly insoluble zein at temperatures up to 50 °C and pH 9–11. It is derived from a bacterial group whose ability to degrade zein was unknown. This study reports a two-step screen resulting in identification of a new marine metagenome-derived protease with zein-hydrolytic properties at common biomass processing temperatures that could be useful for the modern biorefinery industry. Key points • A two-step multi-substrate strategy for discovery of robust proteases. • Feasible approach for shortening enzyme optimization to industrial demands. • A new temperature-tolerant protease efficiently hydrolyzes insoluble zein. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11235-9.
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16
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Glasgow E, Vander Meulen K, Kuch N, Fox BG. Multifunctional cellulases are potent, versatile tools for a renewable bioeconomy. Curr Opin Biotechnol 2021; 67:141-148. [PMID: 33550093 PMCID: PMC8366578 DOI: 10.1016/j.copbio.2020.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 11/21/2022]
Abstract
Enzyme performance is critical to the future bioeconomy based on renewable plant materials. Plant biomass can be efficiently hydrolyzed by multifunctional cellulases (MFCs) into sugars suitable for conversion into fuels and chemicals, and MFCs fall into three functional categories. Recent work revealed MFCs with broad substrate specificity, dual exo-activity/endo-activity on cellulose, and intramolecular synergy, among other novel characteristics. Binding modules and accessory catalytic domains amplify MFC and xylanase activity in a wide variety of ways, and processive endoglucanases achieve autosynergy on cellulose. Multidomain MFCs from Caldicellulosiruptor are heat-tolerant, adaptable to variable cellulose crystallinity, and may provide interchangeable scaffolds for recombinant design. Further studies of MFC properties and their reactivity with plant biomass are recommended for increasing biorefinery yields.
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Affiliation(s)
- Evan Glasgow
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Kirk Vander Meulen
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Nate Kuch
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Brian G Fox
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States.
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17
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A novel thermostable cellulase cocktail enhances lignocellulosic bioconversion and biorefining in a broad range of pH. Int J Biol Macromol 2020; 154:349-360. [DOI: 10.1016/j.ijbiomac.2020.03.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 11/22/2022]
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18
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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19
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Časaitė V, Sadauskas M, Vaitekūnas J, Gasparavičiūtė R, Meškienė R, Skikaitė I, Sakalauskas M, Jakubovska J, Tauraitė D, Meškys R. Engineering of a chromogenic enzyme screening system based on an auxiliary indole-3-carboxylic acid monooxygenase. Microbiologyopen 2019; 8:e00795. [PMID: 30666828 PMCID: PMC6692525 DOI: 10.1002/mbo3.795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 11/24/2022] Open
Abstract
Here, we present a proof‐of‐principle for a new high‐throughput functional screening of metagenomic libraries for the selection of enzymes with different activities, predetermined by the substrate being used. By this approach, a total of 21 enzyme‐coding genes were selected, including members of xanthine dehydrogenase, aldehyde dehydrogenase (ALDH), and amidohydrolase families. The screening system is based on a pro‐chromogenic substrate, which is transformed by the target enzyme to indole‐3‐carboxylic acid. The later compound is converted to indoxyl by a newly identified indole‐3‐carboxylate monooxygenase (Icm). Due to the spontaneous oxidation of indoxyl to indigo, the target enzyme‐producing colonies turn blue. Two types of pro‐chromogenic substrates have been tested. Indole‐3‐carboxaldehydes and the amides of indole‐3‐carboxylic acid have been applied as substrates for screening of the ALDHs and amidohydrolases, respectively. Both plate assays described here are rapid, convenient, easy to perform, and adaptable for the screening of a large number of samples both in Escherichia coli and Rhodococcus sp. In addition, the fine‐tuning of the pro‐chromogenic substrate allows screening enzymes with the desired substrate specificity.
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Affiliation(s)
- Vida Časaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mikas Sadauskas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rita Meškienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Izabelė Skikaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Sakalauskas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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20
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Chuzel L, Ganatra MB, Rapp E, Henrissat B, Taron CH. Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156). J Biol Chem 2018; 293:18138-18150. [PMID: 30249617 PMCID: PMC6254351 DOI: 10.1074/jbc.ra118.003302] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156.
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Affiliation(s)
- Léa Chuzel
- From New England Biolabs, Ipswich, Massachusetts 01938,; the Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | | | - Erdmann Rapp
- the Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany,; glyXera GmbH, 39120 Magdeburg, Germany
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France,; the Institut National de la Recherche Agronomique (INRA), Unité Sous Contrat (USC) 1408, Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France, and; the Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Song J, Kim SY, Kim DH, Lee YS, Sim JS, Hahn BS, Lee CM. Characterization of an inhibitor-resistant endo-1,4-β-mannanase from the gut microflora metagenome of Hermetia illucens. Biotechnol Lett 2018; 40:1377-1387. [DOI: 10.1007/s10529-018-2596-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/25/2018] [Indexed: 01/05/2023]
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Puentes-Téllez PE, Falcao Salles J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. MICROBIAL ECOLOGY 2018; 76:419-429. [PMID: 29392382 PMCID: PMC6061470 DOI: 10.1007/s00248-017-1141-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/29/2017] [Indexed: 06/02/2023]
Abstract
Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.
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Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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23
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Castilla IA, Woods DF, Reen FJ, O'Gara F. Harnessing Marine Biocatalytic Reservoirs for Green Chemistry Applications through Metagenomic Technologies. Mar Drugs 2018; 16:E227. [PMID: 29973493 PMCID: PMC6071119 DOI: 10.3390/md16070227] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 01/24/2023] Open
Abstract
In a demanding commercial world, large-scale chemical processes have been widely utilised to satisfy consumer related needs. Chemical industries are key to promoting economic growth and meeting the requirements of a sustainable industrialised society. The market need for diverse commodities produced by the chemical industry is rapidly expanding globally. Accompanying this demand is an increased threat to the environment and to human health, due to waste produced by increased industrial production. This increased demand has underscored the necessity to increase reaction efficiencies, in order to reduce costs and increase profits. The discovery of novel biocatalysts is a key method aimed at combating these difficulties. Metagenomic technology, as a tool for uncovering novel biocatalysts, has great potential and applicability and has already delivered many successful achievements. In this review we discuss, recent developments and achievements in the field of biocatalysis. We highlight how green chemistry principles through the application of biocatalysis, can be successfully promoted and implemented in various industrial sectors. In addition, we demonstrate how two novel lipases/esterases were mined from the marine environment by metagenomic analysis. Collectively these improvements can result in increased efficiency, decreased energy consumption, reduced waste and cost savings for the chemical industry.
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Affiliation(s)
- Ignacio Abreu Castilla
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - F Jerry Reen
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
- Telethon Kids Institute, Perth, WA 6008, Australia.
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
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Carlos C, Fan H, Currie CR. Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers. Front Microbiol 2018; 9:364. [PMID: 29545786 PMCID: PMC5839234 DOI: 10.3389/fmicb.2018.00364] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/15/2018] [Indexed: 01/05/2023] Open
Abstract
Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.
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Affiliation(s)
- Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,U.S. Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Huan Fan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,U.S. Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
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Jiménez DJ, Chaib De Mares M, Salles JF. Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse. Front Microbiol 2018. [PMID: 29535687 PMCID: PMC5834485 DOI: 10.3389/fmicb.2018.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plant biomass (PB) is an important source of sugars useful for biofuel production, whose degradation efficiency depends on synergistic and dynamic interactions of different enzymes. Here, using a metatranscriptomics-based approach, we explored the expression of PB-degrading enzymes in a five-species synthetic bacterial consortium during cultivation on sugarcane bagasse as a unique carbon source. By analyzing the temporal expression dynamics of a selection of enzymes we revealed the functional role of each consortium member and disentangled the potential interactions between them. Based on normalized expression values and the taxonomic affiliation of all the transcripts within thirty carbohydrate-active enzyme (CAZy) families, we observed a successional profile. For instance, endo-glucanases/-xylanases (e.g., GH8, GH10, and GH16) were significantly expressed at 12 h, whereas exo-glucanases (e.g., GH6 and GH48) and α-arabinosidases/β-xylosidases (e.g., GH43) were highly expressed at 48 h. Indeed, a significant peak of extracellular β-xylosidase activity was observed at this stage. Moreover, we observed a higher expression of several CAZy families at 12-48 h, suggesting easy access to the main plant polysaccharides. Based on this evidence, we predicted that the highest level of collaboration between strains takes place at the initial stages of growth. Here, Paenibacillus, Brevundimonas, and Chryseobacterium were the most important contributors, whereas Stenotrophomonas was highly active at the end of the culture (96-192 h) without contributing to a large extent to the expression of lignocellulolytic enzymes. Our results contribute to the understanding of enzymatic and ecological mechanisms within PB-degrading microbial consortia, yielding new perspectives to improve the PB saccharification processes.
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Affiliation(s)
- Diego Javier Jiménez
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Maryam Chaib De Mares
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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26
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Cortes-Tolalpa L, Norder J, van Elsas JD, Falcao Salles J. Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. Appl Microbiol Biotechnol 2018; 102:2913-2927. [PMID: 29397428 PMCID: PMC5847192 DOI: 10.1007/s00253-017-8714-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/29/2017] [Accepted: 12/11/2017] [Indexed: 12/30/2022]
Abstract
The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were “trained” to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing the associated costs.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Justin Norder
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Joana Falcao Salles
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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27
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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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Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. Biotechnol Adv 2017; 35:950-970. [PMID: 28723577 DOI: 10.1016/j.biotechadv.2017.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022]
Abstract
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.
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Jiménez DJ, Dini-Andreote F, DeAngelis KM, Singer SW, Salles JF, van Elsas JD. Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia. Trends Microbiol 2017. [PMID: 28648267 DOI: 10.1016/j.tim.2017.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plant biomass (PB) is an important resource for biofuel production. However, the frequent lack of efficiency of PB saccharification is still an industrial bottleneck. The use of enzyme cocktails produced from PB-degrading microbial consortia (PB-dmc) is a promising approach to optimize this process. Nevertheless, the proper use and manipulation of PB-dmc depends on a sound understanding of the ecological processes and mechanisms that exist in these communities. This Opinion article provides an overview of arguments as to how spatiotemporal nutritional fluxes influence the successional dynamics and ecological interactions (synergism versus competition) between populations in PB-dmc. The themes of niche occupancy, 'sugar cheaters', minimal effective consortium, and the Black Queen Hypothesis are raised as key subjects that foster our appraisal of such systems. Here we provide a conceptual framework that describes the critical topics underpinning the ecological basis of PB-dmc, giving a solid foundation upon which further prospective experimentation can be developed.
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Affiliation(s)
- Diego Javier Jiménez
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Francisco Dini-Andreote
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Kristen M DeAngelis
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA 01003-9298, USA
| | - Steven W Singer
- Joint BioEnergy Institute,5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
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30
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Tiwari R, Nain L, Labrou NE, Shukla P. Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review. Crit Rev Microbiol 2017; 44:244-257. [DOI: 10.1080/1040841x.2017.1337713] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rameshwar Tiwari
- Department of Microbiology, Laboratory of Enzyme Technology and Protein Bioinformatics, Maharshi Dayanand University, Rohtak, India
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Nikolaos E. Labrou
- Department of Biotechnology, School of Food, Biotechnology and Development, Laboratory of Enzyme Technology, Agricultural University of Athens, Athens, Greece
| | - Pratyoosh Shukla
- Department of Microbiology, Laboratory of Enzyme Technology and Protein Bioinformatics, Maharshi Dayanand University, Rohtak, India
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31
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Maruthamuthu M, van Elsas JD. Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:142. [PMID: 28588643 PMCID: PMC5457731 DOI: 10.1186/s13068-017-0808-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Enzyme discovery is a promising approach to aid in the deconstruction of recalcitrant plant biomass in an industrial process. Novel enzymes can be readily discovered by applying metagenomics on whole microbiomes. Our goal was to select, examine, and characterize eight novel glycoside hydrolases that were previously detected in metagenomic libraries, to serve biotechnological applications with high performance. RESULTS Here, eight glycosyl hydrolase family candidate genes were selected from metagenomes of wheat straw-degrading microbial consortia using molecular cloning and subsequent gene expression studies in Escherichia coli. Four of the eight enzymes had significant activities on either pNP-β-d-galactopyranoside, pNP-β-d-xylopyranoside, pNP-α-l-arabinopyranoside or pNP-α-d-glucopyranoside. These proteins, denoted as proteins 1, 2, 5 and 6, were his-tag purified and their nature and activities further characterized using molecular and activity screens with the pNP-labeled substrates. Proteins 1 and 2 showed high homologies with (1) a β-galactosidase (74%) and (2) a β-xylosidase (84%), whereas the remaining two (5 and 6) were homologous with proteins reported as a diguanylate cyclase and an aquaporin, respectively. The β-galactosidase- and β-xylosidase-like proteins 1 and 2 were confirmed as being responsible for previously found thermo-alkaliphilic glycosidase activities of extracts of E. coli carrying the respective source fosmids. Remarkably, the β-xylosidase-like protein 2 showed activities with both pNP-Xyl and pNP-Ara in the temperature range 40-50 °C and pH range 8.0-10.0. Moreover, proteins 5 and 6 showed thermotolerant α-glucosidase activity at pH 10.0. In silico structure prediction of protein 5 revealed the presence of a potential "GGDEF" catalytic site, encoding α-glucosidase activity, whereas that of protein 6 showed a "GDSL" site, encoding a 'new family' α-glucosidase activity. CONCLUSION Using a rational screening approach, we identified and characterized four thermo-alkaliphilic glycosyl hydrolases that have the potential to serve as constituents of enzyme cocktails that produce sugars from lignocellulosic plant remains.
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Affiliation(s)
- Mukil Maruthamuthu
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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Towards a sustainable biobased industry - Highlighting the impact of extremophiles. N Biotechnol 2017; 40:144-153. [PMID: 28512003 DOI: 10.1016/j.nbt.2017.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/28/2017] [Accepted: 05/03/2017] [Indexed: 11/21/2022]
Abstract
The transition of the oil-based economy towards a sustainable economy completely relying on biomass as renewable feedstock requires the concerted action of academia, industry, politics and civil society. An interdisciplinary approach of various fields such as microbiology, molecular biology, chemistry, genetics, chemical engineering and agriculture in addition to cross-sectional technologies such as economy, logistics and digitalization is necessary to meet the future global challenges. The genomic era has contributed significantly to the exploitation of naturés biodiversity also from extreme habitats. By applying modern technologies it is now feasible to deliver robust enzymes (extremozymes) and robust microbial systems that are active at temperatures up to 120°C, at pH 0 and 12 and at 1000bar. In the post-genomic era, different sophisticated "omics" analyses will allow the identification of countless novel enzymes regardless of the lack of cultivability of most microorganisms. Furthermore, elaborate protein-engineering methods are clearing the way towards tailor-made robust biocatalysts. Applying environmentally friendly and efficient biological processes, terrestrial and marine biomass can be converted to high value products e.g. chemicals, building blocks, biomaterials, pharmaceuticals, food, feed and biofuels. Thus, further application of extremophiles has the potential to improve sustainability of existing biotechnological processes towards a greener biobased industry.
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33
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Ma S, Huang Y, Wang C, Fan H, Dai L, Zhou Z, Liu X, Deng Y. Defluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw. Int J Syst Evol Microbiol 2017; 67:1607-1612. [PMID: 27902335 PMCID: PMC5817277 DOI: 10.1099/ijsem.0.001664] [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] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, anaerobic, fermentative bacterium, strain A6T, was obtained from an anaerobic batch digester treating animal manure and rice straw. Cells were Gram-stain-positive, slightly curved rods with a size of 0.6-1×2.5-8.2 µm, non-motile and produced terminal spores. The temperature, pH and NaCl concentration ranges for growth were 40-60 °C, 6.5-8.0 and 0-15.0 g l-1, with optimum growth noted at 50-55 °C, pH 7.5 and in the absence of NaCl, respectively. Yeast extract was required for growth. d-Glucose, maltose, d-xylose, d-galactose, d-fructose, d-ribose, lactose, raffinose, sucrose, d-arabinose, cellobiose, d-mannose and yeast extract were used as carbon and energy sources. The fermentation products from glucose were ethanol, lactate, acetate, propionate, butyrate, valerate, iso-butyrate, iso-valerate, H2 and CO2. The G+C content of the genomic DNA was 36.6 mol%. The predominant fatty acids were C16 : 0, iso-C17 : 1, C14 : 0, C16 : 1ω7c, C16 : 0 N-alcohol and C13 : 0 3-OH. Respiratory quinones were not detected. The polar lipid profile comprised phosphoglycolipids, phospholipids, glycolipids, a diphosphatidylglycerol, a phosphatidylglycerol and an unidentified lipid. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was closely related to Defluviitalea saccharophila DSM 22681T with a similarity of 96.0 %. Based on the morphological, physiological and taxonomic characterization, strain A6T is considered to represent a novel species of the genus Defluviitalea, for which the name Defluviitalea raffinosedens sp. nov. is proposed. The type strain is A6T (=DSM 28090T=ACCC 19951T).
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Affiliation(s)
- Shichun Ma
- Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Present address: Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nan Road, Chengdu 610041, Sichuan, P.R. China.,Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Yan Huang
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Cong Wang
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, Sichuan, P.R. China.,Present address: College of Light Industry, Textile and Food Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, Sichuan, P.R. China
| | - Hui Fan
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Lirong Dai
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Zheng Zhou
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Xing Liu
- Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China
| | - Yu Deng
- Key Laboratory of Energy Microbiology and Application, Ministry of Agriculture, Chengdu, Sichuan, P.R. China.,Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan, P.R. China
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Sánchez-Reyez A, Batista-García RA, Valdés-García G, Ortiz E, Perezgasga L, Zárate-Romero A, Pastor N, Folch-Mallol JL. A family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism. Proteins 2017; 85:1222-1237. [DOI: 10.1002/prot.25282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/21/2017] [Accepted: 02/27/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Ayixon Sánchez-Reyez
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
- Centro de Investigación en Biotecnología UAEM; CP 62209 Cuernavaca Morelos Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | - Gilberto Valdés-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | - Ernesto Ortiz
- Instituto de Biotecnología. Universidad Nacional Autónoma de México; CP 62210 Cuernavaca Morelos Mexico
| | - Lucía Perezgasga
- Instituto de Biotecnología. Universidad Nacional Autónoma de México; CP 62210 Cuernavaca Morelos Mexico
| | - Andrés Zárate-Romero
- Centro de Investigación en Biotecnología UAEM; CP 62209 Cuernavaca Morelos Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
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Cheng J, Romantsov T, Engel K, Doxey AC, Rose DR, Neufeld JD, Charles TC. Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences. PLoS One 2017; 12:e0172545. [PMID: 28273103 PMCID: PMC5342196 DOI: 10.1371/journal.pone.0172545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/06/2017] [Indexed: 11/19/2022] Open
Abstract
The techniques of metagenomics have allowed researchers to access the genomic potential of uncultivated microbes, but there remain significant barriers to determination of gene function based on DNA sequence alone. Functional metagenomics, in which DNA is cloned and expressed in surrogate hosts, can overcome these barriers, and make important contributions to the discovery of novel enzymes. In this study, a soil metagenomic library carried in an IncP cosmid was used for functional complementation for β-galactosidase activity in both Sinorhizobium meliloti (α-Proteobacteria) and Escherichia coli (γ-Proteobacteria) backgrounds. One β-galactosidase, encoded by six overlapping clones that were selected in both hosts, was identified as a member of glycoside hydrolase family 2. We could not identify ORFs obviously encoding possible β-galactosidases in 19 other sequenced clones that were only able to complement S. meliloti. Based on low sequence identity to other known glycoside hydrolases, yet not β-galactosidases, three of these ORFs were examined further. Biochemical analysis confirmed that all three encoded β-galactosidase activity. Lac36W_ORF11 and Lac161_ORF7 had conserved domains, but lacked similarities to known glycoside hydrolases. Lac161_ORF10 had neither conserved domains nor similarity to known glycoside hydrolases. Bioinformatic and structural modeling implied that Lac161_ORF10 protein represented a novel enzyme family with a five-bladed propeller glycoside hydrolase domain. By discovering founding members of three novel β-galactosidase families, we have reinforced the value of functional metagenomics for isolating novel genes that could not have been predicted from DNA sequence analysis alone.
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Affiliation(s)
- Jiujun Cheng
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - David R. Rose
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Josh D. Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- * E-mail:
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Smart M, Huddy RJ, Cowan DA, Trindade M. Liquid Phase Multiplex High-Throughput Screening of Metagenomic Libraries Using p-Nitrophenyl-Linked Substrates for Accessory Lignocellulosic Enzymes. Methods Mol Biol 2017; 1539:219-228. [PMID: 27900692 DOI: 10.1007/978-1-4939-6691-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
To access the genetic potential contained in large metagenomic libraries, suitable high-throughput functional screening methods are required. Here we describe a high-throughput screening approach which enables the rapid identification of metagenomic library clones expressing functional accessory lignocellulosic enzymes. The high-throughput nature of this method hinges on the multiplexing of both the E. coli metagenomic library clones and the colorimetric p-nitrophenyl linked substrates which allows for the simultaneous screening for β-glucosidases, β-xylosidases, and α-L-arabinofuranosidases. This method is readily automated and compatible with high-throughput robotic screening systems.
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Affiliation(s)
- Mariette Smart
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Robert J Huddy
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Don A Cowan
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa.
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa.
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Ábrego U, Chen Z, Wan C. Consolidated Bioprocessing Systems for Cellulosic Biofuel Production. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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DeCastro ME, Rodríguez-Belmonte E, González-Siso MI. Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes. Front Microbiol 2016; 7:1521. [PMID: 27729905 PMCID: PMC5037290 DOI: 10.3389/fmicb.2016.01521] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/12/2016] [Indexed: 11/24/2022] Open
Abstract
Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.
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Affiliation(s)
- María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
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