1
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Hu L, Zhang S, Chai S, Lyu Y, Wang S, Feng Z. Discovery of two bifunctional/multifunctional cellulases by functional metagenomics. Enzyme Microb Technol 2023; 169:110288. [PMID: 37467538 DOI: 10.1016/j.enzmictec.2023.110288] [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: 04/25/2023] [Revised: 06/12/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
Cellulases are widely used in industry, and the usage in bioconversion of biofuels makes cellulases more valuable. In this study, two tandem genes that encoded cellulases ZF994-1 and ZF994-2, respectively, were identified on a cosmid from a soil metagenomic library. Phylogenetic analysis indicated that ZF994-1 and ZF994-2 belonged to glycoside hydrolase family 12 (GH12), and GH3, respectively. Based on the substrate specificity analysis, the recombinant ZF994-1 exhibited weak endoglucanase activity, moderate β-1,3-glucanase and β-1,4-mannanase activities, and strong β-glucosidase activity, while the recombinant ZF994-2 exhibited moderate endoglucanase activity and strong β-glucosidase activity. More than 45% β-glucosidase activity of the recombinant ZF994-1 retained in the buffer containing 3 M glucose, indicating the good tolerance against glucose. The recombinant ZF994-2 showed high activity in the presence of metal ions and organic reagents, exhibiting potential industrial applications.
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Affiliation(s)
- Lingzhi Hu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Shengxia Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Shumao Chai
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Yunbin Lyu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China.
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2
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Song X, Lu C, Luo J, Gong X, Guo D, Ma Y. Matured compost amendment improves compost nutrient content by changing the bacterial community during the composting of Chinese herb residues. Front Microbiol 2023; 14:1146546. [PMID: 37007496 PMCID: PMC10060987 DOI: 10.3389/fmicb.2023.1146546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Composting is a sustainable strategy to deal with organic waste. Our research aimed to study the influence of an amendment of 10% matured compost (MC) during Chinese herb residue (CHR) compost. Here, a 60-day CHR compost was performed, and MC application was able to reduce the nitrogen loss and enhance the humic acid accumulation during the composting as compared with the non-inoculated control (NC), by 25 and 19%, respectively. Furthermore, the matured compost amendment improved the diversity of the bacterial community, increased the complexity of the co-occurrence network, and changed the keystone and module hub bacteria during composting. The increased abundance levels of Thermopolyspora, Thermobispora, and Thermosporomyces, which were significantly higher in MC than in NC, may contribute to the degradation of cellulose and the formation of humic acid. Overall, this study extends our understanding of the effects of matured compost reflux on compost quality and the bacterial community.
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Affiliation(s)
- Xiuchao Song
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chao Lu
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jia Luo
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Nanjing, China
| | - Xin Gong
- Jiangsu Key Laboratory for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dejie Guo
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Ma
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Nanjing, China
- *Correspondence: Yan Ma,
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3
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Molecular weight, chain length distribution and long-term retrogradation of cassava starch modified by amylomaltase. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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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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Wu MH, Kao MR, Li CW, Yu SM, Ho THD. A unique self-truncation of bacterial GH5 endoglucanases leads to enhanced activity and thermostability. BMC Biol 2022; 20:137. [PMID: 35681203 PMCID: PMC9185962 DOI: 10.1186/s12915-022-01334-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background β-1,4-endoglucanase (EG) is one of the three types of cellulases used in cellulose saccharification during lignocellulosic biofuel/biomaterial production. GsCelA is an EG secreted by the thermophilic bacterium Geobacillus sp. 70PC53 isolated from rice straw compost in southern Taiwan. This enzyme belongs to glycoside hydrolase family 5 (GH5) with a TIM-barrel structure common among all members of this family. GsCelA exhibits excellent lignocellulolytic activity and thermostability. In the course of investigating the regulation of this enzyme, it was fortuitously discovered that GsCelA undergoes a novel self-truncation/activation process that appears to be common among GH5 enzymes. Results Three diverse Gram-positive bacterial GH5 EGs, but not a GH12 EG, undergo an unexpected self-truncation process by removing a part of their C-terminal region. This unique process has been studied in detail with GsCelA. The purified recombinant GsCelA was capable of removing a 53-amino-acid peptide from the C-terminus. Natural or engineered GsCelA truncated variants, with up to 60-amino-acid deletion from the C-terminus, exhibited higher specific activity and thermostability than the full-length enzyme. Interestingly, the C-terminal part that is removed in this self-truncation process is capable of binding to cellulosic substrates of EGs. The protein truncation, which is pH and temperature dependent, occurred between amino acids 315 and 316, but removal of these two amino acids did not stop the process. Furthermore, mutations of E142A and E231A, which are essential for EG activity, did not affect the protein self-truncation process. Conversely, two single amino acid substitution mutations affected the self-truncation activity without much impact on EG activities. In Geobacillus sp. 70PC53, the full-length GsCelA was first synthesized in the cell but progressively transformed into the truncated form and eventually secreted. The GsCelA self-truncation was not affected by standard protease inhibitors, but could be suppressed by EDTA and EGTA and enhanced by certain divalent ions, such as Ca2+, Mg2+, and Cu2+. Conclusions This study reveals novel insights into the strategy of Gram-positive bacteria for directing their GH5 EGs to the substrate, and then releasing the catalytic part for enhanced activity via a spontaneous self-truncation process. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01334-y.
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Affiliation(s)
- Mei-Huey Wu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, Republic of China.,Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China
| | - Mu-Rong Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China
| | - Chen-Wei Li
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China. .,Biotechnology Research Center, National Chung Hsing University, Taichung, 402, Taiwan, Republic of China. .,Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan, Republic of China.
| | - Tuan-Hua David Ho
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, Republic of China. .,Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China. .,Biotechnology Research Center, National Chung Hsing University, Taichung, 402, Taiwan, Republic of China.
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6
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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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7
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Effects of fertilizer practice on fungal and actinobacterial cellulolytic community with different humified particle-size fractions in double-cropping field. Sci Rep 2021; 11:18441. [PMID: 34531457 PMCID: PMC8446020 DOI: 10.1038/s41598-021-97975-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Cellulose plays an important role in maintaining or improving soil carbon (C) cycling and soil fertility of paddy field. There had close relationship between functional cellulose genes (cbhI and GH48) with characterize of soil organic matter chemical components (fulvic acid and humic acid) and soil physical fractions. However, there is still limited information about how functional cellulose degradation response to long-term fertilizer management and their relative importance for C sequestration under the double-cropping rice paddy field in southern of China. Therefore, the objective of this study were investigated the effects of 34-years long-term fertilizer regime on community abundance of cbhI and GH48 genes in five soil particle-size fractions (> 2000 μm, 2000–200 μm, 200–50 μm, 50–2 μm and 2–0.1 μm) by using polarization magic angle spinning 13C nuclear magnetic resonance spectroscopy. The field experiment was included four different fertilizer treatments: chemical fertilizer alone (MF), rice straw and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). The results showed that distribution of soil humus and cellulolytic microbial community abundance was significant increased under long-term application of crop residue and organic manure condition. And the FA, HA and HM C contents in > 2000 μm and 2000–50 μm fractions with MF, RF and OM treatments were significant higher than that of CK treatment. Meanwhile, the alkyl C and Oalkyl C groups of FA and HA in > 2000 μm fraction with MF, RF, OM and CK treatments were higher than that of the other fractions. There had higher AL% and lower ARO% of FA and HA in different particle-size fractions with MF, RF, OM and CK treatments. The results indicated that abundance of cbhI and GH48 genes in different particle-size fractions with RF and OM treatments were significant increased, compared with CK treatment. There had significant positive correlation between soil humus C components (FA and HA) with abundance of cbhI and GH48 genes, and the o-alkyl C and AL% of FA were positively correlated with abundance of cbhI and GH48 genes. As a result, the community abundance of cbhI and GH48 genes were significant increased under combined application of crop residue and organic manure with chemical fertilizer condition.
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8
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Ibrahim E, Mahmoud A, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Kinetics and thermodynamics of thermal inactivation for recombinant Escherichia coli cellulases, cel12B, cel8C, and polygalacturonase, peh28; biocatalysts for biofuel precursor production. J Biochem 2021; 169:109-117. [PMID: 32810224 DOI: 10.1093/jb/mvaa097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/11/2020] [Indexed: 11/13/2022] Open
Abstract
Lignocellulosic biomass conversion using cellulases/polygalacturonases is a process that can be progressively influenced by several determinants involved in cellulose microfibril degradation. This article focuses on the kinetics and thermodynamics of thermal inactivation of recombinant Escherichia coli cellulases, cel12B, cel8C and a polygalacturonase, peh 28, derived from Pectobacterium carotovorum sub sp. carotovorum. Several consensus motifs conferring the enzymes' thermal stability in both cel12B and peh28 model structures have been detailed earlier, which were confirmed for the three enzymes through the current study of their thermal inactivation profiles over the 20-80°C range using the respective activities on carboxymethylcellulose and polygalacturonic acid. Kinetic constants and half-lives of thermal inactivation, inactivation energy, plus inactivation entropies, enthalpies and Gibbs free energies, revealed high stability, less conformational change and protein unfolding for cel12B and peh28 due to thermal denaturation compared to cel8C. The apparent thermal stability of peh28 and cel12B, along with their hydrolytic efficiency on a lignocellulosic biomass conversion as reported previously, makes these enzymes candidates for various industrial applications. Analysis of the Gibbs free energy values suggests that the thermal stabilities of cel12B and peh28 are entropy-controlled over the tested temperature range.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA.,Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Ahmed Mahmoud
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Kim D Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Keith E Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Ebtesam N Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Patrick L Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Jean M Escudero
- Department of Basic Sciences, St. Louis College of Pharmacy, St. Louis, MO 63110-1088, USA
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9
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Foroozandeh Shahraki M, Ariaeenejad S, Fallah Atanaki F, Zolfaghari B, Koshiba T, Kavousi K, Salekdeh GH. MCIC: Automated Identification of Cellulases From Metagenomic Data and Characterization Based on Temperature and pH Dependence. Front Microbiol 2020; 11:567863. [PMID: 33193158 PMCID: PMC7645119 DOI: 10.3389/fmicb.2020.567863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/30/2020] [Indexed: 01/03/2023] Open
Abstract
As the availability of high-throughput metagenomic data is increasing, agile and accurate tools are required to analyze and exploit this valuable and plentiful resource. Cellulose-degrading enzymes have various applications, and finding appropriate cellulases for different purposes is becoming increasingly challenging. An in silico screening method for high-throughput data can be of great assistance when combined with the characterization of thermal and pH dependence. By this means, various metagenomic sources with high cellulolytic potentials can be explored. Using a sequence similarity-based annotation and an ensemble of supervised learning algorithms, this study aims to identify and characterize cellulolytic enzymes from a given high-throughput metagenomic data based on optimum temperature and pH. The prediction performance of MCIC (metagenome cellulase identification and characterization) was evaluated through multiple iterations of sixfold cross-validation tests. This tool was also implemented for a comparative analysis of four metagenomic sources to estimate their cellulolytic profile and capabilities. For experimental validation of MCIC’s screening and prediction abilities, two identified enzymes from cattle rumen were subjected to cloning, expression, and characterization. To the best of our knowledge, this is the first time that a sequence-similarity based method is used alongside an ensemble machine learning model to identify and characterize cellulase enzymes from extensive metagenomic data. This study highlights the strength of machine learning techniques to predict enzymatic properties solely based on their sequence. MCIC is freely available as a python package and standalone toolkit for Windows and Linux-based operating systems with several functions to facilitate the screening and thermal and pH dependence prediction of cellulases.
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Affiliation(s)
- Mehdi Foroozandeh Shahraki
- Laboratory of Complex Biological Systems and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Behrouz Zolfaghari
- Computer Science and Engineering Department, Indian Institute of Technology Guwahati, Guwahati, India
| | - Takeshi Koshiba
- Department of Mathematics, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization, Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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10
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Lutz S, Thuerig B, Oberhaensli T, Mayerhofer J, Fuchs JG, Widmer F, Freimoser FM, Ahrens CH. Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics. Front Microbiol 2020; 11:1810. [PMID: 32849417 PMCID: PMC7406687 DOI: 10.3389/fmicb.2020.01810] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protective effect. Yet, the targeted use of composts against soil-borne diseases is hampered by the unpredictability of the efficacy. Several studies have identified and/or isolated beneficial microorganisms (i.e., bacteria, oomycetes, and fungi) from disease suppressive composts capable of suppressing pathogens (e.g., Pythium and Fusarium) in various crops (e.g., tomato, lettuce, and cucumber), and some of them have been developed into commercial products. Yet, there is growing evidence that synthetic or complex microbial consortia can be more effective in controlling diseases than single strains, but the underlying molecular mechanisms are poorly understood. Currently, a major bottleneck concerns the lack of functional assays to identify the most potent beneficial microorganisms and/or key microbial consortia from complex soil and compost microbiomes, which can harbor tens of thousands of species. This focused review describes microorganisms, which have been isolated from, amended to or found to be abundant in disease-suppressive composts and for which a beneficial effect has been documented. We point out opportunities to increasingly harness compost microbiomes for plant protection through an integrated systems approach that combines the power of functional assays to isolate biocontrol and plant growth promoting strains and further prioritize them, with functional genomics approaches that have been successfully applied in other fields of microbiome research. These include detailed metagenomics studies (i.e., amplicon and shotgun sequencing) to achieve a better understanding of the complex system compost and to identify members of taxa enriched in suppressive composts. Whole-genome sequencing and complete assembly of key isolates and their subsequent functional profiling can elucidate the mechanisms of action of biocontrol strains. Integrating the benefits of these approaches will bring the long-term goals of employing microorganisms for a sustainable control of plant pathogens and developing reliable diagnostic assays to assess the suppressiveness of composts within reach.
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Affiliation(s)
- Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Barbara Thuerig
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | - Thomas Oberhaensli
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | | | - Jacques G Fuchs
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | - Franco Widmer
- Agroscope, Research Group Molecular Ecology, Zurich, Switzerland
| | - Florian M Freimoser
- Agroscope, Research Group Phytopathology and Zoology in Fruit and Vegetable Production, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
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11
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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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12
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Sahoo K, Sahoo RK, Gaur M, Subudhi E. Cellulolytic thermophilic microorganisms in white biotechnology: a review. Folia Microbiol (Praha) 2019; 65:25-43. [DOI: 10.1007/s12223-019-00710-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
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13
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Slabu I, Galman JL, Lloyd RC, Turner NJ. Discovery, Engineering, and Synthetic Application of Transaminase Biocatalysts. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02686] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Iustina Slabu
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - James L. Galman
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Richard C. Lloyd
- Dr.
Reddy’s Laboratories, Chirotech Technology Centre, CB4 0PE Cambridge, United Kingdom
| | - Nicholas J. Turner
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
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14
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Tian X, Yang T, He J, Chu Q, Jia X, Huang J. Fungal community and cellulose-degrading genes in the composting process of Chinese medicinal herbal residues. BIORESOURCE TECHNOLOGY 2017; 241:374-383. [PMID: 28578278 DOI: 10.1016/j.biortech.2017.05.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
The fungal community and the population of 16S rRNA, 18S rRNA and cellulose-degrading genes during the 30-day composting process of Chinese medicinal herbal residues were investigated using Illumina MiSeq and quantitative real-time PCR. An obvious succession of fungal communities occurred during the composting process. Unidentified fungi predominated in the raw materials. As composting progressed, Ascomycota became the most dominant phylum, with Aspergillus being the most dominant genus, and Aspergillus fumigatus making up 99.65% of that genus. Because of the inoculation of cellulolytic fungi in the mature stage, the cellulose degradation rate in inoculation groups was faster and the relative abundances of Aspergillus and the glycoside hydrolase family 7 genes were significantly higher than those in the control groups. These indicated that the fungal inoculants facilitated the degradation of cellulose, increased cellulolytic fungi and optimized the community structure.
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Affiliation(s)
- Xueping Tian
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Tao Yang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Jingzhong He
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Qian Chu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Xiaojun Jia
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Jun Huang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
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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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16
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Ibrahim E, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:52. [PMID: 28413443 PMCID: PMC5327597 DOI: 10.1186/s13068-017-0732-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The high crystallinity of cellulosic biomass myofibrils as well as the complexity of their intermolecular structure is a significant impediment for biofuel production. Cloning of celB-, celC-encoded cellulases (cel12B and cel8C) and peh-encoded polygalacturonase (peh28) from Pectobacterium carotovorum subsp. carotovorum (Pcc) was carried out in our previous study using Escherichia coli as a host vector. The current study partially characterizes the enzymes' molecular structures as well as their catalytic performance on different substrates which can be used to improve their potential for lignocellulosic biomass conversion. RESULTS β-Jelly roll topology, (α/α)6 antiparallel helices and right-handed β-helices were the folds identified for cel12B, cel8C, and peh28, respectively, in their corresponding protein model structures. Purifications of 17.4-, 6.2-, and 6.0-fold, compared to crude extract, were achieved for cel12B and cel8C, and peh28, respectively, using specific membrane ultrafiltrations and size-exclusion chromatography. Avicel and carboxymethyl cellulose (CMC) were substrates for cel12B, whereas for cel8C catalytic activity was only shown on CMC. The enzymes displayed significant synergy on CMC but not on Avicel when tested for 3 h at 45 °C. No observed β-glucosidase activities were identified for cel8C and cel12B when tested on p-nitrophenyl-β-d-glucopyranoside. Activity stimulation of 130% was observed when a recombinant β-glucosidase from Pcc was added to cel8C and cel12B as tested for 3 h at 45 °C. Optimum temperature and pH of 45 °C and 5.4, respectively, were identified for all three enzymes using various substrates. Catalytic efficiencies (kcat/Km) were calculated for cel12B and cel8C on CMC as 0.141 and 2.45 ml/mg/s respectively, at 45 °C and pH 5.0 and for peh28 on polygalacturonic acid as 4.87 ml/mg/s, at 40 °C and pH 5.0. Glucose and cellobiose were the end-products identified for cel8C, cel12B, and β-glucosidase acting together on Avicel or CMC, while galacturonic acid and other minor co-products were identified for peh28 action on pectin. CONCLUSIONS This study provides some insight into which parameters should be optimized when application of cel8C, cel12B, and peh28 to biomass conversion is the goal.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Kim D. Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Keith E. Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4 Canada
| | - Ebtesam N. Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Patrick L. Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Jean M. Escudero
- Department of Basic Science, St. Louis College of Pharmacy, St. Louis, MO 63110-1088 USA
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17
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Ghosh S, Kuisiene N, Cheeptham N. The cave microbiome as a source for drug discovery: Reality or pipe dream? Biochem Pharmacol 2016; 134:18-34. [PMID: 27867014 DOI: 10.1016/j.bcp.2016.11.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/15/2016] [Indexed: 01/04/2023]
Abstract
This review highlights cave habitats, cave microbiomes and their potential for drug discovery. Such studies face many challenges, including access to remote and pristine caves, and sample collection and transport. Inappropriate physical and chemical growth conditions in the laboratory for the isolation and cultivation of cave microorganisms pose many complications including length of cultivation; some cave microorganisms can take weeks and even months to grow. Additionally, DNA extraction from cave environmental samples may be difficult due to the high concentration of various minerals that are natural DNA blocking agents. Once cave microorganisms are grown in the lab, other problems often arise, such as maintenance of pure culture, consistency of antimicrobial activity and fermentation conditions for antimicrobial production. In this review, we suggest that, although based on what has been done in the field, there is potential in using cave microorganisms to produce antimicrobial agents, one needs to be highly committed and prepared.
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Affiliation(s)
- Soumya Ghosh
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Nomeda Kuisiene
- Department of Microbiology and Biotechnology, Vilnius University, Lithuania
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada.
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18
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Zhao Y, Lu Q, Wei Y, Cui H, Zhang X, Wang X, Shan S, Wei Z. Effect of actinobacteria agent inoculation methods on cellulose degradation during composting based on redundancy analysis. BIORESOURCE TECHNOLOGY 2016; 219:196-203. [PMID: 27494100 DOI: 10.1016/j.biortech.2016.07.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/23/2016] [Accepted: 07/27/2016] [Indexed: 06/06/2023]
Abstract
In this study, actinobacteria agent including Streptomyces sp. and Micromonospora sp. were inoculated during chicken manure composting by different inoculation methods. The effect of different treatments on cellulose degradation and the relationship between inoculants and indigenous actinobacteria were investigated during composting. The results showed that inoculation in different stages of composting all improved the actinobacteria community diversity particularly in the cooling stage of composting (M3). Moreover, inoculation could distinctly accelerate the degradation of organic matters (OM) especially celluloses. Redundancy analysis indicated that the correlation between indigenous actinobacteria and degradation of OM and cellulose were regulated by inoculants and there were significant differences between different inoculation methods. Furthermore, synergy between indigenous actinobacteria and inoculants for degradation of OM and cellulose in M3 was better than other treatments. Conclusively, we suggested an inoculation method to regulate the indigenous actinobacteria based on the relationship between inoculants and indigenous actinobacteria and degradation content.
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Affiliation(s)
- Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Qian Lu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yuquan Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Hongyang Cui
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xu Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xueqin Wang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Si Shan
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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Jeffries JWE, Dawson N, Orengo C, Moody TS, Quinn DJ, Hailes HC, Ward JM. Metagenome Mining: A Sequence Directed Strategy for the Retrieval of Enzymes for Biocatalysis. ChemistrySelect 2016. [DOI: 10.1002/slct.201600515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jack W. E. Jeffries
- Department of Biochemical Engineering; University College London, Bernard Katz Building; Gordon Street London WC1H 0AH UK
| | - Natalie Dawson
- Department of Structural and Molecular Biology; University College London; Gower Street WC1E 6BT UK
| | - Christine Orengo
- Department of Structural and Molecular Biology; University College London; Gower Street WC1E 6BT UK
| | - Thomas S. Moody
- Department of Biocatalysis and Isotope Chemistry; Almac; 20 Seagoe Industrial Estate Craigavon Northern Ireland (UK
| | - Derek J. Quinn
- Department of Biocatalysis and Isotope Chemistry; Almac; 20 Seagoe Industrial Estate Craigavon Northern Ireland (UK
| | - Helen C. Hailes
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | - John M. Ward
- Department of Biochemical Engineering; University College London, Bernard Katz Building; Gordon Street London WC1H 0AH UK
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20
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A Metagenomic Advance for the Cloning and Characterization of a Cellulase from Red Rice Crop Residues. Molecules 2016; 21:molecules21070831. [PMID: 27347917 PMCID: PMC6274478 DOI: 10.3390/molecules21070831] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 01/28/2023] Open
Abstract
Many naturally-occurring cellulolytic microorganisms are not readily cultivable, demanding a culture-independent approach in order to study their cellulolytic genes. Metagenomics involves the isolation of DNA from environmental sources and can be used to identify enzymes with biotechnological potential from uncultured microbes. In this study, a gene encoding an endoglucanase was cloned from red rice crop residues using a metagenomic strategy. The amino acid identity between this gene and its closest published counterparts is lower than 70%. The endoglucanase was named EglaRR01 and was biochemically characterized. This recombinant protein showed activity on carboxymethylcellulose, indicating that EglaRR01 is an endoactive lytic enzyme. The enzymatic activity was optimal at a pH of 6.8 and at a temperature of 30 °C. Ethanol production from this recombinant enzyme was also analyzed on EglaRR01 crop residues, and resulted in conversion of cellulose from red rice into simple sugars which were further fermented by Saccharomyces cerevisiae to produce ethanol after seven days. Ethanol yield in this study was approximately 8 g/L. The gene found herein shows strong potential for use in ethanol production from cellulosic biomass (second generation ethanol).
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21
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Yu C, Reddy AP, Simmons CW, Simmons BA, Singer SW, VanderGheynst JS. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:206. [PMID: 26633993 PMCID: PMC4667496 DOI: 10.1186/s13068-015-0392-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. RESULTS High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. CONCLUSIONS A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.
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Affiliation(s)
- Chaowei Yu
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Amitha P. Reddy
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
| | - Christopher W. Simmons
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Department of Food Science and Technology, University of California, Davis, CA 95616 USA
| | - Blake A. Simmons
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551 USA
| | - Steven W. Singer
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jean S. VanderGheynst
- />Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
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22
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Biocatalysts for biomass deconstruction from environmental genomics. Curr Opin Chem Biol 2015; 29:18-25. [DOI: 10.1016/j.cbpa.2015.06.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023]
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23
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Kathiravan MN, Gim GH, Ryu J, Kim PI, Lee CW, Kim SW. Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil. J Microbiol 2015; 53:767-75. [DOI: 10.1007/s12275-015-5454-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/02/2015] [Accepted: 10/02/2015] [Indexed: 11/29/2022]
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Montella S, Amore A, Faraco V. Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development. Crit Rev Biotechnol 2015; 36:998-1009. [PMID: 26381035 DOI: 10.3109/07388551.2015.1083939] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.
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Affiliation(s)
- Salvatore Montella
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Antonella Amore
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Vincenza Faraco
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
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25
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Zhang X, Zhong Y, Yang S, Zhang W, Xu M, Ma A, Zhuang G, Chen G, Liu W. Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production. BIORESOURCE TECHNOLOGY 2014; 170:183-195. [PMID: 25129234 DOI: 10.1016/j.biortech.2014.07.093] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 05/05/2023]
Abstract
The development of communities of three important composting players including actinobacteria, fungi and clostridia was explored during the composting of wheat straw for mushroom production. The results revealed the presence of highly diversified actinobacteria and fungal communities during the composting process. The diversity of the fungal community, however, sharply decreased in the mature compost. Furthermore, an apparent succession of both actinobacteria and fungi with intensive changes in the composition of communities was demonstrated during composting. Notably, cellulolytic actinomycetal and fungal genera represented by Thermopolyspora, Microbispora and Humicola were highly enriched in the mature compost. Analysis of the key cellulolytic genes revealed their prevalence at different composting stages including several novel glycoside hydrolase family 48 exocellulase lineages. The community of cellulolytic microbiota also changed substantially over time. The prevalence of the diversified cellulolytic microorganisms holds the great potential of mining novel lignocellulose decomposing enzymes from this specific ecosystem.
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Affiliation(s)
- Xi Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China.
| | - Shida Yang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Meiqing Xu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Anzhou Ma
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, No. 85, Shuangqing Road, Beijing, PR China
| | - Guoqiang Zhuang
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, No. 85, Shuangqing Road, Beijing, PR China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China.
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Abstract
Metagenomics deals with the isolation of genetic material directly recovered from environmental samples. Metagenomics as an approach has emerged over the past two decades to elucidate a host of microbial communities inhabiting a specific niche with the goal of understanding their genetic diversity, population structure, and ecological role played by them. A number of new and novel molecules with significant functionalities and applications have been identified through this approach. In fact, many investigators are engaged in this field to unlock the untapped genetic resources with funding from governments sector. The sustainable economic future of modern industrialized societies requires the development of novel molecules, enzymes, processes, products, and applications. Metagenomics can also be applied to solve practical challenges in the field of medicine, agriculture, sustainability, and ecology. Metagenomics promises to provide new molecules and novel enzymes with diverse functions and enhanced features compared to the enzymes from the culturable microorganisms. Besides the application of metagenomics for unlocking novel biocatalysts from nature, it also has found applications in fields as diverse as bioremediation, personalized medicine, xenobiotic metabolism, and so forth.
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27
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Wang SD, Guo GS, Li L, Cao LC, Tong L, Ren GH, Liu YH. Identification and characterization of an unusual glycosyltransferase-like enzyme with β-galactosidase activity from a soil metagenomic library. Enzyme Microb Technol 2014; 57:26-35. [DOI: 10.1016/j.enzmictec.2014.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/13/2014] [Accepted: 01/16/2014] [Indexed: 11/25/2022]
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28
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Mehta CM, Palni U, Franke-Whittle IH, Sharma AK. Compost: its role, mechanism and impact on reducing soil-borne plant diseases. WASTE MANAGEMENT (NEW YORK, N.Y.) 2014; 34:607-22. [PMID: 24373678 DOI: 10.1016/j.wasman.2013.11.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/28/2013] [Accepted: 11/28/2013] [Indexed: 05/14/2023]
Abstract
Soil-borne plant pathogens are responsible for causing many crop plant diseases, resulting in significant economic losses. Compost application to agricultural fields is an excellent natural approach, which can be taken to fight against plant pathogens. The application of organic waste products is also an environmentally friendly alternative to chemical use, which unfortunately is the most common approach in agriculture today. This review analyses pioneering and recent compost research, and also the mechanisms and mode of action of compost microbial communities for reducing the activity of plant pathogens in agricultural crops. In addition, an approach for improving the quality of composts through the microbial communities already present in the compost is presented. Future agricultural practices will almost definitely require integrated research strategies to help combat plant diseases.
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Affiliation(s)
- C M Mehta
- Department of Biological Sciences, College of Basic Science and Humanities, G. B. P. U. A. & T. Pantnagar, U.S. Nagar, Uttarakhand, India; Department of Botany, D.S.B. Campus, Kumaun University Nainital, Uttarakhand, India
| | - Uma Palni
- Department of Botany, D.S.B. Campus, Kumaun University Nainital, Uttarakhand, India
| | - I H Franke-Whittle
- Leopold-Franzens University, Institute of Microbiology, Technikerstraße 25, 6020 Innsbruck, Austria
| | - A K Sharma
- Department of Biological Sciences, College of Basic Science and Humanities, G. B. P. U. A. & T. Pantnagar, U.S. Nagar, Uttarakhand, India.
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