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Hussain A, Parveen F, Saxena A, Ashfaque M. A review of nanotechnology in enzyme cascade to address challenges in pre-treating biomass. Int J Biol Macromol 2024; 270:132466. [PMID: 38761904 DOI: 10.1016/j.ijbiomac.2024.132466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]
Abstract
Nanotechnology has become a revolutionary technique for improving the preliminary treatment of lignocellulosic biomass in the production of biofuels. Traditional methods of pre-treatment have encountered difficulties in effectively degrading the intricate lignocellulosic composition, thereby impeding the conversion of biomass into fermentable sugars. Nanotechnology has enabled the development of enzyme cascade processes that present a potential solution for addressing the limitations. The focus of this review article is to delve into the utilization of nanotechnology in the pretreatment of lignocellulosic biomass through enzyme cascade processes. The review commences with an analysis of the composition and structure of lignocellulosic biomass, followed by a discussion on the drawbacks associated with conventional pre-treatment techniques. The subsequent analysis explores the importance of efficient pre-treatment methods in the context of biofuel production. We thoroughly investigate the utilization of nanotechnology in the pre-treatment of enzyme cascades across three distinct sections. Nanomaterials for enzyme immobilization, enhanced enzyme stability and activity through nanotechnology, and nanocarriers for controlled enzyme delivery. Moreover, the techniques used to analyse nanomaterials and the interactions between enzymes and nanomaterials are introduced. This review emphasizes the significance of comprehending the mechanisms underlying the synergy between nanotechnology and enzymes establishing sustainable and environmentally friendly nanotechnology applications.
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Affiliation(s)
- Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
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2
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Braga LPP, Pereira RV, Martins LF, Moura LMS, Sanchez FB, Patané JSL, da Silva AM, Setubal JC. Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC Genomics 2021; 22:652. [PMID: 34507539 PMCID: PMC8434746 DOI: 10.1186/s12864-021-07957-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. RESULTS Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. CONCLUSIONS The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.
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Affiliation(s)
- Lucas Palma Perez Braga
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Livia Maria Silva Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Beltrame Sanchez
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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3
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Kuntothom T, Cairns JK. Expression and characterization of TbCel12A, a thermophilic endoglucanase with potential in biomass hydrolysis. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Zhu Z, Qu J, Yu L, Jiang X, Liu G, Wang L, Qu Y, Qin Y. Three glycoside hydrolase family 12 enzymes display diversity in substrate specificities and synergistic action between each other. Mol Biol Rep 2019; 46:5443-5454. [PMID: 31359382 DOI: 10.1007/s11033-019-04999-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/23/2019] [Indexed: 12/01/2022]
Abstract
PoCel12A, PoCel12B, and PoCel12C are genes that encode glycoside hydrolase family 12 (GH12) enzymes in Penicillium oxalicum. PoCel12A and PoCel12B are typical GH12 enzymes that belong to fungal subfamilies 12-1 and 12-2, respectively. PoCel12C contains a low-complexity region (LCR) domain, which is not found in PoCel12A or PoCel12B and independent of fungal subfamily 12-1 or 12-2. Recombinant enzymes (named rCel12A, rCel12B and rCel12C) demonstrate existing diversity in the substrate specificities. Although most members in GH family 12 are typical endoglucanases and preferentially hydrolyze β-1,4-glucan (e.g., carboxymethylcellulose), recombinant PoCel12A is a non-typical endo-(1-4)-β-glucanase; it preferentially hydrolyzes mix-linked β-glucan (barley β-glucan, β-1,3-1,4-glucan) and slightly hydrolyzes β-1,4-glucan (carboxymethylcellulose). Recombinant PoCel12B possesses a significantly high activity against xyloglucan. A specific activity of rCel12B toward xyloglucan (239 µmol/min/mg) is the second-highest value known. Recombinant PoCel12C shows low activity toward β-glucan, carboxymethylcellulose, or xyloglucan. All three enzymes can degrade phosphoric acid-swollen cellulose (PASC). However, the hydrolysis products toward PASC by enzymes are different: the main hydrolysis products are cellotriose, cellotetraose, and cellobiose for rCel12A, rCel12B, and rCel12C, correspondingly. A synergistic action toward PASC among rCel12A and rCel12B is observed, thereby suggesting a potential application for preparing enzyme cocktails used in lignocellulose hydrolysis.
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Affiliation(s)
- Zhu Zhu
- National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.,State Key Lab of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Jingyao Qu
- National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.,State Key Lab of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Lele Yu
- National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.,State Key Lab of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.,Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash Biomedicine Discovery Institute, Monash University, Melbourne, 3800, Australia
| | - Guodong Liu
- National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.,State Key Lab of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Lushan Wang
- National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Yinbo Qu
- National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.,State Key Lab of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China. .,State Key Lab of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.
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5
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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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6
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Bohra V, Dafale NA, Hathi Z, Purohit HJ. Genomic annotation and validation of bacterial consortium NDMC-1 for enhanced degradation of sugarcane bagasse. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01462-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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7
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Qu W, Lin D, Zhang Z, Di W, Gao B, Zeng R. Metagenomics Investigation of Agarlytic Genes and Genomes in Mangrove Sediments in China: A Potential Repertory for Carbohydrate-Active Enzymes. Front Microbiol 2018; 9:1864. [PMID: 30177916 PMCID: PMC6109693 DOI: 10.3389/fmicb.2018.01864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/25/2018] [Indexed: 12/31/2022] Open
Abstract
Monosaccharides and oligosaccharides produced by agarose degradation exhibit potential in the fields of bioenergy, medicine, and cosmetics. Mangrove sediments (MGSs) provide a special environment to enrich enzymes for agarose degradation. However, representative investigations of the agarlytic genes in MGSs have been rarely reported. In this study, agarlytic genes in MGSs were researched in detail from the aspects of diversity, abundance, activity, and location through deep metagenomics sequencing. Functional genes in MGSs were usually incomplete but were shown as results, which could cause virtually high number of results in previous studies because multiple fragmented sequences could originate from the same genes. In our work, only complete and nonredundant (CNR) genes were analyzed to avoid virtually high amount of the results. The number of CNR agarlytic genes in our datasets was significantly higher than that in the datasets of previous studies. Twenty-one recombinant agarases with agarose-degrading activity were detected using heterologous expression based on numerous complete open-reading frames, which are rarely obtained in metagenomics sequencing of samples with complex microbial communities, such as MGSs. Aga2, which had the highest crude enzyme activity among the 21 recombinant agarases, was further purified and subjected to enzymatic characterization. With its high agarose-degrading activity, resistance to temperature changes and chemical agents, Aga2 could be a suitable option for industrial production. The agarase ratio with signal peptides to that without signal peptides in our MGS datasets was lower than that of other reported agarases. Six draft genomes, namely, Clusters 1-6, were recovered from the datasets. The taxonomic annotation of these genomes revealed that Clusters 1, 3, 5, and 6 were annotated as Desulfuromonas sp., Treponema sp., Ignavibacteriales spp., and Polyangiaceae spp., respectively. Meanwhile, Clusters 2 and 4 were potential new species. All these genomes were first reported and found to have abilities of degrading various important polysaccharides. The metabolic pathway of agarose in Cluster 4 was also speculated. Our results showed the capacity and activity of agarases in the MGS microbiome, and MGSs exert potential as a repertory for mining not only agarlytic genes but also almost all genes of the carbohydrate-active enzyme family.
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Affiliation(s)
- Wu Qu
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Dan Lin
- Novogene Bioinformatics Technology Co. Ltd., Tianjin, China
| | - Zhouhao Zhang
- Novogene Bioinformatics Technology Co. Ltd., Tianjin, China
| | - Wenjie Di
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Boliang Gao
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Runying Zeng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.,Key Laboratory of Marine Genetic Resources, Xiamen, China
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8
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Conway JM, Crosby JR, Hren AP, Southerland RT, Lee LL, Lunin VV, Alahuhta P, Himmel ME, Bomble YJ, Adams MWW, Kelly RM. Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic
Caldicellulosiruptor
species. AIChE J 2018. [DOI: 10.1002/aic.16354] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jonathan M. Conway
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | - James R. Crosby
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | - Andrew P. Hren
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | - Robert T. Southerland
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | - Laura L. Lee
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
| | | | - Petri Alahuhta
- Biosciences CenterNational Renewable Energy LaboratoryGoldenCO80401
| | | | | | - Michael W. W. Adams
- Dept. of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGA30602
| | - Robert M. Kelly
- Dept. of Chemical and Biomolecular EngineeringNorth Carolina State UniversityRaleighNC27695
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9
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Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. PLoS One 2017; 12:e0189604. [PMID: 29281693 PMCID: PMC5744941 DOI: 10.1371/journal.pone.0189604] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 12/03/2022] Open
Abstract
Efficient deconstruction of plant biomass is a major barrier to the development of viable lignocellulosic biofuels. Pretreatment with ionic liquids reduces lignocellulose recalcitrance to enzymatic hydrolysis, increasing yields of sugars for conversion into biofuels. However, commercial cellulases are not compatible with many ionic liquids, necessitating extensive water washing of pretreated biomass prior to hydrolysis. To circumvent this issue, previous research has demonstrated that several thermophilic bacterial cellulases can efficiently deconstruct lignocellulose in the presence of the ionic liquid, 1-ethyl-3-methylimadizolium acetate. As promising as these enzymes are, they would need to be produced at high titer in an industrial enzyme production host before they could be considered a viable alternative to current commercial cellulases. Aspergillus niger has been used to produce high titers of secreted enzymes in industry and therefore, we assessed the potential of this organism to be used as an expression host for these ionic liquid-tolerant cellulases. We demonstrated that 29 of these cellulases were expressed at detectable levels in a wild-type strain of A. niger, indicating a basic level of compatibility and potential to be produced at high levels in a host engineered to produce high titers of enzymes. We then profiled one of these enzymes in detail, the β-glucosidase A5IL97, and compared versions expressed in both A. niger and Escherichia coli. This comparison revealed the enzymatic activity of A5IL97 purified from E. coli and A. niger is equivalent, suggesting that A. niger could be an excellent enzyme production host for enzymes originally characterized in E. coli, facilitating the transition from the laboratory to industry.
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10
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Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW. A bacterial pioneer produces cellulase complexes that persist through community succession. Nat Microbiol 2017; 3:99-107. [PMID: 29109478 PMCID: PMC6794216 DOI: 10.1038/s41564-017-0052-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022]
Abstract
Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, ‘Candidatus Reconcilibacillus cellulovorans’, possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the ‘Ca. Reconcilibacillus cellulovorans’ multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology. Cultivation of a cellulolytic consortium reveals successional community dynamics and the presence of multidomain glycoside hydrolases assembled into stable complexes distinct from cellulosomes, which are produced by a potential pioneer population.
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Affiliation(s)
- Sebastian Kolinko
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Evelyn Denzel
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Jennifer Hiras
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Corning Incorporated, Corning, NY, USA
| | - Raphael Gabriel
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Bäcker
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephanie A Eichorst
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network "Chemistry meets Microbiology", University of Vienna, Vienna, Austria
| | - Dario Frey
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Qiushi Chen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Todd R Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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11
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Lemos LN, Pereira RV, Quaggio RB, Martins LF, Moura LMS, da Silva AR, Antunes LP, da Silva AM, Setubal JC. Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting. Front Microbiol 2017; 8:644. [PMID: 28469608 PMCID: PMC5395642 DOI: 10.3389/fmicb.2017.00644] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/29/2017] [Indexed: 11/22/2022] Open
Abstract
Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source. The microbial community composition of this consortium was investigated by shotgun metagenomics and genome-centric analysis. Six near-complete (over 90%) genomes were reconstructed. Similarity and phylogenetic analyses show that four of these six genomes are novel, with the following hypothesized identifications: a new Thermobacillus species; the first Bacillus thermozeamaize genome (for which currently only 16S sequences are available) or else the first representative of a new family in the Bacillales order; the first representative of a new genus in the Paenibacillaceae family; and the first representative of a new deep-branching family in the Clostridia class. The reconstructed genomes from known species were identified as Geobacillus thermoglucosidasius and Caldibacillus debilis. The metabolic potential of these recovered genomes based on COG and CAZy analyses show that these genomes encode several glycoside hydrolases (GHs) as well as other genes related to lignocellulose breakdown. The new Thermobacillus species stands out for being the richest in diversity and abundance of GHs, possessing the greatest potential for biomass degradation among the six recovered genomes. We also investigated the presence and activity of the organisms corresponding to these genomes in the composting operation from which the consortium was built, using compost metagenome and metatranscriptome datasets generated in a previous study. We obtained strong evidence that five of the six recovered genomes are indeed present and active in that composting process. We have thus discovered three (perhaps four) new thermophillic bacterial species that add to the increasing repertoire of known lignocellulose degraders, whose biotechnological potential can now be investigated in further studies.
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Affiliation(s)
- Leandro N Lemos
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São PauloSão Paulo, Brazil
| | - Roberta V Pereira
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Ronaldo B Quaggio
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Layla F Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Livia M S Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São PauloSão Paulo, Brazil
| | - Amanda R da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São PauloSão Paulo, Brazil
| | - Luciana P Antunes
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Aline M da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil.,Biocomplexity Institute, Virginia TechBlacksburg, VA, USA
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