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Shamshitov A, Kadžienė G, Supronienė S. The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management. PLANTS (BASEL, SWITZERLAND) 2024; 13:766. [PMID: 38592825 PMCID: PMC10974107 DOI: 10.3390/plants13060766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
The global escalation in cereal production, essential to meet growing population demands, simultaneously augments the generation of cereal crop residues, estimated annually at approximately 3107 × 106 Mg/year. Among different crop residue management approaches, returning them to the soil can be essential for various ecological benefits, including nutrient recycling and soil carbon sequestration. However, the recalcitrant characteristics of cereal crop residues pose significant challenges in their management, particularly in the decomposition rate. Therefore, in this review, we aim to summarize the influence of different agricultural practices on enhancing soil microbial decomposer communities, thereby effectively managing cereal crop residues. Moreover, this manuscript provides indirect estimates of cereal crop residue production in Northern Europe and Lithuania, and highlights the diverse roles of lignocellulolytic microorganisms in the decomposition process, with a particular focus on enzymatic activities. This review bridges the knowledge gap and indicates future research directions concerning the influence of agricultural practices on cereal crop residue-associated microbial consortia.
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Affiliation(s)
- Arman Shamshitov
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
| | - Gražina Kadžienė
- Department of Soil and Crop Management, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania
| | - Skaidrė Supronienė
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
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Santos-Pereira C, Sousa J, Costa ÂMA, Santos AO, Rito T, Soares P, Franco-Duarte R, Silvério SC, Rodrigues LR. Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12627-9. [PMID: 37417976 PMCID: PMC10390414 DOI: 10.1007/s00253-023-12627-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. KEY POINTS: • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.
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Affiliation(s)
- Cátia Santos-Pereira
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Joana Sousa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Ângela M A Costa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Andréia O Santos
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Teresa Rito
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro Soares
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sara C Silvério
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal.
| | - Lígia R Rodrigues
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
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Chen Y, Li J, Zhao T, Zhang Y, Zhang L, Xu L. The temporal profile of GH 1 gene abundance and the shift in GH 1 cellulase-producing microbial communities during vermicomposting of corn stover and cow dung. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:84035-84045. [PMID: 37354300 DOI: 10.1007/s11356-023-28341-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023]
Abstract
Vermicomposting is a promising method for corn stover management to achieve bioresource recovery and environmental protection. Most β-glucosidases, which limit the cellulose degradation rate during vermicomposting of corn stover, belong to glycoside hydrolase family 1 (GH1). This study was conducted with different earthworm densities to quantify the GH1 gene abundance and investigate the evolution of GH1 cellulase-producing microbial communities using qPCR and pyrosequencing. The results showed that β-glucosidase activity, GH1 gene abundance, TOC, and microbial communities carrying the GH1 gene were affected by processing time and earthworm density. After introducing earthworms, β-glucosidase activity increased to 1.90-2.13 U/g from 0.54 U/g. The GH1 gene abundance of treatments with earthworms (5.82E+09-6.70E+09 copies/g) was significantly higher than that of treatments without earthworms (2.48E+09 copies/g) on Day 45. Earthworms increased the richness of microbial communities. The relative abundances of Sphingobium and Dyadobacter, which are dominant genera harboring the GH1 gene, were increased by earthworms to peak values of 23.90% and 11.20%, respectively. Correlation analysis showed that Sphingobium, Dyadobacter, Trichoderma, and Starkeya were positively associated with β-glucosidases. This work sheds new light on the mechanism of cellulose degradation during vermicomposting at the molecular level.
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Affiliation(s)
- Yuxiang Chen
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China
| | - Jiaolin Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China
| | - Tingting Zhao
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China
| | - Yan Zhang
- Costal Research and Extension Center, Mississippi State University, Mississippi, MS, 39567, USA
| | - Lei Zhang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China
| | - Lixin Xu
- College of Life Sciences, Jilin University, Changchun, 130012, China.
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Dixit M, Shukla P. Analysis of endoglucanases production using metatranscriptomics and proteomics approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:211-231. [PMID: 38220425 DOI: 10.1016/bs.apcsb.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The cellulases are among the most used enzyme in industries for various purposes. They add up to the green economy perspective and cost-effective production of enterprises. Biorefineries, paper industries, and textile industries are foremost in their usage. The production of endoglucanases from microorganisms is a valuable resource and can be exploited with the help of biotechnology. The present review provides some insight into the uses of endoglucanases in different industries and the potent fungal source of these enzymes. The advances in the enzyme technology has helped towards understanding some pathways to increase the production of industrial enzymes from microorganisms. The proteomics analysis and systems biology tools also help to identify these pathways for the enhanced production of such enzymes. This review deciphers the use of proteomics tools to analyze the potent microorganisms and identify suitable culture conditions to increase the output of endoglucanases. The review also includes the role of quantitative proteomics which is a powerful technique to get results faster and more timely. The role of metatranscriptomic approaches are also described which are helpful in the enzyme engineering for their efficient use under industrial conditions. Conclusively, this review helps to understand the challenges faced in the industrial use of endoglucanases and their further improvement.
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Affiliation(s)
- Mandeep Dixit
- Department of Botany, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India.
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Wang Y, Jiménez DJ, Zhang Z, van Elsas JD. Functioning of a tripartite lignocellulolytic microbial consortium cultivated under two shaking conditions: a metatranscriptomic study. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:54. [PMID: 36991472 DOI: 10.1186/s13068-023-02289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/25/2023] [Indexed: 03/30/2023]
Abstract
Abstract
Background
In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).
Results
The results indicated that, at 60 rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible (aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180 rpm, at 60 rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180 rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) β-xylosidase/β-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60 rpm.
Conclusions
We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.
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Zhang X, Chen X, Li S, Bello A, Liu J, Gao L, Fan Z, Wang S, Liu L, Ma B, Li H. Mechanism of differential expression of β-glucosidase genes in functional microbial communities in response to carbon catabolite repression. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:3. [PMID: 35418139 PMCID: PMC8756671 DOI: 10.1186/s13068-021-02101-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/29/2021] [Indexed: 11/10/2022]
Abstract
Abstract
Background
β-Glucosidase is the rate-limiting enzyme of cellulose degradation. It has been stipulated and established that β-glucosidase-producing microbial communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes. However, it is still unknown if this differential expression of functional microbial community happens accidentally or as a general regulatory mechanism, and of what biological significance it has. To investigate the composition and function of microbial communities and how they respond to different carbon metabolism pressures and the transcriptional regulation of functional genes, the different carbon metabolism pressure was constructed by setting up the static chamber during composting.
Results
The composition and function of functional microbial communities demonstrated different behaviors under the carbon metabolism pressure. Functional microbial community up-regulated glucose tolerant β-glucosidase genes expression to maintain the carbon metabolism rate by enhancing the transglycosylation activity of β-glucosidase to compensate for the decrease of hydrolysis activity under carbon catabolite repression (CCR). Micrococcales play a vital role in the resistance of functional microbial community under CCR. The transcription regulation of GH1 family β-glucosidase genes from Proteobacteria showed more obvious inhibition than other phyla under CCR.
Conclusion
Microbial functional communities differentially regulate the expression of glucose/non-glucose tolerant β-glucosidase genes under CCR, which is a general regulatory mechanism, not accidental. Furthermore, the differentially expressed β-glucosidase gene exhibited species characteristics at the phylogenetic level.
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Adeniyi A, Bello I, Mukaila T, Hammed A. A Review of Microbial Molecular Profiling during Biomass Valorization. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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Zhang X, Su E, Li S, Chen X, Fan Z, Liu M, Ma B, Li H. Molecular analyses of the diversity and function of the family 1 β-glucosidase-producing microbial community in compost. Can J Microbiol 2021; 67:713-723. [PMID: 33905664 DOI: 10.1139/cjm-2020-0576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The diversity and transcription efficiency of GH1 family β-glucosidase genes were investigated in natural and inoculated composts using a DNA clone library and real-time qPCR. Compositional differences were observed in the functional community between both composting processes. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla. Twenty representative β-glucosidase genes were quantitatively analyzed from DNA and RNA pools. Principal component analysis and Pearson's correlation analysis showed that cellulose degradation is correlated with the composition and succession of functional microbial communities, and this correlation was mainly observed in Proteobacteria and Actinobacteria. Compared with inoculated compost, the functional microbial communities in natural compost with a low diversity index exhibited weak buffering capacity for function in response to environmental changes. This may explain the consistency and dysfunction of cellulose degradation and transcriptional regulation by dominant β-glucosidase genes. Except for the β-glucosidase genes encoding constitutive enzymes, individual β-glucosidase genes responded to environmental changes more drastically than the group β-glucosidase genes. Correlation results suggested that β-glucosidase genes belonging to Micrococcales played an important role in the regulation of intracellular β-glucosidase. These results indicated that the responses of functional microorganisms were different during both composting processes, and were reflected at both the individual and group levels.
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Affiliation(s)
- Xinyue Zhang
- Northeast Agricultural University, 12430, Harbin, China;
| | - Erlie Su
- Northeast Agricultural University, 12430, Harbin, China;
| | - Shanshan Li
- Northeast Agricultural University, 12430, Harbin, China;
| | - Xiehui Chen
- Northeast Agricultural University, 12430, Harbin, China;
| | - Zhihua Fan
- Northeast Agricultural University, 12430, Harbin, China;
| | - Meiting Liu
- Northeast Agricultural University, 12430, Harbin, Harbin, China;
| | - Bo Ma
- Northeast Agricultural University, 12430, Harbin, China, 150030;
| | - Hongtao Li
- Northeast Agricultural University, 12430, Harbin, China, 150030;
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de Abreu VAC, Perdigão J, Almeida S. Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview. Front Genet 2021; 11:575592. [PMID: 33537056 PMCID: PMC7848172 DOI: 10.3389/fgene.2020.575592] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.
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Affiliation(s)
- Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - José Perdigão
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - Sintia Almeida
- Central de Genômica e Bioinformática (CeGenBio), Núcleo de Pesquisa e Desenvolvimento de Medicamentos (NPDM), Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, Brazil
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11
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A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases. Extremophiles 2021; 25:101-114. [PMID: 33416984 DOI: 10.1007/s00792-020-01214-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2020] [Indexed: 01/02/2023]
Abstract
Next-generation sequencing and computational biology have facilitated the implementation of new combinatorial screening approaches to discover novel enzymes of biotechnological interest. In this study, we describe the successful establishment of a multi-omic approach for the identification of thermostable hydrolase-encoding genes by determination of gene expression levels. We applied this combinatorial approach using an anaerobic enrichment culture from an Azorean hot spring sample grown on green coffee beans as recalcitrant substrate. An in-depth analysis of the microbial community resulted in microorganisms capable of metabolizing the selected substrate, such as the genera Caloramator, Dictyoglomus and Thermoanaerobacter as active and abundant microorganisms. To discover glycoside hydrolases, 90,342 annotated genes were screened for specific reaction types. A total number of 106 genes encoding cellulases (EC 3.2.1.4), beta-glucosidases (EC 3.2.1.21) and endo-1,4-beta-mannosidases (EC 3.2.1.78) were selected. Mapping of RNA-Seq reads to the related metagenome led to expression levels for each gene. Amongst those, 14 genes, encoding glycoside hydrolases, showed highest expression values, and were used for further cloning. Four proteins were biochemically characterized and were identified as thermoactive glycoside hydrolases with a broad substrate range. This work demonstrated that a combinatory omic approach is a suitable strategy identifying unique thermoactive enzymes from environmental samples.
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Tuveng TR, Jensen MS, Fredriksen L, Vaaje-Kolstad G, Eijsink VGH, Forsberg Z. A thermostable bacterial lytic polysaccharide monooxygenase with high operational stability in a wide temperature range. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:194. [PMID: 33292445 PMCID: PMC7708162 DOI: 10.1186/s13068-020-01834-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are oxidative, copper-dependent enzymes that function as powerful tools in the turnover of various biomasses, including lignocellulosic plant biomass. While LPMOs are considered to be of great importance for biorefineries, little is known about industrial relevant properties such as the ability to operate at high temperatures. Here, we describe a thermostable, cellulose-active LPMO from a high-temperature compost metagenome (called mgLPMO10). RESULTS MgLPMO10 was found to have the highest apparent melting temperature (83 °C) reported for an LPMO to date, and is catalytically active up to temperatures of at least 80 °C. Generally, mgLPMO10 showed good activity and operational stability over a wide temperature range. The LPMO boosted cellulose saccharification by recombinantly produced GH48 and GH6 cellobiohydrolases derived from the same metagenome, albeit to a minor extent. Cellulose saccharification studies with a commercial cellulase cocktail (Celluclast®) showed that the performance of this thermostable bacterial LPMO is comparable with that of a frequently utilized fungal LPMO from Thermoascus aurantiacus (TaLPMO9A). CONCLUSIONS The high activity and operational stability of mgLPMO10 are of both fundamental and applied interest. The ability of mgLPMO10 to perform oxidative cleavage of cellulose at 80 °C and the clear synergy with Celluclast® make this enzyme an interesting candidate in the development of thermostable enzyme cocktails for use in lignocellulosic biorefineries.
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Affiliation(s)
- Tina Rise Tuveng
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Aas, Norway
| | - Marianne Slang Jensen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Aas, Norway
| | - Lasse Fredriksen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Aas, Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Aas, Norway.
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Aas, Norway.
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Bunterngsook B, Mhuantong W, Kanokratana P, Iseki Y, Watanabe T, Champreda V. Identification and characterization of a novel AA9-type lytic polysaccharide monooxygenase from a bagasse metagenome. Appl Microbiol Biotechnol 2020; 105:197-210. [PMID: 33230603 DOI: 10.1007/s00253-020-11002-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 11/25/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are auxiliary enzymes catalyzing oxidative cleavages of cellulose chains in crystalline regions, resulting in their increasing accessibility to the hydrolytic enzyme counterparts and hence higher released sugars from biomass saccharification. In this study, a novel auxiliary protein family 9 LPMO (BgAA9) was identified from a metagenomic library derived from a thermophilic microbial community in bagasse collection site where diverse AA9 and AA10 putative sequences were annotated. The enzyme showed highest similarity to a glycoside hydrolase family 61 from Chaetomium thermophilum. Recombinant BgAA9 expressed in Pichia pastoris cleaved cellohexaose (DP6) into shorter cellooligosaccharides (DP2, DP3, and DP4). Supplementation BgAA9 to a commercial cellulase, Accellerase® 1500 showed strong synergistic effect on saccharification of Avicel® PH101, decrystallized cellulose, filter paper, and alkaline-pretreated sugarcane bagasse, resulting in 63-93% increase in the total reducing sugar yield after incubation at 50 °C for 72 h. Strong synergism was shown between BgAA9 and the cellulase with the highest total fermentable sugar yield obtained from 75:25% of Accellerase®1500:BgAA9 which released 39 mg glucose/FPU (filter paper unit) equivalent to 38.7% higher than Accellerase®1500 alone at the same total protein dosage of 5 mg/g substrate according to the mixture design study. The enzyme represented the first characterized LPMO from environmental metagenome and a potent auxiliary component for biomass saccharification. KEY POINTS: • BgAA9 represents the first characterized LPMO from metagenome. • 12 AA families were annotated in thermophilic bagasse fosmid library by NGS. • BgAA9 showed homology to Cel61 in Chaetomium thermophilum. • BgAA9 oxidized cellohexaose and PASC to DP2, DP4, and DP6. • BgAA9 showed strong synergism to Accellerase on bagasse hydrolysis.
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Affiliation(s)
- Benjarat Bunterngsook
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Pattanop Kanokratana
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Yu Iseki
- Laboratory of Biomass Conversion, Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Watanabe
- Laboratory of Biomass Conversion, Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Verawat Champreda
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani, 12120, Thailand.
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14
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Oh HN, Park D, Seong HJ, Kim D, Sul WJ. Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes. J Microbiol 2019; 57:865-873. [PMID: 31571125 DOI: 10.1007/s12275-019-9217-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/03/2019] [Accepted: 07/04/2019] [Indexed: 11/25/2022]
Abstract
Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil's metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.
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Affiliation(s)
- Han Na Oh
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Doyoung Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dockyu Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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15
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Fernández-Bayo JD, Hestmark KV, Claypool JT, Harrold DR, Randall TE, Achmon Y, Stapleton JJ, Simmons CW, VanderGheynst JS. The initial soil microbiota impacts the potential for lignocellulose degradation during soil solarization. J Appl Microbiol 2019; 126:1729-1741. [PMID: 30895681 DOI: 10.1111/jam.14258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 02/02/2023]
Abstract
AIMS Soil biosolarization (SBS) is a pest control technology that includes the incorporation of organic matter into soil prior to solarization. The objective of this study was to measure the impact of the initial soil microbiome on the temporal evolution of genes encoding lignocellulose-degrading enzymes during SBS. METHODS AND RESULTS Soil biosolarization field experiments were completed using green waste (GW) as a soil amendment and in the presence and absence of compost activating inoculum. Samples were collected over time and at two different soil depths for measurement of the microbial community and the predicted lignocellulosic-degrading microbiome. Compost inoculum had a significant positive effect on several predicted genes encoding enzymes involved in cellulose, hemicellulose and lignin degradation. These included beta-glucosidase, endo-1,3(4)-beta-glucanase, alpha-galactosidase and laccase. CONCLUSION Amendment of micro-organisms found in compost to soil prior to SBS enhanced the degradation potential of cellulose, hemicellulose and lignin found in GW. SIGNIFICANCE AND IMPACT OF THE STUDY The type of organic matter amended and its biotransformation by soil micro-organisms impact the efficacy of SBS. The results suggest that co-amending highly recalcitrant biomass with micro-organisms found in compost improves biomass conversion during SBS.
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Affiliation(s)
- J D Fernández-Bayo
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - K V Hestmark
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA
| | - J T Claypool
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - D R Harrold
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA
| | - T E Randall
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA
| | - Y Achmon
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.,Department of Food Science and Technology, University of California, Davis, CA, USA.,Department of Biotechnology and Food Engineering, Guangdong Technion Israel Institute of Technology, Shantou, China
| | - J J Stapleton
- Statewide Integrated Pest Management Program, University of California, Kearney Agricultural Research and Extension Center, Parlier, CA, USA
| | - C W Simmons
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - J S VanderGheynst
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.,Department of Bioengineering, University of Massachusetts, Dartmouth, MA, USA
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16
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Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome. PLoS One 2018; 13:e0197862. [PMID: 29795644 PMCID: PMC5968413 DOI: 10.1371/journal.pone.0197862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022] Open
Abstract
Enzymatic depolymerization of recalcitrant polysaccharides plays a key role in accessing the renewable energy stored within lignocellulosic biomass, and natural biodiversities may be explored to discover microbial enzymes that have evolved to conquer this task in various environments. Here, a metagenome from a thermophilic microbial community was mined to yield a novel, thermostable cellulase, named mgCel6A, with activity on an industrial cellulosic substrate (sulfite-pulped Norway spruce) and a glucomannanase side activity. The enzyme consists of a glycoside hydrolase family 6 catalytic domain (GH6) and a family 2 carbohydrate binding module (CBM2) that are connected by a linker rich in prolines and threonines. MgCel6A exhibited maximum activity at 85°C and pH 5.0 on carboxymethyl cellulose (CMC), but in prolonged incubations with the industrial substrate, the highest yields were obtained at 60°C, pH 6.0. Differential scanning calorimetry (DSC) indicated a Tm(app) of 76°C. Both functional data and the crystal structure, solved at 1.88 Å resolution, indicate that mgCel6A is an endoglucanase. Comparative studies with a truncated variant of the enzyme showed that the CBM increases substrate binding, while not affecting thermal stability. Importantly, at higher substrate concentrations the full-length enzyme was outperformed by the catalytic domain alone, underpinning previous suggestions that CBMs may be less useful in high-consistency bioprocessing.
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17
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Jiménez DJ, Chaib De Mares M, Salles JF. Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse. Front Microbiol 2018. [PMID: 29535687 PMCID: PMC5834485 DOI: 10.3389/fmicb.2018.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plant biomass (PB) is an important source of sugars useful for biofuel production, whose degradation efficiency depends on synergistic and dynamic interactions of different enzymes. Here, using a metatranscriptomics-based approach, we explored the expression of PB-degrading enzymes in a five-species synthetic bacterial consortium during cultivation on sugarcane bagasse as a unique carbon source. By analyzing the temporal expression dynamics of a selection of enzymes we revealed the functional role of each consortium member and disentangled the potential interactions between them. Based on normalized expression values and the taxonomic affiliation of all the transcripts within thirty carbohydrate-active enzyme (CAZy) families, we observed a successional profile. For instance, endo-glucanases/-xylanases (e.g., GH8, GH10, and GH16) were significantly expressed at 12 h, whereas exo-glucanases (e.g., GH6 and GH48) and α-arabinosidases/β-xylosidases (e.g., GH43) were highly expressed at 48 h. Indeed, a significant peak of extracellular β-xylosidase activity was observed at this stage. Moreover, we observed a higher expression of several CAZy families at 12-48 h, suggesting easy access to the main plant polysaccharides. Based on this evidence, we predicted that the highest level of collaboration between strains takes place at the initial stages of growth. Here, Paenibacillus, Brevundimonas, and Chryseobacterium were the most important contributors, whereas Stenotrophomonas was highly active at the end of the culture (96-192 h) without contributing to a large extent to the expression of lignocellulolytic enzymes. Our results contribute to the understanding of enzymatic and ecological mechanisms within PB-degrading microbial consortia, yielding new perspectives to improve the PB saccharification processes.
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Affiliation(s)
- Diego Javier Jiménez
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Maryam Chaib De Mares
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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18
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Zang X, Liu M, Fan Y, Xu J, Xu X, Li H. The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:51. [PMID: 29492106 PMCID: PMC5828080 DOI: 10.1186/s13068-018-1045-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 02/06/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Compost habitats sustain a vast ensemble of microbes that engender the degradation of cellulose, which is an important part of global carbon cycle. β-Glucosidase is the rate-limiting enzyme of degradation of cellulose. Thus, analysis of regulation of β-glucosidase gene expression in composting is beneficial to a better understanding of cellulose degradation mechanism. Genetic diversity and expression of β-glucosidase-producing microbial communities, and relationships of cellulose degradation, metabolic products and the relative enzyme activity during natural composting and inoculated composting were evaluated. RESULTS Compared with natural composting, adding inoculation agent effectively improved the degradation of cellulose, and maintained high level of the carboxymethyl cellulose (CMCase) and β-glucosidase activities in thermophilic phase. Gene expression analysis showed that glycoside hydrolase family 1 (GH1) family of β-glucosidase genes contributed more to β-glucosidase activity in the later thermophilic phase in inoculated compost. In the cooling phase of natural compost, glycoside hydrolase family 3 (GH3) family of β-glucosidase genes contributed more to β-glucosidase activity. Intracellular β-glucosidase activity played a crucial role in the regulation of β-glucosidase gene expression, and upregulation or downregulation was also determined by extracellular concentration of glucose. At sufficiently high glucose concentrations, the functional microbial community in compost was altered, which may contribute to maintaining β-glucosidase activity despite the high glucose content. CONCLUSION This research provides an ecological functional map of microorganisms involved in carbon metabolism in cattle manure-rice straw composting. The performance of the functional microbial groups in the two composting treatments is different, which is related to the cellulase activity and cellulose degradation, respectively.
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Affiliation(s)
- Xiangyun Zang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Meiting Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Yihong Fan
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Jie Xu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Xiuhong Xu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Hongtao Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
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19
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Zang X, Liu M, Wang H, Fan Y, Zhang H, Liu J, Xing E, Xu X, Li H. The distribution of active β-glucosidase-producing microbial communities in composting. Can J Microbiol 2017; 63:998-1008. [PMID: 28892642 DOI: 10.1139/cjm-2017-0368] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. Cellulose degradation is an important part of the global carbon cycle, and β-glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. This work analyzes the succession of β-glucosidase-producing microbial communities that persist throughout cattle manure - rice straw composting, and evaluates their metabolic activities and community advantage during the various phases of composting. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families 1 and 3 (GH1 and GH3) amplified from DNA were classified and gene abundance levels were analyzed. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Deinococcus-Thermus. This indicates that a diverse microbial community utilizes cellobiose. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting; there was a shift to Actinomycetes in the maturing stage. Proteobacteria accounted for the highest proportions during the heating and thermophilic phases of composting. By contrast, the fungal phylum Ascomycota was a minor microbial community constituent in thermophilic phase of composting. Combined with the analysis of the temperature, cellulose degradation rate and the carboxymethyl cellulase and β-glucosidase activities showed that the bacterial GH1 family β-glucosidase genes make greater contribution in cellulose degradation at the later thermophilic stage of composting. In summary, even GH1 bacteria families β-glucosidase genes showing low abundance in DNA may be functionally important in the later thermophilic phase of composting. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in compost. Several β-glucosidase-producing bacteria and fungi identified in this study may represent potential indicators of composting in cellulose degradation.
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Affiliation(s)
- Xiangyun Zang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Meiting Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Han Wang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yihong Fan
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Haichang Zhang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jiawen Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Enlu Xing
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xiuhong Xu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Hongtao Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
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20
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Zhou M, Guo P, Wang T, Gao L, Yin H, Cai C, Gu J, Lü X. Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:198. [PMID: 28852421 PMCID: PMC5568718 DOI: 10.1186/s13068-017-0885-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/10/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND Degradation of pectin in lignocellulosic materials is one of the key steps for biofuel production. Biological hydrolysis of pectin, i.e., degradation by pectinolytic microbes and enzymes, is an attractive paradigm because of its obvious advantages, such as environmentally friendly procedures, low in energy demand for lignin removal, and the possibility to be integrated in consolidated process. In this study, a metagenomics sequence-guided strategy coupled with enrichment culture technique was used to facilitate targeted discovery of pectinolytic microbes and enzymes. An apple pomace-adapted compost (APAC) habitat was constructed to boost the enrichment of pectinolytic microorganisms. RESULTS Analyses of 16S rDNA high-throughput sequencing revealed that microbial communities changed dramatically during composting with some bacterial populations being greatly enriched. Metagenomics data showed that apple pomace-adapted compost microbial community (APACMC) was dominated by Proteobacteria and Bacteroidetes. Functional analysis and carbohydrate-active enzyme profiles confirmed that APACMC had been successfully enriched for the targeted functions. Among the 1756 putative genes encoding pectinolytic enzymes, 129 were predicted as novel (with an identity <30% to any CAZy database entry) and only 1.92% were more than 75% identical with proteins in NCBI environmental database, demonstrating that they have not been observed in previous metagenome projects. Phylogenetic analysis showed that APACMC harbored a broad range of pectinolytic bacteria and many of them were previously unrecognized. CONCLUSIONS The immensely diverse pectinolytic microbes and enzymes found in our study will expand the arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. Our study provides a powerful approach for targeted mining microbes and enzymes in numerous industries.
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Affiliation(s)
- Man Zhou
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Peng Guo
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Tao Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Lina Gao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Huijun Yin
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Cheng Cai
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi Province China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province China
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21
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Cruz-Ramírez CA, Gómez-Ramírez LF, Uribe-Vélez D. Manejo biológico del tamo de arroz bajo diferentes relaciones C:N empleando co-inóculos microbianos y promotores de crecimiento vegetal. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2017. [DOI: 10.15446/rev.colomb.biote.v19n2.70168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El tamo de arroz es uno de los residuos agrícolas lignocelulósicos más abundantes en el planeta, luego de los residuos producidos por los cultivos de maíz y trigo, con una producción mundial estimada de 1000 millones de toneladas según estadísticas de la FAO. En el contexto de la agricultura moderna es determinante lograr un manejo ambientalmente sostenible de este recurso mediante su incorporación al suelo, de tal forma que se logre el reciclaje de nutrientes, evitando la incorporación de patógenos al sistema y la inmovilización de elementos como el nitrógeno por la comunidad microbiana. El objetivo de este trabajo consistió en la evaluación de un inoculo microbiano mixto a partir de productos comerciales basados en hongos del género Trichoderma y bacterias aerobias formadoras de endosporas, con potencial degradador del tamo de arroz, así como el empleo de bacterias promotoras de crecimiento vegetal al momento de la siembra, que pudieran aprovechar los nutrientes del proceso de descomposición del tamo de arroz, potenciando su actividad biológica. Los tratamientos fueron evaluados bajo diferentes relaciones C:N del tamo de arroz que favorecieran el proceso de degradación, mediante la adición de nitrógeno inorgánico. Los resultados del trabajo permitieron identificar que la aplicación de una enmienda de nitrógeno a una relación C:N 35 más una dosis adicional de urea al momento de la siembra de las semillas de arroz, fue el tratamiento más adecuado para potenciar el efecto de los microorganismos e incrementar las variables agronómicas obtenidas mediante un esquema de fertilización convencional del cultivo.
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22
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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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23
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Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau. Appl Environ Microbiol 2017; 83:AEM.03020-16. [PMID: 28087533 DOI: 10.1128/aem.03020-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/10/2017] [Indexed: 02/03/2023] Open
Abstract
Among the bacteria, members of the order Actinomycetales are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by Actinomycetales (other than Streptomyces spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 Actinomycetales strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the Streptomycetaceae, Pseudonocardiaceae, Micromonosporaceae, and Promicromonosporaceae families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the Micromonosporaceae). When incubated in a hydrated mixture of blended Stipa and Hilaria grass biomass over a 5-week period, Streptomyces and Saccharothrix (a member of the Pseudonocardiaceae) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of Actinomycetales sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 Actinomycetales genomes in the CAZy database and 5 genomes from our isolates, we posit that Streptomyces spp. and select members of the Pseudonocardiaceae and Micromonosporaceae likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils.IMPORTANCE Shifts in the relative abundance of Actinomycetales taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse Actinomycetales taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of Actinomycetales isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available Actinomycetales genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of Actinomycetales ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of Actinomycetales phylogeny with lignocellulolytic functional potential.
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24
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Mello BL, Alessi AM, Riaño-Pachón DM, deAzevedo ER, Guimarães FEG, Espirito Santo MC, McQueen-Mason S, Bruce NC, Polikarpov I. Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:254. [PMID: 29118851 PMCID: PMC5667448 DOI: 10.1186/s13068-017-0944-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/24/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult. Metatranscriptomic studies of microbial communities can unveil the metabolic functions employed by lignocellulolytic consortia and identify novel biocatalysts that could improve industrial lignocellulose conversion. RESULTS In this study, a microbial community from compost was grown in minimal medium with sugarcane bagasse sugarcane bagasse as the sole carbon source. Solid-state nuclear magnetic resonance was used to monitor lignocellulose degradation; analysis of metatranscriptomic data led to the selection and functional characterization of several target genes, revealing the first glycoside hydrolase from Carbohydrate Active Enzyme family 11 with exo-1,4-β-xylanase activity. The xylanase crystal structure was resolved at 1.76 Å revealing the structural basis of exo-xylanase activity. Supplementation of a commercial cellulolytic enzyme cocktail with the xylanase showed improvement in Avicel hydrolysis in the presence of inhibitory xylooligomers. CONCLUSIONS This study demonstrated that composting microbiomes continue to be an excellent source of biotechnologically important enzymes by unveiling the diversity of enzymes involved in in situ lignocellulose degradation.
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Affiliation(s)
- Bruno L. Mello
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, São Carlos, SP 13560-970 Brazil
| | - Anna M. Alessi
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | - Diego M. Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Rua Giuseppe Máximo Scalfaro 10000, Campinas, SP 13083-100 Brazil
- Laboratório de Biologia de Sistemas Regulatórios, Departamento de Química, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP 05508-000 Brazil
| | - Eduardo R. deAzevedo
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, São Carlos, SP 13560-970 Brazil
| | - Francisco E. G. Guimarães
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, São Carlos, SP 13560-970 Brazil
| | - Melissa C. Espirito Santo
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, São Carlos, SP 13560-970 Brazil
| | | | - Neil C. Bruce
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, São Carlos, SP 13560-970 Brazil
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25
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Mello BL, Alessi AM, McQueen-Mason S, Bruce NC, Polikarpov I. Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia. Sci Rep 2016; 6:38781. [PMID: 27941835 PMCID: PMC5150498 DOI: 10.1038/srep38781] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/14/2016] [Indexed: 01/09/2023] Open
Abstract
Microbial communities (MCs) create complex metabolic networks in natural habitats and respond to environmental changes by shifts in the community structure. Although members of MCs are often not amenable for cultivation in pure culture, it is possible to obtain a greater diversity of species in the laboratory setting when microorganisms are grown as mixed cultures. In order to mimic the environmental conditions, an appropriate growth medium must be applied. Here, we examined the hypothesis that a greater diversity of microorganisms can be sustained under nutrient-limited conditions. Using a 16 S rRNA amplicon metagenomic approach, we explored the structure of a compost-derived MC. During a five-week time course the MC grown in minimal medium with sugarcane bagasse (SCB) as a sole carbon source showed greater diversity and enrichment in lignocellulose-degrading microorganisms. In contrast, a MC grown in nutrient rich medium with addition of SCB had a lower microbial diversity and limited number of lignocellulolytic species. Our approach provides evidence that factors such as nutrient availability has a significant selective pressure on the biodiversity of microorganisms in MCs. Consequently, nutrient-limited medium may displace bacterial generalist species, leading to an enriched source for mining novel enzymes for biotechnology applications.
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Affiliation(s)
- Bruno L Mello
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, São Carlos, SP, 13560-970, Brazil
| | - Anna M Alessi
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Simon McQueen-Mason
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Neil C Bruce
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, São Carlos, SP, 13560-970, Brazil
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26
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Antunes LP, Martins LF, Pereira RV, Thomas AM, Barbosa D, Lemos LN, Silva GMM, Moura LMS, Epamino GWC, Digiampietri LA, Lombardi KC, Ramos PL, Quaggio RB, de Oliveira JCF, Pascon RC, Cruz JBD, da Silva AM, Setubal JC. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Sci Rep 2016; 6:38915. [PMID: 27941956 PMCID: PMC5150989 DOI: 10.1038/srep38915] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
Abstract
Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.
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Affiliation(s)
| | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Andrew Maltez Thomas
- 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
| | - Deibs Barbosa
- 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
| | - Leandro Nascimento Lemos
- 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
| | - Gianluca Major Machado Silva
- 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
| | - 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
| | - George Willian Condomitti Epamino
- 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
| | | | - Karen Cristina Lombardi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Ronaldo Bento Quaggio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Aline Maria da Silva
- 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
| | - João Carlos Setubal
- 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.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA
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27
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Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches. Appl Microbiol Biotechnol 2016; 100:10463-10477. [PMID: 27418359 PMCID: PMC5119850 DOI: 10.1007/s00253-016-7713-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 06/16/2016] [Accepted: 06/27/2016] [Indexed: 02/01/2023]
Abstract
The selection of microbes by enrichment on plant biomass has been proposed as an efficient way to develop new strategies for lignocellulose saccharification. Here, we report an in-depth analysis of soil-derived microbial consortia that were trained to degrade once-used wheat straw (WS1-M), switchgrass (SG-M) and corn stover (CS-M) under aerobic and mesophilic conditions. Molecular fingerprintings, bacterial 16S ribosomal RNA (rRNA) gene amplicon sequencing and metagenomic analyses showed that the three microbial consortia were taxonomically distinct. Based on the taxonomic affiliation of protein-encoding sequences, members of the Bacteroidetes (e.g. Chryseobacterium, Weeksella, Flavobacterium and Sphingobacterium) were preferentially selected on WS1-M, whereas SG-M and CS-M favoured members of the Proteobacteria (e.g. Caulobacter, Brevundimonas, Stenotrophomonas and Xanthomonas). The highest degradation rates of lignin (~59 %) were observed with SG-M, whereas CS-M showed a high consumption of cellulose and hemicellulose. Analyses of the carbohydrate-active enzymes in the three microbial consortia showed the dominance of glycosyl hydrolases (e.g. of families GH3, GH43, GH13, GH10, GH29, GH28, GH16, GH4 and GH92). In addition, proteins of families AA6, AA10 and AA2 were detected. Analysis of secreted protein fractions (metasecretome) for each selected microbial consortium mainly showed the presence of enzymes able to degrade arabinan, arabinoxylan, xylan, β-glucan, galactomannan and rhamnogalacturonan. Notably, these metasecretomes contain enzymes that enable us to produce oligosaccharides directly from wheat straw, sugarcane bagasse and willow. Thus, the underlying microbial consortia constitute valuable resources for the production of enzyme cocktails for the efficient saccharification of plant biomass.
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28
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Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin. J Biol Chem 2015; 291:5234-46. [PMID: 26637355 PMCID: PMC4777856 DOI: 10.1074/jbc.m115.694307] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 11/23/2022] Open
Abstract
Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.
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Affiliation(s)
- Kate E Helmich
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726
| | - Jose Henrique Pereira
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Daniel L Gall
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Richard A Heins
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Ryan P McAndrew
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Craig Bingman
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Kai Deng
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Keefe C Holland
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Daniel R Noguera
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Blake A Simmons
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Kenneth L Sale
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - John Ralph
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726
| | - Timothy J Donohue
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Bacteriology, University of Wisconsin, Madison, Wisconsin 53706,
| | - Paul D Adams
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720, and
| | - George N Phillips
- the Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251
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29
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Cragg SM, Beckham GT, Bruce NC, Bugg TDH, Distel DL, Dupree P, Etxabe AG, Goodell BS, Jellison J, McGeehan JE, McQueen-Mason SJ, Schnorr K, Walton PH, Watts JEM, Zimmer M. Lignocellulose degradation mechanisms across the Tree of Life. Curr Opin Chem Biol 2015; 29:108-19. [PMID: 26583519 PMCID: PMC7571853 DOI: 10.1016/j.cbpa.2015.10.018] [Citation(s) in RCA: 297] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/11/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022]
Abstract
Organisms use diverse mechanisms involving multiple complementary enzymes, particularly glycoside hydrolases (GHs), to deconstruct lignocellulose. Lytic polysaccharide monooxygenases (LPMOs) produced by bacteria and fungi facilitate deconstruction as does the Fenton chemistry of brown-rot fungi. Lignin depolymerisation is achieved by white-rot fungi and certain bacteria, using peroxidases and laccases. Meta-omics is now revealing the complexity of prokaryotic degradative activity in lignocellulose-rich environments. Protists from termite guts and some oomycetes produce multiple lignocellulolytic enzymes. Lignocellulose-consuming animals secrete some GHs, but most harbour a diverse enzyme-secreting gut microflora in a mutualism that is particularly complex in termites. Shipworms however, house GH-secreting and LPMO-secreting bacteria separate from the site of digestion and the isopod Limnoria relies on endogenous enzymes alone. The omics revolution is identifying many novel enzymes and paradigms for biomass deconstruction, but more emphasis on function is required, particularly for enzyme cocktails, in which LPMOs may play an important role.
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Affiliation(s)
- Simon M Cragg
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK.
| | - Gregg T Beckham
- National Renewable Energy Laboratory, National Bioenergy Centre, Golden, CO 80401 USA
| | - Neil C Bruce
- University of York, Department of Biological Sciences, Centre for Novel Agricultural Products, York YO10 5DD, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel L Distel
- Ocean Genome Legacy, Marine Science Center, Northeastern University, Boston, MA, USA
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Amaia Green Etxabe
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Barry S Goodell
- Department of Sustainable Biomaterials, 216 ICTAS II Bldg., Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - Jody Jellison
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - John E McGeehan
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Simon J McQueen-Mason
- University of York, Department of Biological Sciences, Centre for Novel Agricultural Products, York YO10 5DD, UK
| | | | - Paul H Walton
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Martin Zimmer
- Leibniz-Center for Tropical Marine Ecology (ZMT) GmbH, Fahrenheitstrasse 6, 28359 Bremen, Germany
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30
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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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31
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Jiménez DJ, Maruthamuthu M, van Elsas JD. Metasecretome analysis of a lignocellulolytic microbial consortium grown on wheat straw, xylan and xylose. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:199. [PMID: 26628913 PMCID: PMC4666044 DOI: 10.1186/s13068-015-0387-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/16/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Synergistic action of different enzymes is required to complete the degradation of plant biomass in order to release sugars which are useful for biorefining. However, the use of single strains is often not efficient, as crucial parts of the required enzymatic machinery can be absent. The use of microbial consortia bred on plant biomass is a way to overcome this hurdle. In these, secreted proteins constitute sources of relevant enzyme cocktails. Extensive analyses of the proteins secreted by effective microbial consortia will contribute to a better understanding of the mechanism of lignocellulose degradation. RESULTS Here, we report an analysis of the proteins secreted by a microbial consortium (metasecretome) that was grown on either wheat straw (RWS), xylose or xylan as the carbon sources. Liquid chromatography-tandem mass spectrometry was used to analyze the proteins in the supernatants. Totals of 768 (RWS), 477 (xylose) and 103 (xylan) proteins were identified and taxonomically and functionally classified. In RWS, the proteins were mostly affiliated with Sphingobacterium-like consortium members (~50 %). Specific abundant protein clusters were predicted to be involved in polysaccharide transport and/or sensing (TonB-dependent receptors). In addition, proteins predicted to degrade plant biomass, i.e. endo-1,4-beta-xylanases, alpha-l-arabinofuranosidases and alpha-l-fucosidases, were prominent. In the xylose-driven consortium, most secreted proteins were affiliated with those from Enterobacteriales (mostly Klebsiella species), whereas in the xylan-driven one, they were related to Flavobacterium-like ones. Notably, the metasecretomes of the consortia growing on xylose and xylan contained proteins involved in diverse metabolic functions (e.g. membrane proteins, isomerases, dehydrogenases and oxidoreductases). CONCLUSIONS An analysis of the metasecretomes of microbial consortia originating from the same source consortium and subsequently bred on three different carbon sources indicated that the major active microorganisms in the three final consortia differed. Importantly, diverse glycosyl hydrolases, predicted to be involved in (hemi)cellulose degradation (e.g. of CAZy families GH3, GH10, GH43, GH51, GH67 and GH95), were identified in the RWS metasecretome. Based on these results, we catalogued the RWS consortium as a true microbial enzyme factory that constitute an excellent source for the production of an efficient enzyme cocktail for the pretreatment of plant biomass.
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Affiliation(s)
- Diego Javier Jiménez
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Mukil Maruthamuthu
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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