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Daley SR, Kirby S, Sparling R. Adaptive evolution of Clostridium thermocellum ATCC 27405 on alternate carbon sources leads to altered fermentation profiles. Can J Microbiol 2024. [PMID: 38832648 DOI: 10.1139/cjm-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Consolidated bioprocessing candidate, Clostridium thermocellum, is a cellulose hydrolysis specialist, with the ability to ferment the released sugars to produce bioethanol. C. thermocellum is generally studied with model substrates Avicel and cellobiose to understand the metabolic pathway leading to ethanol. In the present study, adaptive laboratory evolution, allowing C. thermocellum DSM 1237 to adapt to growth on glucose, fructose, and sorbitol, with the prospect that some strains will adapt their metabolism to yield more ethanol. Adaptive growth on glucose and sorbitol resulted in an approximately 1 mM and 2 mM increase in ethanol yield per millimolar glucose equivalent, respectively, accompanied by a shift in the production of the other expected fermentation end products. The increase in ethanol yield observed for sorbitol adapted cells was due to the carbon source being more reduced compared to cellobiose. Glucose and cellobiose have similar oxidation states thus the increase in ethanol yield is due to the rerouting of electrons from other reduced metabolic products excluding H2 which did not decrease in yield. There was no increase in ethanol yield observed for fructose adapted cells, but there was an unanticipated elimination of formate production, also observed in sorbitol adapted cells suggesting that fructose has regulatory implications on formate production either at the transcription or protein level.
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Affiliation(s)
- Steve R Daley
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Samantha Kirby
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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2
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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Stoichiometric Analysis and Production of Bacterial Cellulose by Gluconacetobacter liquefaciens using Borassus flabellifer L. Jaggery. Appl Biochem Biotechnol 2022; 194:3645-3667. [PMID: 35482222 DOI: 10.1007/s12010-022-03896-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/14/2022] [Indexed: 11/02/2022]
Abstract
The objective of the work is to examine the potential utilization of Palmyra palm jaggery (PPJ) for the enhancement of bacterial cellulose (BC) production by Gluconacetobacter liquefaciens. To evaluate the culturing condition, the production of BC fermentation was carried out in batch mode using different carbon sources namely glucose, sucrose and PPJ. PPJ in the HS medium (PHS medium) resulted maximum concentration of BC (14.35 ± 0.18 g/L) under shaking condition than other carbon sources in HS medium. The influence of different medium variables including initial pH and nitrogen sources on BC production was investigated using PHS medium under shaking condition. The maximum BC concentration of 17.79 ± 2.4 g/L was obtained in shaking condition at an initial pH of 5.6 using yeast extract as nitrogen source. Stoichiometric equation for the cell growth and BC synthesis was developed using elemental balance approach. The metabolic heat of reaction (40 kcal generated per liter of medium) was evaluated using electron balance approach. Based on the process economic analysis and the yield of BC during the fermentation, PHS medium without nitrogen source could be a promising cost-effective nutrient than HS medium. Thermal stability, crystallinity index and structural characterizations of produced BC using PPJ medium were evaluated using TGA, XRD and FTIR and the obtained results were compared with HS medium containing glucose and sucrose.
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Biyada S, Merzouki M, Dėmčėnko T, Vasiliauskienė D, Marčiulaitienė E, Vasarevičius S, Urbonavičius J. The Effect of Feedstock Concentration on the Microbial Community Dynamics During Textile Waste Composting. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.813488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In this study, the effect of initial feedstock concentration on the microbial community structure and dynamics during textile waste composting processes was investigated using the next-generation sequencing approach. For this, three mixtures were prepared with different textile waste concentrations mixed with green waste and paper and cardboard waste for composting, to choose the proportion that will provide a mature final compost. A comprehensive characterization of the microbial communities associated with different textile waste concentrations during composting was achieved. It was noted that by increasing the concentration of textile waste, microbial communities (bacterial and fungal) change. Genera and species belonging to Actinobacteria, Firmicutes, Chloroflexia, Rozellomycota, Mortierellomycota, Aphelidiomycota, Ascomycota, and Mucoromycota were the most abundant in the mixtures containing either 40 or 60% of textile waste, whereas some of the species were absent at 80% of textile waste in the mix; this difference was also reflected by their enzymatic activities. Generally, these phyla are associated with composting, and they play a major role in recalcitrant molecular decaying. Ultimately, it can be concluded that the shift most likely occurred in microbial communities during composting probably owing to the interaction between changes in the nutrient concentration and microbial communities. This investigation proves that the concentration of textile waste significantly affects the microbial communities and demonstrates that a high concentration of textile waste is not suitable to grant a good maturity of compost.
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Biyada S, Merzouki M, Dėmčėnko T, Vasiliauskienė D, Ivanec-Goranina R, Urbonavičius J, Marčiulaitienė E, Vasarevičius S, Benlemlih M. Microbial community dynamics in the mesophilic and thermophilic phases of textile waste composting identified through next-generation sequencing. Sci Rep 2021; 11:23624. [PMID: 34880393 PMCID: PMC8654937 DOI: 10.1038/s41598-021-03191-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023] Open
Abstract
Composting is a promising source of mesophilic and thermophilic microorganisms directly involved in the decay of organic matter. However, there is a paucity of information related to bacterial and fungal diversity in compost and their enzymatic activities during the composting process. In this work, bacterial and fungal diversity during the mesophilic and thermophilic phases of textile waste composting was investigated as a way to explain the physical–chemical results obtained during the composting process. This was accomplished using a next-generation sequencing approach that targets either the 16S rRNA or ITS genomic regions of bacteria and fungi, respectively. It was observed that Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant bacterial phyla present at the mesophilic phase but not at the thermophilic one. Composting textile waste exhibits a sustained thermophilic profile (above 55 °C) that usually precludes fungal activity. Nonetheless, the presence of fungi at the thermophilic phase was observed. Rozellomycota, Basidiomycota, and Ascomycota were the most dominant phyla during both composting phases. Such thermophilic fungi with great ability to decay organic matter could be isolated as pure cultures and used for the bioaugmentation of textile waste composting to achieve an advanced maturity level of textile waste compost.
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Affiliation(s)
- Saloua Biyada
- Laboratory of Biotechnology, Environment, Agrifood, and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Atlas, BP: 1796, 30 000, Fez, Morocco.
| | - Mohammed Merzouki
- Laboratory of Biotechnology, Environment, Agrifood, and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Atlas, BP: 1796, 30 000, Fez, Morocco
| | - Taisija Dėmčėnko
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Dovilė Vasiliauskienė
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Rūta Ivanec-Goranina
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Jaunius Urbonavičius
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Eglė Marčiulaitienė
- Department of Environmental Protection and Water Engineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Saulius Vasarevičius
- Department of Environmental Protection and Water Engineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Mohamed Benlemlih
- Laboratory of Biotechnology, Environment, Agrifood, and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Atlas, BP: 1796, 30 000, Fez, Morocco
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Pimentel PSSR, de Oliveira JB, Astolfi-Filho S, Pereira N. Enzymatic Hydrolysis of Lignocellulosic Biomass Using an Optimized Enzymatic Cocktail Prepared from Secretomes of Filamentous Fungi Isolated from Amazonian Biodiversity. Appl Biochem Biotechnol 2021; 193:3915-3935. [PMID: 34410613 DOI: 10.1007/s12010-021-03642-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022]
Abstract
The use of lignocellulosic biomass (LCB) has emerged as one of the main strategies for generating renewable biofuels. For the efficient use of such feedstock, pre-treatments are essential. The hydrolysis of cellulose - major component of LCB - demands enzymatic cocktails with improved efficiency to generate fermentable sugars. In this scenario, lignocellulolytic fungi have enormous potential for the development of efficient enzyme platforms. In this study, two enzymatic cocktails were developed for hydrolysis of two lignocellulosic biomasses: industrial cellulose pulp and cassava peel. The solid biomass ratio in relation to the protein content of the enzyme cocktail was performed by experimental design. The optimized cocktail for the hydrolysis of cellulose pulp (AMZ 1) was composed, in protein base, by 43% of Aspergillus sp. LMI03 enzyme extract and 57% of T. reesei QM9414, while the optimal enzyme cocktail for cassava peel hydrolysis (AMZ 2) was composed by 50% of Aspergillus sp. LMI03 enzyme extract, 25% of the extract of P. citrinum LMI01 and 25% of T. reesei. The ratio between solids and protein loading for AMZ 1 cocktail performance was 52 g/L solids and 30 mg protein/g solids, resulting in a hydrolytic efficiency of 93%. For the AMZ 2 cocktail, the hydrolytic efficiency was 78% for an optimized ratio of 78 g/L solids and 19 mg protein/g solids. These results indicate that cocktails formulated with enzymatic extracts of P. citrinum LMI01, Aspergillus sp. LMI03, and T. reesei QM9414 are excellent alternatives for efficient hydrolysis of plant biomass and for other processes that depend on biocatalysis.
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Affiliation(s)
| | - Jessica Batista de Oliveira
- Multi Institutional Biotechnology Graduate Program, Federal University of Amazonas, Manaus, 69067-005, Brazil
| | - Spartaco Astolfi-Filho
- Centro de Apoio Multidisciplinar (CAM), Federal University of Amazonas, Manaus, 69067-005, Brazil
| | - Nei Pereira
- Laboratory of Bioprocess Development, Center of Biofuels, Oil and Derivatives, School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-594, Brazil
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Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:5163-5184. [PMID: 32337628 DOI: 10.1007/s00253-020-10602-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.
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8
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Escobar ELN, da Silva TA, Pirich CL, Corazza ML, Pereira Ramos L. Supercritical Fluids: A Promising Technique for Biomass Pretreatment and Fractionation. Front Bioeng Biotechnol 2020; 8:252. [PMID: 32391337 PMCID: PMC7191036 DOI: 10.3389/fbioe.2020.00252] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/11/2020] [Indexed: 11/17/2022] Open
Abstract
Lignocellulosic biomasses are primarily composed of cellulose, hemicelluloses and lignin and these biopolymers are bonded together in a heterogeneous matrix that is highly recalcitrant to chemical or biological conversion processes. Thus, an efficient pretreatment technique must be selected and applied to this type of biomass in order to facilitate its utilization in biorefineries. Classical pretreatment methods tend to operate under severe conditions, leading to sugar losses by dehydration and to the release of inhibitory compounds such as furfural (2-furaldehyde), 5-hydroxy-2-methylfurfural (5-HMF), and organic acids. By contrast, supercritical fluids can pretreat lignocellulosic materials under relatively mild pretreatment conditions, resulting in high sugar yields, low production of fermentation inhibitors and high susceptibilities to enzymatic hydrolysis while reducing the consumption of chemicals, including solvents, reagents, and catalysts. This work presents a review of biomass pretreatment technologies, aiming to deliver a state-of-art compilation of methods and results with emphasis on supercritical processes.
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Affiliation(s)
- Estephanie Laura Nottar Escobar
- Applied Kinetics and Thermodynamics Laboratory, Department of Chemical Engineering, Federal University of Paraná, Curitiba, Brazil
| | - Thiago Alessandre da Silva
- Department of Chemistry, Research Center in Applied Chemistry, Federal University of Paraná, Curitiba, Brazil
| | - Cleverton Luiz Pirich
- Department of Chemistry, Research Center in Applied Chemistry, Federal University of Paraná, Curitiba, Brazil
| | - Marcos Lúcio Corazza
- Applied Kinetics and Thermodynamics Laboratory, Department of Chemical Engineering, Federal University of Paraná, Curitiba, Brazil
| | - Luiz Pereira Ramos
- Department of Chemistry, Research Center in Applied Chemistry, Federal University of Paraná, Curitiba, Brazil
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Cellulose as Potential Feedstock for Cellulase Enzyme Production: Versatility and Properties of Various Cellulosic Biomass – Part II. Fungal Biol 2019. [DOI: 10.1007/978-3-030-14726-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Wirth R, Kádár G, Kakuk B, Maróti G, Bagi Z, Szilágyi Á, Rákhely G, Horváth J, Kovács KL. The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing. Front Microbiol 2018; 9:2285. [PMID: 30319585 PMCID: PMC6165872 DOI: 10.3389/fmicb.2018.02285] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022] Open
Abstract
The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a “back-up” team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.
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Affiliation(s)
- Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Balázs Kakuk
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - József Horváth
- Faculty of Agriculture, University of Szeged, Hódmezövásárhely, Hungary
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary
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Ordoñez-Arévalo B, Guillén-Navarro K, Huerta E, Cuevas R, Calixto-Romo MA. Enzymatic dynamics into the Eisenia fetida (Savigny, 1826) gut during vermicomposting of coffee husk and market waste in a tropical environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:1576-1586. [PMID: 29098584 DOI: 10.1007/s11356-017-0572-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/24/2017] [Indexed: 06/07/2023]
Abstract
Epigeic worms modify microbial communities through their digestive processes, thereby influencing the decomposition of organic matter in vermicomposting systems. Nevertheless, the enzyme dynamics within the gut of tropically adapted earthworms is unknown, and the enzymes involved have not been simultaneously studied. The activities of 19 hydrolytic enzymes within three different sections of the intestine of Eisenia fetida were determined over a fasting period and at 24 h and 30, 60, and 90 days of vermicomposting, and data were evaluated by multivariate analyses. There were found positive correlations between the maximal activity of glycosyl hydrolases and one esterase with the anterior intestine (coincident with the reduction of hemicellulose in the substrate) and the activity of the protease α-chymotrypsin with posterior intestine. The results suggest that activities of enzymes change in a coordinated manner within each gut section, probably influenced by selective microbial enzyme enrichment and by the availability of nutrients throughout vermicomposting.
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Affiliation(s)
- Berenice Ordoñez-Arévalo
- Grupo Académico de Biotecnología Ambiental, Unidad Tapachula, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km 2.5, C.P 30700, Tapachula, Chiapas, Mexico
| | - Karina Guillén-Navarro
- Grupo Académico de Biotecnología Ambiental, Unidad Tapachula, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km 2.5, C.P 30700, Tapachula, Chiapas, Mexico.
| | - Esperanza Huerta
- Grupo Académico de Agroecología, El Colegio de la Frontera Sur, Unidad Campeche, Av. Polígono s/n, Ciudad Industrial, C.P. 24500, Lerma, Campeche, Mexico
| | - Raúl Cuevas
- Grupo Académico de Biotecnología Ambiental, Unidad Tapachula, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km 2.5, C.P 30700, Tapachula, Chiapas, Mexico
| | - M Angeles Calixto-Romo
- Grupo Académico de Biotecnología Ambiental, Unidad Tapachula, El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto Km 2.5, C.P 30700, Tapachula, Chiapas, Mexico
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Herlet J, Kornberger P, Roessler B, Glanz J, Schwarz WH, Liebl W, Zverlov VV. A new method to evaluate temperature vs. pH activity profiles for biotechnological relevant enzymes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:234. [PMID: 29046720 PMCID: PMC5637330 DOI: 10.1186/s13068-017-0923-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Glycoside hydrolases are important for various industrial and scientific applications. Determination of their temperature as well as pH optima and range is crucial to evaluate whether an enzyme is suitable for application in a biotechnological process. These basic characteristics of enzymes are generally determined by two separate measurements. However, these lead to a two-dimensional assessment of the pH range at one temperature (and vice versa) and do not allow prediction of the relative enzymatic performance at any pH/temperature combination of interest. In this work, we demonstrate a new method that is based on experimental data and visualizes the relationship among pH, temperature, and activity at a glance in a three-dimensional contour plot. RESULTS In this study, we present a method to determine the relative activity of an enzyme at 96 different combinations of pH and temperature in parallel. For this purpose, we used a gradient PCR cycler and a citrate-phosphate-based buffer system in microtiter plates. The approach was successfully tested with various substrates and diverse assays for glycoside hydrolases. Furthermore, its applicability was demonstrated for single enzymes using the endoglucanase Cel8A from Clostridium thermocellum as well as the commercially available complex enzyme mixture Celluclast®. Thereby, we developed a fast and adaptable method to determine simultaneously both pH and temperature ranges of enzymes over a wide range of conditions, an easy transformation of the experimental data into a contour plot for visualization, and the necessary controls. With our method, the suitability of an enzyme or enzyme mixture for any chosen combination of temperature and pH can easily be assessed at a glance. CONCLUSIONS We propose a method that offers significant advantages over commonly used methods to determine the pH and temperature ranges of enzymes. The overall relationship among pH, temperature, and activity is visualized. Our method could be applied to evaluate exactly what conditions have to be met for optimal utilization of an enzyme or enzyme mixture for both lab-scale and industrial processes. Adaptation to other enzymes, including proteases, should be possible and the method may also lead to a platform for additional applications, such as inactivation kinetics analysis.
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Affiliation(s)
- J. Herlet
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - P. Kornberger
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - B. Roessler
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - J. Glanz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - W. H. Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - W. Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - V. V. Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow, Russia
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Antony B, Johny J, Aldosari SA, Abdelazim MM. Identification and expression profiling of novel plant cell wall degrading enzymes from a destructive pest of palm trees, Rhynchophorus ferrugineus. INSECT MOLECULAR BIOLOGY 2017; 26:469-484. [PMID: 28556365 DOI: 10.1111/imb.12314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plant cell wall degrading enzymes (PCWDEs) from insects were recently identified as a multigene family of proteins that consist primarily of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) and play essential roles in the degradation of the cellulose/hemicellulose/pectin network in the invaded host plant. Here we applied transcriptomic and degenerate PCR approaches to identify the PCWDEs from a destructive pest of palm trees, Rhynchophorus ferrugineus, followed by a gut-specific and stage-specific differential expression analysis. We identified a total of 27 transcripts encoding GH family members and three transcripts of the CE family with cellulase, hemicellulase and pectinase activities. We also identified two GH9 candidates, which have not previously been reported from Curculionidae. The gut-specific quantitative expression analysis identified key cellulases, hemicellulases and pectinases from R. ferrugineus. The expression analysis revealed a pectin methylesterase, RferCE8u02, and a cellulase, GH45c34485, which showed the highest gut enriched expression. Comparison of PCWDE expression patterns revealed that cellulases and pectinases are significantly upregulated in the adult stages, and we observed specific high expression of the hemicellulase RferGH16c4170. Overall, our study revealed the potential of PCWDEs from R. ferrugineus, which may be useful in biotechnological applications and may represent new tools in R. ferrugineus pest management strategies.
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Affiliation(s)
- B Antony
- Department of Plant Protection, Chair of Date Palm Research, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - J Johny
- Department of Plant Protection, Chair of Date Palm Research, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - S A Aldosari
- Department of Plant Protection, Chair of Date Palm Research, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - M M Abdelazim
- Department of Plant Protection, Chair of Date Palm Research, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JBH, Martiny AC. Cellulolytic potential under environmental changes in microbial communities from grassland litter. Front Microbiol 2014; 5:639. [PMID: 25505459 PMCID: PMC4243572 DOI: 10.3389/fmicb.2014.00639] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 11/06/2014] [Indexed: 12/02/2022] Open
Abstract
In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.
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Affiliation(s)
- Renaud Berlemont
- Department of Earth System Science, University of California, IrvineIrvine, CA, USA
- Department of Biological Science, California State UniversityLong Beach, CA, USA
| | - Steven D. Allison
- Department of Earth System Science, University of California, IrvineIrvine, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Ying Lu
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Eoin L. Brodie
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of CaliforniaBerkeley, CA, USA
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Adam C. Martiny
- Department of Earth System Science, University of California, IrvineIrvine, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
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