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Isola D, Lee HJ, Chung YJ, Zucconi L, Pelosi C. Once upon a Time, There Was a Piece of Wood: Present Knowledge and Future Perspectives in Fungal Deterioration of Wooden Cultural Heritage in Terrestrial Ecosystems and Diagnostic Tools. J Fungi (Basel) 2024; 10:366. [PMID: 38786721 PMCID: PMC11122135 DOI: 10.3390/jof10050366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Wooden Cultural Heritage (WCH) represents a significant portion of the world's historical and artistic heritage, consisting of immovable and movable artefacts. Despite the expertise developed since ancient times to enhance its durability, wooden artefacts are inevitably prone to degradation. Fungi play a pivotal role in the deterioration of WCH in terrestrial ecosystems, accelerating its decay and leading to alterations in color and strength. Reviewing the literature of the last 25 years, we aimed to provide a comprehensive overview of fungal diversity affecting WCH, the biochemical processes involved in wood decay, and the diagnostic tools available for fungal identification and damage evaluation. Climatic conditions influence the occurrence of fungal species in threatened WCH, characterized by a prevalence of wood-rot fungi (e.g., Serpula lacrymans, Coniophora puteana) in architectural heritage in temperate and continental climates and Ascomycota in indoor and harsh environments. More efforts are needed to address the knowledge fragmentation concerning biodiversity, the biology of the fungi involved, and succession in the degradative process, which is frequently centered solely on the main actors. Multidisciplinary collaboration among engineers, restorers, and life sciences scientists is vital for tackling the challenges posed by climate change with increased awareness. Traditional microbiology and culture collections are fundamental in laying solid foundations for a more comprehensive interpretation of big data.
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Affiliation(s)
- Daniela Isola
- Department of Economics, Engineering, Society and Business Organization (DEIM), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
| | - Hyun-Ju Lee
- Institute of Preventive Conservation for Cultural Heritage, Korea National University of Cultural Heritage, Buyeo 33115, Republic of Korea;
| | - Yong-Jae Chung
- Department of Heritage Conservation and Restoration, Graduate School of Cultural Heritage, Korea National University of Cultural Heritage, Buyeo 33115, Republic of Korea;
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
| | - Claudia Pelosi
- Department of Economics, Engineering, Society and Business Organization (DEIM), University of Tuscia, Largo dell’Università Snc, 01100 Viterbo, Italy;
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Zhang L, Li J, Wang Z, Zhang D, Liu H, Wang J, Wu F, Wang X, Zhou X. Litter mixing promoted decomposition and altered microbial community in common bean root litter. BMC Microbiol 2023; 23:148. [PMID: 37217839 DOI: 10.1186/s12866-023-02871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Decomposition of plant litter is a key driver of carbon and nutrient cycling in terrestrial ecosystems. Mixing litters of different plant species may alter the decomposition rate, but its effect on the microbial decomposer community in plant litter is not fully understood. Here, we tested the effects of mixing with maize (Zea mays L.) and soybean [Glycine max (Linn.) Merr.] stalk litters on the decomposition and microbial decomposer communities of common bean (Phaseolus vulgaris L.) root litter at the early decomposition stage in a litterbag experiment. RESULTS Mixing with maize stalk litter, soybean stalk litter, and both of these litters increased the decomposition rate of common bean root litter at 56 day but not 14 day after incubation. Litter mixing also increased the decomposition rate of the whole liter mixture at 56 day after incubation. Amplicon sequencing found that litter mixing altered the composition of bacterial (at 56 day after incubation) and fungal communities (at both 14 and 56 day after incubation) in common bean root litter. Litter mixing increased the abundance and alpha diversity of fungal communities in common bean root litter at 56 day after incubation. Particularly, litter mixing stimulated certain microbial taxa, such as Fusarium, Aspergillus and Stachybotrys spp. In addition, a pot experiment with adding litters in the soil showed that litter mixing promoted growth of common bean seedlings and increased soil nitrogen and phosphorus contents. CONCLUSIONS This study showed that litter mixing can promote the decomposition rate and cause shifts in microbial decomposer communities, which may positively affect crop growth.
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Affiliation(s)
- Linlin Zhang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Jiawei Li
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Zhilin Wang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Dinghong Zhang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Hui Liu
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Jia Wang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Fengzhi Wu
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Xue Wang
- Northeast Agricultural University Library, Northeast Agricultural University, Harbin, China.
| | - Xingang Zhou
- Department of Horticulture, Northeast Agricultural University, Harbin, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.
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Merino N, Wang N, Gao Y, Wang M, Mahendra S. Roles of various enzymes in the biotransformation of 6:2 fluorotelomer alcohol (6:2 FTOH) by a white-rot fungus. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131007. [PMID: 36871371 DOI: 10.1016/j.jhazmat.2023.131007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Six-carbon-chained polyfluoroalkyl substances, such as 6:2 fluorotelomer alcohol (6:2 FTOH), are being used to replace longer chained compounds in the manufacture of various commercial products. This study examined the effects of growth substrates and nutrients on specific intracellular and extracellular enzymes mediating 6:2 FTOH aerobic biotransformation by the white-rot fungus, Phanerochaete chrysosporium. Cellulolytic conditions with limited glucose were a suitable composition, resulting in high 5:3 FTCA yield (37 mol%), which is a key intermediate in 6:2 FTOH degradation without forming significant amounts of terminal perfluorocarboxylic acids (PFCAs). Sulfate and ethylenediaminetetraacetic acid (EDTA) were also essential for 5:3 FTCA production, but, at lower levels, resulted in the buildup of 5:2 sFTOH (52 mol%) and 6:2 FTUCA (20 mol%), respectively. In non-ligninolytic nutrient-rich medium, 45 mol% 6:2 FTOH was transformed but produced only 12.7 mol% 5:3 FTCA. Enzyme activity studies imply that cellulolytic conditions induce the intracellular cytochrome P450 system. In contrast, extracellular peroxidase synthesis is independent of 6:2 FTOH exposure. Gene expression studies further verified that peroxidases were relevant in catalyzing the downstream transformations from 5:3 FTCA. Collectively, the identification of nutrients and enzymatic systems will help elucidate underlying mechanisms and biogeochemical conditions favorable for fungal transformation of PFCA precursors in the environment.
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Affiliation(s)
- Nancy Merino
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Ning Wang
- DuPont Haskell Global Centers for Health and Environmental Sciences, Newark, DE 19711, United States
| | - Yifan Gao
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Meng Wang
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States.
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Yan H, Zhang Q, Wang Y, Cui X, Liu Y, Yu Z, Xu S, Ruan R. Rice straw as microalgal biofilm bio-carrier: Effects of indigenous microorganisms on rice straw and microalgal biomass production. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 341:118075. [PMID: 37141712 DOI: 10.1016/j.jenvman.2023.118075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 05/06/2023]
Abstract
Microalgal biofilm cultivation is a promising method for efficient microalgae production. However, expensive, difficult-to-obtain and non-durable carriers hinder its up-scaling. This study adopted both sterilized and unsterilized rice straw (RS) as a carrier for the development of microalgal biofilm, with polymethyl methacrylate as control. The biomass production and chemical composition of Chlorella sorokiniana, as well as the microbial community composition during cultivation were examined. The physicochemical properties of RS before and after utilized as carrier were investigated. The biomass productivity of unsterilized RS biofilm exceeded that of suspended culture by 4.85 g m-2·d-1. The indigenous microorganisms, mainly fungus, could effectively fixed microalgae to the bio-carrier and enhance its biomass production. They could also degrade RS into dissolved matters for microalgal utilization, leading to the physicochemical properties change of RS in the direction which favored its energy conversion. This study showed that RS can be used effectively as a microalgal biofilm carrier, thus presenting a new possibility for the recycling of rice straw.
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Affiliation(s)
- Hongbin Yan
- State Key Laboratory of Food Science and Technology, Engineering Research Center for Biomass Conversion, Ministry of Education, Nanchang University, Nanchang, Jiangxi, 330047, PR China
| | - Qi Zhang
- State Key Laboratory of Food Science and Technology, Engineering Research Center for Biomass Conversion, Ministry of Education, Nanchang University, Nanchang, Jiangxi, 330047, PR China.
| | - Yunpu Wang
- State Key Laboratory of Food Science and Technology, Engineering Research Center for Biomass Conversion, Ministry of Education, Nanchang University, Nanchang, Jiangxi, 330047, PR China
| | - Xian Cui
- State Key Laboratory of Food Science and Technology, Engineering Research Center for Biomass Conversion, Ministry of Education, Nanchang University, Nanchang, Jiangxi, 330047, PR China
| | - Yuhuan Liu
- State Key Laboratory of Food Science and Technology, Engineering Research Center for Biomass Conversion, Ministry of Education, Nanchang University, Nanchang, Jiangxi, 330047, PR China.
| | - Zhigang Yu
- Advanced Water Management Centre, The University of Queensland, Brisbane, 4072, Australia
| | - Shuming Xu
- Bureau of Agriculture and Rural Affairs, Dingnan County, Ganzhou, Jiangxi, 341900, PR China
| | - Roger Ruan
- Center for Biorefining and Dept. of Bioproducts and Biosystems Engineering, University of Minnesota, Paul, 55108, USA
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Koubová A, Lorenc F, Horváthová T, Chroňáková A, Šustr V. Millipede gut-derived microbes as a potential source of cellulolytic enzymes. World J Microbiol Biotechnol 2023; 39:169. [PMID: 37186294 DOI: 10.1007/s11274-023-03620-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023]
Abstract
Lignocellulose biomass has recently been considered a cost-effective and renewable energy source within circular economy management. Cellulases are important key enzymes for simple, fast, and clean biomass decomposition. The intestinal tract of millipedes is the environment which can provide promising microbial strains with cellulolytic potential. In the present study, we used the tropical millipede Telodeinopus aoutii as an experimental organism. Within a feeding test in which millipedes were fed with oak and maple leaf litter, we focused on isolating culturable cellulolytic microbiota from the millipede gut. Several growth media selecting for actinobacteria, bacteria, and fungi have been used to cultivate microbial strains with cellulolytic activities. Our results showed that oak-fed millipedes provided a higher number of culturable bacteria and a more diversified microbial community than maple-fed ones. The screening for cellulolytic activity using Congo red revealed that about 30% of bacterial and fungal phylotypes isolated from the gut content of T. aoutii, produced active cellulases in vitro. Actinobacteria Streptomyces and Kitasatospora were the most active cellulolytic genera on Congo red test. In contrast, fungi Aspergillus, Penicillium, Cheatomium, Clonostachys, and Trichoderma showed the highest protein-specific cellulase activity quantified by 4-Methylumbelliferyl β-D-cellobioside (4-MUC). Our findings provide a basis for future research on the enzyme activities of microbes isolated from the digestive tracts of invertebrates and their biocatalytic role in biomass degradation.
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Affiliation(s)
- Anna Koubová
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 702/7, 370 05, České Budějovice, Czech Republic
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - František Lorenc
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 702/7, 370 05, České Budějovice, Czech Republic
- Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, Studentská 1668, 370 05, České Budějovice, Czech Republic
| | - Terézia Horváthová
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 702/7, 370 05, České Budějovice, Czech Republic
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Alica Chroňáková
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 702/7, 370 05, České Budějovice, Czech Republic
| | - Vladimír Šustr
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 702/7, 370 05, České Budějovice, Czech Republic.
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Tong X, He Z, Zheng L, Pande H, Ni Y. Enzymatic treatment processes for the production of cellulose nanomaterials: A review. Carbohydr Polym 2023; 299:120199. [PMID: 36876810 DOI: 10.1016/j.carbpol.2022.120199] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022]
Abstract
Cellulose nanomaterials have attracted much attention in recent years because of their unique properties. Commercial or semi-commercial production of nanocellulose has been reported in recent years. Mechanical treatments for nanocellulose production are viable but highly energy-intensive. Chemical processes are well reported; however, these chemical processes are not only costly, but also cause environmental concerns and end-use related challenges. This review summarizes recent researches on enzymatic treatment of cellulose fibers for the production of cellulose nanomaterials, with focus on novel enzymatic processes with xylanase and lytic polysaccharide monooxygenases (LPMO) to enhance the efficacy of cellulase. Different enzymes are discussed, including endoglucanase, exoglucanase and xylanase, as well as LPMO, with emphasis on the accessibility and hydrolytic specificity of LPMO enzymes to cellulose fiber structures. LPMO acts in a synergistic way with cellulase to cause significant physical and chemical changes to the cellulose fiber cell-wall structures, which facilitate the nano-fibrillation of the fibers.
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Affiliation(s)
- Xin Tong
- Department of Chemical Engineering, Limerick Pulp and Paper Centre, University of New Brunswick, Fredericton, NB E3B5A3, Canada; Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou 310023, PR China
| | - Zhibin He
- Department of Chemical Engineering, Limerick Pulp and Paper Centre, University of New Brunswick, Fredericton, NB E3B5A3, Canada.
| | - Linqiang Zheng
- Department of Chemical Engineering, Limerick Pulp and Paper Centre, University of New Brunswick, Fredericton, NB E3B5A3, Canada
| | - Harshad Pande
- Domtar Corporation, 395 Blvd Maisonneuve West, Montreal, PQ H3A 1L6, Canada
| | - Yonghao Ni
- Department of Chemical Engineering, Limerick Pulp and Paper Centre, University of New Brunswick, Fredericton, NB E3B5A3, Canada
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Xiao R, Guo Y, Zhang M, Pan W, Wang JJ. Stronger network connectivity with lower diversity of soil fungal community was presented in coastal marshes after sixteen years of freshwater restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140623. [PMID: 32693270 DOI: 10.1016/j.scitotenv.2020.140623] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Freshwater input for salt marsh restoration in the Yellow River Delta induced Phragmites australis expansion and thus may cause shifts of soil fungi from halophilic to desalination-adapted species for increased litter decomposition. In this study, soil fungal communities of restored and natural salt marshes were determined to reveal further details of shift in soil fungal community and its probable prediction for salt marsh restoration. Our results showed a stronger network within Ascomycota (e.g. Sordariales, Aspergillus, Hypocreales and Cladosporium herbarum) in restored marshes, but with a lower diversity of halophilic taxa (e.g. Chytridiomycota and Nematoda) in comparison with natural salt marshes. Contrarily, the occurrence of Chytridiomycota, Ichthyosporea and Discicristoidea in the soil fungal networks of the natural salt marsh emphasized the importance of salt tolerant species at the land-sea transition zone. The Sordariales was dominant and had a strong correlation with other fungal species and aggregate associated soil organic carbon (SOC), which probably contributed to SOC accumulation in restored marshes. But the reduced halophilic species specific to salt marsh elucidated that the formation of monospecific stands of P. australis along with the freshwater input induced desalination to the saline habitats changed the native patterns of vegetation and soil organisms. As the buffer between terrestrial and marine systems, a single habitat type such as dense monocultures of P. australis must be avoided and diverse saltmarsh habitats across a salinity gradient should be reserved. In this way, the diversity and specificity of coastal halophytes and related microorganisms could be maintained and thus might confer benefits in balancing various functions of the salt marsh ecosystem and preserving the system's elasticity and resistance to stress.
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Affiliation(s)
- Rong Xiao
- College of Environment and Resources, Fuzhou University, Fuzhou 350108, China.
| | - Yutong Guo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Mingxiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Wenbin Pan
- College of Environment and Resources, Fuzhou University, Fuzhou 350108, China
| | - Jian Jim Wang
- School of Plant, Environmental and Soil Sciences, Louisiana State Univ. Agricultural Center, Baton Rouge, LA 70803, USA
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Tao W, Kasuga T, Li S, Huang H, Fan Z. Homoethanol production from cellobionate and glycerol using recombinant Klebsiella oxytoca strains. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Chen L, Jiang Y, Liang C, Luo Y, Xu Q, Han C, Zhao Q, Sun B. Competitive interaction with keystone taxa induced negative priming under biochar amendments. MICROBIOME 2019; 7:77. [PMID: 31109381 PMCID: PMC6526607 DOI: 10.1186/s40168-019-0693-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/08/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Biochar amendments have been widely proposed as a conventional and efficient strategy to promote soil organic carbon (SOC) sequestration via negative priming. Unfortunately, the extent and biological mechanisms responsible for biochar-induced negative priming are still not fully understood. Despite traditional explanations focused on the environmental filtering mechanisms of biochar amendments on microbial biomass and community composition underlying the priming effect on SOC dynamics, whether and how a biochar-induced competitive interaction with keystone taxa determines SOC mineralization in natural ecosystems has been minimally explored. RESULTS Here, we paid particular attention to the relationships between the diversity and network structure of soil bacterial and fungal communities and SOC mineralization. A 3-year field experiment was conducted comprising five treatments: no fertilization, conventional fertilization, and conventional fertilization with three rates of biochar amendments. Biochar amendments considerably increased soil moisture capacity and pH and subsequently shaped the composition and co-occurrence networks of soil bacterial and fungal communities. Importantly, network analysis revealed that the biochar amendments triggered the competitive interaction with putative keystone taxa in the bacterial and fungal networks. Structural equation modeling suggested that the competitive interaction with keystone taxa promoted bacterial and fungal diversity and consequently reduced carbohydrate catabolism and soil metabolic quotient. Stable isotope probing incubations further provided consistent evidence of competition by keystone taxa with the increases in bacterial and fungal diversity under the biochar amendments. CONCLUSIONS We found that biochar-induced competition with keystone taxa stimulated the bacterial and fungal diversity and consequently decreased SOC mineralization. The comprehensive understanding of the unexplored biological mechanisms underlying the biochar-induced negative priming may provide crucial implications for enabling SOC sequestration.
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Affiliation(s)
- Lijun Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing, 210008, China.
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yu Luo
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Qinsong Xu
- College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Cheng Han
- School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
| | - Qiguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing, 210008, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing, 210008, China.
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Zhou FF, Zhang YD, Zhang Q, Lu J, Liu Y, Wang JH. Structure characterization and immunological activity of a β-glucan from White H. marmoreus and its silver nanoparticle derivatives. Carbohydr Polym 2019; 210:1-8. [DOI: 10.1016/j.carbpol.2019.01.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/02/2019] [Accepted: 01/16/2019] [Indexed: 10/27/2022]
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Homoethanol Production from Glycerol and Gluconate Using Recombinant Klebsiella oxytoca Strains. Appl Environ Microbiol 2019; 85:AEM.02122-18. [PMID: 30578264 DOI: 10.1128/aem.02122-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022] Open
Abstract
Gluconic acid, an oxidized cellulose degradation product, could be produced from cellulosic biomass. Glycerol is an inexpensive and renewable resource for fuels and chemicals production and is available as a byproduct of biodiesel production. Gluconate is a more oxidized substrate than glucose, whereas glycerol is a more reduced substrate than glucose. Although the production of homoethanol from glucose can be achieved, the conversion of gluconate to ethanol is accompanied by the production of oxidized byproduct such as acetate, and reduced byproducts such as 1,3-propanediol are produced, along with ethanol, when glycerol is used as the carbon source. When gluconate and glycerol are used as the sole carbon source by Klebsiella oxytoca BW21, the ethanol yield is about 62 to 64%. Coutilization of both gluconate and glycerol in batch fermentation increased the yield of ethanol to about 78.7% and decreased by-product accumulation (such as acetate and 1,3-propanediol) substantially. Decreasing by-product formation by deleting the pta, frd, ldh, pflA, and pduC genes in strain BW21 increased the ethanol yield to 89.3% in the batch fermentation of a glycerol-gluconate mixture. These deletions produced the strain K. oxytoca WT26. However, the utilization rate of glycerol was significantly slower than that of gluconate in batch fermentation. In addition, substantial amounts of glycerol remain unutilized after gluconate was depleted in batch fermentation. Continuous fed-batch fermentation was used to solve the utilization rate mismatch problem for gluconate and glycerol. An ethanol yield of 97.2% was achieved in continuous fed-batch fermentation of these two substrates, and glycerol was completely used at the end of the fermentation.IMPORTANCE Gluconate is a biomass-derived degradation product, and glycerol can be obtained as a biodiesel byproduct. Compared to glucose, using them as the sole substrate is accompanied by the production of by-products. Our study shows that through pathway engineering and adoption of a fed-batch culture system, high-yield homoethanol production that usually can be achieved by using glucose as the substrate is achievable using gluconate and glycerol as cosubstrates. The same strategy is expected to be able to achieve homofermentative production of other products, such as lactate and 2,3-butanediol, which can be typically achieved using glucose as the substrate and inexpensive biodiesel-derived glycerol and biomass-derived gluconate as the cosubstrates.
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Bulakhov AG, Gusakov AV, Rozhkova AM, Volkov PV, Matys VY, Zorov IN, Sinitsyn AP. Properties of Chimeric Polysaccharide Monooxygenase with an Attached Cellulose Binding Module and Its Use in the Hydrolysis of Cellulose-Containing Materials in the Composition of Cellulase Complexes. CATALYSIS IN INDUSTRY 2018. [DOI: 10.1134/s2070050418020034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Souza MFD, Silva ASD, Bon EP. A novel Trichoderma harzianum strain from the Amazon Forest with high cellulolytic capacity. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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15
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Fungal lytic polysaccharide monooxygenases from family AA9: Recent developments and application in lignocelullose breakdown. Int J Biol Macromol 2017; 102:771-778. [DOI: 10.1016/j.ijbiomac.2017.04.077] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022]
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16
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Reyes-Sosa FM, López Morales M, Platero Gómez AI, Valbuena Crespo N, Sánchez Zamorano L, Rocha-Martín J, Molina-Heredia FP, Díez García B. Management of enzyme diversity in high-performance cellulolytic cocktails. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:156. [PMID: 28649275 PMCID: PMC5477296 DOI: 10.1186/s13068-017-0845-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/12/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Modern biorefineries require enzymatic cocktails of improved efficiency to generate fermentable sugars from lignocellulosic biomass. Cellulolytic fungi, among other microorganisms, have demonstrated the highest potential in terms of enzymatic productivity, complexity and efficiency. On the other hand, under cellulolytic-inducing conditions, they often produce a considerable diversity of carbohydrate-active enzymes which allow them to adapt to changing environmental conditions. However, industrial conditions are fixed and adjusted to the optimum of the whole cocktail, resulting in underperformance of individual enzymes. RESULTS One of these cellulolytic cocktails from Myceliophthora thermophila has been analyzed here by means of LC-MS/MS. Pure GH6 family members detected have been characterized, confirming previous studies, and added to whole cocktails to compare their contribution in the hydrolysis of industrial substrates. Finally, independent deletions of two GH6 family members, as an example of the enzymatic diversity management, led to the development of a strain producing a more efficient cellulolytic cocktail. CONCLUSIONS These data indicate that the deletion of noncontributive cellulases (here EG VI) can increase the cellulolytic efficiency of the cocktail, validating the management of cellulase diversity as a strategy to obtain improved fungal cellulolytic cocktails.
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Affiliation(s)
| | - Macarena López Morales
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Ana Isabel Platero Gómez
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Noelia Valbuena Crespo
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Laura Sánchez Zamorano
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Javier Rocha-Martín
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Fernando P. Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla y CSIC, Américo Vespucio 49, 41092 Seville, Spain
| | - Bruno Díez García
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
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17
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Zhang W, Sathitsuksanoh N, Barone JR, Renneckar S. Enhanced enzymatic saccharification of pretreated biomass using glycerol thermal processing (GTP). BIORESOURCE TECHNOLOGY 2016; 199:148-154. [PMID: 26384086 DOI: 10.1016/j.biortech.2015.08.141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 06/05/2023]
Abstract
Biomass was heated (200-240°C) in the presence of glycerol, for 4-12 min, under shear to disrupt the native cell wall architecture. The impact of this method, named glycerol thermal processing (GTP), on saccharification efficiency of the hardwood Liquidambar styraciflua, and a control cellulose sample was studied as a function of treatment severity. Furthermore, the enzymatic conversion of samples with varying compositions was studied after extraction of the structural polymers. Interestingly, the sweet gum processed materials crystallinity index increased by 10% of the initial value. The experiments revealed that the residual lignin was not a barrier to limiting the digestibility of cellulose after pretreatment yielding up to 70% glucose based on the starting wood material. Further xylan removal greatly improved the cellulose hydrolysis rate, converting nearly 70% of the cellulose into glucose within 24h, and reaching 78% of ultimate glucan digestibility after 72 h.
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Affiliation(s)
- Wei Zhang
- Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24061, United States; Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, VA 24061, United States
| | - Noppadon Sathitsuksanoh
- Department of Chemical Engineering, University of Louisville, Louisville, KY 40292, United States
| | - Justin R Barone
- Department of Biological Science and Engineering, Virginia Tech, Blacksburg 24061, United States
| | - Scott Renneckar
- Department of Wood Science, University of British Columbia, Vancouver V6T1Z4, Canada.
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18
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Miura T, Niswati A, Swibawa IG, Haryani S, Gunito H, Shimano S, Fujie K, Kaneko N. Diversity of Fungi on Decomposing Leaf Litter in a Sugarcane Plantation and Their Response to Tillage Practice and Bagasse Mulching: Implications for Management Effects on Litter Decomposition. MICROBIAL ECOLOGY 2015; 70:646-658. [PMID: 25933637 DOI: 10.1007/s00248-015-0620-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 04/20/2015] [Indexed: 06/04/2023]
Abstract
To minimize the degradation of soil organic matter (SOM) content in conventional sugarcane cropping, it is important to understand how the fungal community contributes to SOM dynamics during the decomposition of sugarcane leaf litter. However, our knowledge of fungal diversity in tropical agroecosystems is currently limited. Thus, we determined the fungal community structure on decomposing sugarcane leaf litter and their response to different soil management systems using the internal transcribed spacer region 1 (ITS1) amplicon sequencing method afforded by Ion Torrent Personal Genome Machine (PGM). The results indicate that no-tillage had positive effects on the relative abundance of Zygomycota and of some taxa that may prefer a moist environment over conventional tillage, whereas bagasse mulching decreased the richness of operational taxonomic units (OTUs) and had positive effect on the relative abundance of slow-growing taxa, which may prefer poor nutrient substrates. Furthermore, a combination of no-tillage and bagasse mulching increased the abundance of unique OTUs. We suggest that the alteration of fungal communities through the changes in soil management practices produces an effect on litter decomposition.
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Affiliation(s)
- Toshiko Miura
- Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan.
| | - Ainin Niswati
- Department of Soil Science, University of Lampung, Bandar Lampung, Indonesia
| | - I G Swibawa
- Department of Plant Pest and Diseases, University of Lampung, Bandar Lampung, Indonesia
| | - Sri Haryani
- Research and Development Division of PT Gunung Madu Plantations, Sumatra, Indonesia
| | - Heru Gunito
- Research and Development Division of PT Gunung Madu Plantations, Sumatra, Indonesia
| | - Satoshi Shimano
- Environmental Education Center, Miyagi University of Education, Sendai, Japan
| | - Koichi Fujie
- Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Nobuhiro Kaneko
- Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
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19
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Li X, Chomvong K, Yu VY, Liang JM, Lin Y, Cate JHD. Cellobionic acid utilization: from Neurospora crassa to Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:120. [PMID: 26279678 PMCID: PMC4537572 DOI: 10.1186/s13068-015-0303-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/31/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Economical production of fuels and chemicals from plant biomass requires the efficient use of sugars derived from the plant cell wall. Neurospora crassa, a model lignocellulosic degrading fungus, is capable of breaking down the complex structure of the plant cell wall. In addition to cellulases and hemicellulases, N. crassa secretes lytic polysaccharide monooxygenases (LPMOs), which cleave cellulose by generating oxidized sugars-particularly aldonic acids. However, the strategies N. crassa employs to utilize these sugars are unknown. RESULTS We identified an aldonic acid utilization pathway in N. crassa, comprised of an extracellular hydrolase (NCU08755), cellobionic acid transporter (CBT-1, NCU05853) and cellobionic acid phosphorylase (CAP, NCU09425). Extracellular cellobionic acid could be imported directly by CBT-1 or cleaved to gluconic acid and glucose by a β-glucosidase (NCU08755) outside the cells. Intracellular cellobionic acid was further cleaved to glucose 1-phosphate and gluconic acid by CAP. However, it remains unclear how N. crassa utilizes extracellular gluconic acid. The aldonic acid pathway was successfully implemented in Saccharomyces cerevisiae when N. crassa gluconokinase was co-expressed, resulting in cellobionic acid consumption in both aerobic and anaerobic conditions. CONCLUSIONS We successfully identified a branched aldonic acid utilization pathway in N. crassa and transferred its essential components into S. cerevisiae, a robust industrial microorganism.
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Affiliation(s)
- Xin Li
- />Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Kulika Chomvong
- />Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Vivian Yaci Yu
- />Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Julie M Liang
- />Department of Chemistry, University of California, Berkeley, CA USA
| | - Yuping Lin
- />Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Jamie H D Cate
- />Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
- />Department of Chemistry, University of California, Berkeley, CA USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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20
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Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2014.08.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR. Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev 2014; 78:614-49. [PMID: 25428937 PMCID: PMC4248655 DOI: 10.1128/mmbr.00035-14] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SUMMARY Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer Yuzon
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
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22
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Kricka W, Fitzpatrick J, Bond U. Metabolic engineering of yeasts by heterologous enzyme production for degradation of cellulose and hemicellulose from biomass: a perspective. Front Microbiol 2014; 5:174. [PMID: 24795706 PMCID: PMC4001029 DOI: 10.3389/fmicb.2014.00174] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/31/2014] [Indexed: 11/13/2022] Open
Abstract
This review focuses on current approaches to metabolic engineering of ethanologenic yeast species for the production of bioethanol from complex lignocellulose biomass sources. The experimental strategies for the degradation of the cellulose and xylose-components of lignocellulose are reviewed. Limitations to the current approaches are discussed and novel solutions proposed.
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Affiliation(s)
- William Kricka
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
| | - James Fitzpatrick
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
| | - Ursula Bond
- School of Genetics and Microbiology, Department of Microbiology, Trinity College Dublin Dublin, Ireland
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23
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Fitzpatrick J, Kricka W, James TC, Bond U. Expression of three Trichoderma reesei cellulase genes in Saccharomyces pastorianus for the development of a two-step process of hydrolysis and fermentation of cellulose. J Appl Microbiol 2014; 117:96-108. [PMID: 24666670 DOI: 10.1111/jam.12494] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 11/26/2022]
Abstract
AIMS To compare the production of recombinant cellulase enzymes in two Saccharomyces species so as to ascertain the most suitable heterologous host for the degradation of cellulose-based biomass and its conversion into bioethanol. METHOD AND RESULTS cDNA copies of genes representing the three major classes of cellulases (Endoglucanases, Cellobiohydrolases and β-glucosidases) from Trichoderma reesei were expressed in Saccharomyces pastorianus and Saccharomyces cerevisiae. The recombinant enzymes were secreted by the yeast hosts into the medium and were shown to act in synergy to hydrolyse cellulose. The conditions required to achieve maximum release of glucose from cellulose by the recombinant enzymes were defined and the activity of the recombinant enzymes was compared to a commercial cocktail of T. reesei cellulases. CONCLUSIONS We demonstrate that significantly higher levels of cellulase activity were achieved by expression of the genes in S. pastorianus compared to S. cerevisiae. Hydrolysis of cellulose by the combined activity of the recombinant enzymes was significantly better at 50°C than at 30°C, the temperature used for mesophilic yeast fermentations, reflecting the known temperature profiles of the native enzymes. SIGNIFICANCE AND IMPACT OF THE STUDY The results demonstrate that host choice is important for the heterologous production of cellulases. On the basis of the low activity of the T. reesei recombinant enzymes at fermentation temperatures, we propose a two-step process for the hydrolysis of cellulose and its fermentation into alcohol using cellulases produced in situ.
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Affiliation(s)
- J Fitzpatrick
- School of Genetics and Microbiology, Moyne Institute, Trinity College Dublin, College Green, Dublin 2, Ireland
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24
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Gómez-Mendoza DP, Junqueira M, do Vale LHF, Domont GB, Ferreira Filho EX, Sousa MVD, Ricart CAO. Secretomic survey of Trichoderma harzianum grown on plant biomass substrates. J Proteome Res 2014; 13:1810-22. [PMID: 24593137 DOI: 10.1021/pr400971e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The present work aims at characterizing T. harzianum secretome when the fungus is grown in synthetic medium supplemented with one of the four substrates: glucose, cellulose, xylan, and sugarcane bagasse (SB). The characterization was done by enzymatic assays and proteomic analysis using 2-DE/MALDI-TOF and gel-free shotgun LC-MS/MS. The results showed that SB induced the highest cellulolytic and xylanolytic activities when compared with the other substrates, while remarkable differences in terms of number and distribution of protein spots in 2-DE gels were also observed among the samples. Additionally, treatment of the secretomes with PNGase F revealed that most spot trails in 2-DE gels corresponded to N-glycosylated proteoforms. The LC-MS/MS analysis of the samples identified 626 different protein groups, including carbohydrate-active enzymes and accessory, noncatalytic, and cell-wall-associated proteins. Although the SB-induced secretome displayed the highest cellulolytic and xylanolytic activities, it did not correspond to a higher proteome complexity because CM-cellulose-induced secretome was significantly more diverse. Among the identified proteins, 73% were exclusive to one condition, while only 5% were present in all samples. Therefore, this study disclosed the variation of T. harzianum secretome in response to different substrates and revealed the diversity of the fungus enzymatic toolbox.
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Affiliation(s)
- Diana Paola Gómez-Mendoza
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Asa Norte, Brasília, 70910-900 DF, Brazil
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25
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Baldrian P, López-Mondéjar R. Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods. Appl Microbiol Biotechnol 2014; 98:1531-7. [PMID: 24384749 DOI: 10.1007/s00253-013-5457-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/30/2013] [Accepted: 12/05/2013] [Indexed: 11/28/2022]
Abstract
Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Vídeňská 1083, 14220, Prague 4, Czech Republic,
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26
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Ju X, Bowden M, Engelhard M, Zhang X. Investigating commercial cellulase performances toward specific biomass recalcitrance factors using reference substrates. Appl Microbiol Biotechnol 2013; 98:4409-20. [PMID: 24337347 DOI: 10.1007/s00253-013-5450-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 11/29/2022]
Abstract
Three commercial cellulase preparations, Novozymes Cellic(®) Ctec2, Dupont Accellerase(®) 1500, and DSM Cytolase CL, were evaluated for their hydrolytic activity using a set of reference biomass substrates with controlled substrate characteristics. It was found that lignin remains a significant recalcitrance factor to all the preparations, although different enzyme preparations respond to the inhibitory effect of lignin differently. Also, different types of biomass lignin can inhibit cellulase enzymes in different manners. Enhancing enzyme activity toward biomass fiber swelling is an area significantly contributing to potential improvement in cellulase performance. While the degree of polymerization of cellulose in the reference substrates did not present a major recalcitrance factor to Novozymes Cellic(®) Ctec2, cellulose crystallite has been shown to have a significant lower reactivity toward all enzyme mixtures. The presence of polysaccharide monooxygenases (PMOs) in Novozymes Ctec2 appears to enhance enzyme activity toward decrystallization of cellulose. This study demonstrated that reference substrates with controlled chemical and physical characteristics of structural features can be applied as an effective and practical strategy to identify cellulosic enzyme activities toward specific biomass recalcitrance factor(s) and provide specific targets for enzyme improvement.
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Affiliation(s)
- Xiaohui Ju
- Voiland School of Chemical Engineering and Bioengineering, Bioproducts, Science and Engineering Laboratory, Washington State University, Richland, WA, 99354, USA
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27
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Nihira T, Saito Y, Nishimoto M, Kitaoka M, Igarashi K, Ohtsubo K, Nakai H. Discovery of cellobionic acid phosphorylase in cellulolytic bacteria and fungi. FEBS Lett 2013; 587:3556-61. [PMID: 24055472 DOI: 10.1016/j.febslet.2013.09.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/25/2022]
Abstract
A novel phosphorylase was characterized as new member of glycoside hydrolase family 94 from the cellulolytic bacterium Xanthomonas campestris and the fungus Neurospora crassa. The enzyme catalyzed reversible phosphorolysis of cellobionic acid. We propose 4-O-β-D-glucopyranosyl-D-gluconic acid: phosphate α-D-glucosyltransferase as the systematic name and cellobionic acid phosphorylase as the short names for the novel enzyme. Several cellulolytic fungi of the phylum Ascomycota also possess homologous proteins. We, therefore, suggest that the enzyme plays a crucial role in cellulose degradation where cellobionic acid as oxidized cellulolytic product is converted into α-D-glucose 1-phosphate and D-gluconic acid to enter glycolysis and the pentose phosphate pathway, respectively.
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Affiliation(s)
- Takanori Nihira
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
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28
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Dimarogona M, Topakas E, Christakopoulos P. Recalcitrant polysaccharide degradation by novel oxidative biocatalysts. Appl Microbiol Biotechnol 2013; 97:8455-65. [PMID: 23995228 DOI: 10.1007/s00253-013-5197-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 12/13/2022]
Abstract
The classical hydrolytic mechanism for the degradation of plant polysaccharides by saprophytic microorganisms has been reconsidered after the recent landmark discovery of a new class of oxidases termed lytic polysaccharide monooxygenases (LPMOs). LPMOs are of increased biotechnological interest due to their implication in lignocellulosic biomass decomposition for the production of biofuels and high-value chemicals. They act on recalcitrant polysaccharides by a combination of hydrolytic and oxidative function, generating oxidized and non-oxidized chain ends. They are copper-dependent and require molecular oxygen and an external electron donor for their proper function. In this review, we present the recent findings concerning the mechanism of action of these oxidative enzymes and identify issues and questions to be addressed in the future.
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Affiliation(s)
- Maria Dimarogona
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str, Zografou Campus, 15700, Athens, Greece
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29
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Hemsworth GR, Davies GJ, Walton PH. Recent insights into copper-containing lytic polysaccharide mono-oxygenases. Curr Opin Struct Biol 2013; 23:660-8. [PMID: 23769965 DOI: 10.1016/j.sbi.2013.05.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/15/2013] [Accepted: 05/16/2013] [Indexed: 12/18/2022]
Abstract
Recently the role of oxidative enzymes in the degradation of polysaccharides by saprophytic bacteria and fungi was uncovered, challenging the classical model of polysaccharide degradation of being solely via a hydrolytic pathway. 3D structural analyses of lytic polysaccharide mono-oxygenases of both bacterial AA10 (formerly CBM33) and fungal AA9 (formerly GH61) enzymes revealed structures with β-sandwich folds containing an active site with a metal coordinated by an N-terminal histidine. Following some initial confusion about the identity of the metal ion it has now been shown that these enzymes are copper-dependent oxygenases. Here we assess recent developments in the academic literature, focussing on the structures of the copper active sites. We provide critical comparisons with known small-molecules studies of copper-oxygen complexes and with copper methane monoxygenase, another of nature's powerful copper oxygenases.
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Affiliation(s)
- Glyn R Hemsworth
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
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30
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Ekwe E, Morgenstern I, Tsang A, Storms R, Powlowski J. Non-Hydrolytic Cellulose Active Proteins: Research Progress and Potential Application in Biorefineries. Ind Biotechnol (New Rochelle N Y) 2013. [DOI: 10.1089/ind.2013.0010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Enongene Ekwe
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Ingo Morgenstern
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Reginald Storms
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
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31
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Cerato-platanin shows expansin-like activity on cellulosic materials. Appl Microbiol Biotechnol 2013; 98:175-84. [DOI: 10.1007/s00253-013-4822-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/26/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
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32
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Liu G, Qin Y, Li Z, Qu Y. Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era. Biotechnol Adv 2013; 31:962-75. [PMID: 23507038 DOI: 10.1016/j.biotechadv.2013.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/09/2013] [Accepted: 03/10/2013] [Indexed: 11/19/2022]
Abstract
The current high cost of lignocellulolytic enzymes is a major bottleneck in the economic bioconversion of lignocellulosic biomass to fuels and chemicals. Fungal lignocellulolytic enzyme systems are secreted at high levels, making them the most promising starting points for further development of highly efficient lignocellulolytic enzyme systems. In this paper, recent advances in improvement of fungal lignocellulolytic enzyme systems are reviewed, with an emphasis on the achievements made using genomic approaches. A general strategy for lignocellulolytic enzyme system development is proposed, including the improvement of the hydrolysis efficiencies and productivities of current enzyme systems. The applications of genomic, transcriptomic and proteomic analysis methods in examining the composition of native enzyme systems, discovery of novel enzymes and synergistic proteins from natural sources, and understanding of regulatory mechanisms for lignocellulolytic enzyme biosynthesis are summarized. By combining systems biology and synthetic biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.
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Affiliation(s)
- Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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