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Ríos-Alvarado J, Avitia-Rodríguez ON, Urtiz-Estrada N, Zazueta-Álvarez DE, López-Miranda J, Vázquez-Ortega PG, Rojas-Contreras JA. Expression and characterization of a novel β-1,4-endoglucanase from Bacillus subtilis strain isolated from a pulp and paper mill wastewater. Protein Expr Purif 2024; 220:106490. [PMID: 38697589 DOI: 10.1016/j.pep.2024.106490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The production of fermentable sugars from lignocellulosic biomass is achieved by the synergistic action of a group of enzymes called cellulases. Cellulose is a long chain of chemically linked glucoses by β-1,4 bonds. The enzyme β-1,4-endoglucanase is the first cellulase involved in the degradation, breaking the bond of the amorphous regions. A β-1,4-endoglucanase enzyme with high activity was obtained from a Bacillus subtilis strain isolated from wastewater of a pulp and paper mill. Sequencing and bioinformatic analysis showed that the gene amplified by PCR consisting of 1407 nucleotides and coding for a β-1,4-endoglucanase enzyme of approximately 55 kDa. The open reading frame (ORF) encoding the mature endoglucanase (eglS) was successfully inserted in a modified cloning plasmid (pITD03) and into the pYD1 plasmid used for its expression in yeast. Carboxymethylcellulose (CMC) plate assay, SDS-PAGE, and zymogram confirmed the production and secretion by the transformed E. coli BL21-SI strain of a 39 kDa β-1,4-endoglucanase consistent with the catalytic domain without the cellulose-binding module (CBM). The results showed that the truncated β-1,4-endoglucanase had higher activity and stability.
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Affiliation(s)
- Joel Ríos-Alvarado
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico
| | - Olga Noelia Avitia-Rodríguez
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico
| | - Norma Urtiz-Estrada
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Veterinaria S/N, Col. Valle del Sur, 34120, Durango, Dgo., Mexico
| | - David Enrique Zazueta-Álvarez
- Universidad Politécnica de Durango, Departamento de Ingeniería en Tecnología Ambiental, Carretera Durango-México Km 9.5. Col, Los Encinos, C.P. 34300, Durango, Dgo, Mexico
| | - Javier López-Miranda
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico
| | - Perla Guadalupe Vázquez-Ortega
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico.
| | - Juan Antonio Rojas-Contreras
- Tecnológico Nacional de México/Instituto Tecnológico de Durango, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, 34080, Durango, Dgo., Mexico.
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Kathirgamanathan M, Weerasinghe S, Bowange TK, Abayasekara CL, Kulasooriya SA, Ratnayake RR. Evaluation of co-culture of cellulolytic fungi for enhanced cellulase and xylanase activity and saccharification of untreated lignocellulosic material. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01183-y. [PMID: 38954242 DOI: 10.1007/s12223-024-01183-y] [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: 09/11/2023] [Accepted: 06/11/2024] [Indexed: 07/04/2024]
Abstract
Bioethanol production from lignocellulosic materials is hindered by the high costs of pretreatment and the enzymes. The present study aimed to evaluate whether co-cultivation of four selected cellulolytic fungi yields higher cellulase and xylanase activities compared to the monocultures and to investigate whether the enzymes from the co-cultures yield higher saccharification on selected plant materials without thermo-chemical pretreatment. The fungal isolates, Trichoderma reesei F118, Penicillium javanicum FS7, Talaromyces sp. F113, and Talaromyces pinophilus FM9, were grown as monocultures and binary co-cultures under submerged conditions for 7 days. The cellulase and xylanase activities of the culture filtrates were measured, and the culture filtrates were employed for the saccharification of sugarcane leaves, Guinea grass leaves, and water hyacinth stems and leaves. Total reducing sugars and individual sugars released from each plant material were quantified. The co-culture of Talaromyces sp. F113 with Penicillium javanicum FS7 and of T. reesei F118 with T. pinophilus FM9 produced significantly higher cellulase activities compared to the corresponding monocultures whereas no effect was observed on xylanase activities. Overall, the highest amounts of total reducing sugars and individual sugars were obtained from Guinea grass leaves saccharified with the co-culture of T. reesei F118 with T. pinophilus FM9, yielding 63.5% saccharification. Guinea grass leaves were found to be the most susceptible to enzymatic saccharification without pre-treatment, while water hyacinth stems and leaves were the least. Accordingly, the study suggests that fungal co-cultivation could be a promising approach for the saccharification of lignocellulosic materials for bioethanol production.
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Affiliation(s)
- M Kathirgamanathan
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - S Weerasinghe
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - T K Bowange
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - C L Abayasekara
- Department of Botany, Faculty of Science, University of Peradeniya, Kandy, Sri Lanka
| | - S A Kulasooriya
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - R R Ratnayake
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka.
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Zhang F, Zhang Y, He T, Ji Q, Hou S, Gui L. Changes in Rumen Microbiology and Metabolism of Tibetan Sheep with Different Lys/Met Ratios in Low-Protein Diets. Animals (Basel) 2024; 14:1533. [PMID: 38891581 PMCID: PMC11171176 DOI: 10.3390/ani14111533] [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: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
In ruminants, supplementing appropriate amounts of amino acids improves growth, feed utilization efficiency, and productivity. This study aimed to assess the effects of different Lys/Met ratios on the ruminal microbial community and the metabolic profiling in Tibetan sheep using 16S rDNA sequencing and non-target metabolomics. Ninety-two-month-old Tibetan rams (initial weight = 15.37 ± 0.92 kg) were divided into three groups and fed lysine/methionine (Lys/Met) of 1:1 (LP-L), 2:1 (LP-M), and 3:1 (LP-H) in low-protein diet, respectively. Results: The T-AOC, GSH-Px, and SOD were significantly higher in the LP-L group than in LP-H and LP-M groups (p < 0.05). Cellulase activity was significantly higher in the LP-L group than in the LP-H group (p < 0.05). In the fermentation parameters, acetic acid concentration was significantly higher in the LP-L group than in the LP-H group (p < 0.05). Microbial sequencing analysis showed that Ace and Chao1 indicators were significantly higher in LP-L than in LP-H and LP-M (p < 0.05). At the genus level, the abundance of Rikenellaceae RC9 gut group flora and Succiniclasticum were significantly higher in LP-L than in LP-M group (p < 0.05). Non-target metabolomics analyses revealed that the levels of phosphoric acid, pyrocatechol, hydrocinnamic acid, banzamide, l-gulono-1,4-lactone, cis-jasmone, Val-Asp-Arg, and tropinone content were higher in LP-L. However, l-citrulline and purine levels were lower in the LP-L group than in the LP-M and LP-H groups. Banzamide, cis-jasmone, and Val-Asp-Arg contents were positively correlated with the phenotypic contents, including T-AOC, SOD, and cellulase. Phosphoric acid content was positively correlated with cellulase and lipase activities. In conclusion, the Met/Lys ratio of 1:1 in low-protein diets showed superior antioxidant status and cellulase activity in the rumen by modulating the microbiota and metabolism of Tibetan sheep.
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Affiliation(s)
| | | | | | | | | | - Linsheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810000, China; (F.Z.); (Y.Z.); (Q.J.); (S.H.)
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Bautista-Cruz A, Aquino-Bolaños T, Hernández-Canseco J, Quiñones-Aguilar EE. Cellulolytic Aerobic Bacteria Isolated from Agricultural and Forest Soils: An Overview. BIOLOGY 2024; 13:102. [PMID: 38392320 PMCID: PMC10886624 DOI: 10.3390/biology13020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20-30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.
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Affiliation(s)
- Angélica Bautista-Cruz
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Teodulfo Aquino-Bolaños
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Jessie Hernández-Canseco
- Doctoral Programme in Conservation and Use of Natural Resources, Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, Zapopan 45019, Jalisco, Mexico
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An P, Yang C, Li W, Zhao D, Xiang H. The Isolation and Characterization of a Novel Psychrotolerant Cellulolytic Bacterium, Microbacterium sp. QXD-8 T. Microorganisms 2024; 12:303. [PMID: 38399707 PMCID: PMC10892437 DOI: 10.3390/microorganisms12020303] [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: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 02/25/2024] Open
Abstract
Cellulolytic microorganisms play a crucial role in agricultural waste disposal. Strain QXD-8T was isolated from soil in northern China. Similarity analyses of the 16S rRNA gene, as well as the 120 conserved genes in the whole-genome sequence, indicate that it represents a novel species within the genus Microbacterium. The Microbacterium sp. QXD-8T was able to grow on the CAM plate with sodium carboxymethyl cellulose as a carbon source at 15 °C, forming a transparent hydrolysis circle after Congo red staining, even though the optimal temperature for the growth and cellulose degradation of strain QXD-8T was 28 °C. In the liquid medium, it effectively degraded cellulose and produced reducing sugars. Functional annotation revealed the presence of encoding genes for the GH5, GH6, and GH10 enzyme families with endoglucanase activity, as well as the GH1, GH3, GH39, and GH116 enzyme families with β-glucosidase activity. Additionally, two proteins in the GH6 family, one in the GH10, and two of nine proteins in the GH3 were predicted to contain a signal peptide and transmembrane region, suggesting their potential for extracellularly degrade cellulose. Based on the physiological features of the type strain QXD-8T, we propose the name Microbacterium psychrotolerans for this novel species. This study expands the diversity of psychrotolerant cellulolytic bacteria and provides a potential microbial resource for straw returning in high-latitude areas at low temperatures.
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Affiliation(s)
- Peng An
- College of Life Science, Sichuan Normal University, Chengdu 610101, China; (P.A.); (W.L.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Changjialian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- College of Life Science, Sichuan Normal University, Chengdu 610101, China; (P.A.); (W.L.)
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
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Ramanathan N, Sreeramulu B, Mani M, Sundaram J. Potential of insect endogenous cellulases for lignocellulosic break down deciphered using molecular docking studies. Nat Prod Res 2023:1-9. [PMID: 37967019 DOI: 10.1080/14786419.2023.2280169] [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: 07/22/2023] [Accepted: 10/30/2023] [Indexed: 11/17/2023]
Abstract
Insects possess cellulolytic system capable of producing variegate enzymes with multifarious specificities to break down complex lignocellulosic products. Astonishingly, endoglucanases, exoglucanases and β-glycosidases act sequentially in a synergistic system to facilitate the breakdown of cellulose to utilisable energy source glucose. In silico docking studies of endo-β-1,4-glucanase from 19 different insects belonging to six different orders identified that it possesses high affinity for all the six substrates, including CMC, cellulose, cellotriose, cellotetraose, cellopentose and cellohexaose. Additionally, β-glucosidase from nearly all the reported insect sources also showed considerable affinity towards cellobiose. Van der Waals, conventional hydrogen bonds and carbon-hydrogen bonds stabilise the interaction between the enzyme and different substrates. Molecular dynamics simulations also held up the stability of various complexes. Efficient breakdown of lignocelluloses-based substrates becoming a major focus of industrial and academic communities worldwide, this study can perhaps complement the propensity of insect cellulases for prospected applications.
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Peng Q, Lin L, Tu Q, Wang X, Zhou Y, Chen J, Jiao N, Zhou J. Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates. mSystems 2023; 8:e0128322. [PMID: 37417747 PMCID: PMC10469889 DOI: 10.1128/msystems.01283-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/12/2023] [Indexed: 07/08/2023] Open
Abstract
Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.
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Affiliation(s)
- Qiannan Peng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaopeng Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Yueyue Zhou
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Jiyu Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Joint Lab for Ocean Research and Education at Shandong University, Xiamen University and Dalhousie University, Qingdao, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
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Korsa G, Konwarh R, Masi C, Ayele A, Haile S. Microbial cellulase production and its potential application for textile industries. ANN MICROBIOL 2023; 73:13. [DOI: 10.1186/s13213-023-01715-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 03/22/2023] [Indexed: 09/03/2023] Open
Abstract
Abstract
Purpose
The textile industry’s previous chemical use resulted in thousands of practical particulate emissions, such as machine component damage and drainage system blockage, both of which have practical implications. Enzyme-based textile processing is cost-effective, environmentally friendly, non-hazardous, and water-saving. The purpose of this review is to give evidence on the potential activity of microbial cellulase in the textile industry, which is mostly confined to the realm of research.
Methods
This review was progressive by considering peer-reviewed papers linked to microbial cellulase production, and its prospective application for textile industries was appraised and produced to develop this assessment. Articles were divided into two categories based on the results of trustworthy educational journals: methods used to produce the diversity of microorganisms through fermentation processes and such approaches used to produce the diversity of microbes through microbial fermentation. Submerged fermentation (SMF) and solid-state fermentation (SSF) techniques are currently being used to meet industrial demand for microbial cellulase production in the bio textile industry.
Results
Microbial cellulase is vital for increasing day to day due to its no side effect on the environment and human health becoming increasingly important. In conventional textile processing, the gray cloth was subjected to a series of chemical treatments that involved breaking the dye molecule’s amino group with Cl − , which started and accelerated dye(-resistant) bond cracking. A cellulase enzyme is primarily derived from a variety of microbial species found in various ecological settings as a biotextile/bio-based product technology for future needs in industrial applications.
Conclusion
Cellulase has been produced for its advantages in cellulose-based textiles, as well as for quality enhancement and fabric maintenance over traditional approaches. Cellulase’s role in the industry was microbial fermentation processes in textile processing which was chosen as an appropriate and environmentally sound solution for a long and healthy lifestyle.
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Gauttam R, Eng T, Zhao Z, Ul Ain Rana Q, Simmons BA, Yoshikuni Y, Mukhopadhyay A, Singer SW. Development of genetic tools for heterologous protein expression in a pentose-utilizing environmental isolate of Pseudomonas putida. Microb Biotechnol 2023; 16:645-661. [PMID: 36691869 PMCID: PMC9948227 DOI: 10.1111/1751-7915.14205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 01/25/2023] Open
Abstract
Pseudomonas putida has emerged as a promising host for the conversion of biomass-derived sugars and aromatic intermediates into commercially relevant biofuels and bioproducts. Most of the strain development studies previously published have focused on P. putida KT2440, which has been engineered to produce a variety of non-native bioproducts. However, P. putida is not capable of metabolizing pentose sugars, which can constitute up to 25% of biomass hydrolysates. Related P. putida isolates that metabolize a larger fraction of biomass-derived carbon may be attractive as complementary hosts to P. putida KT2440. Here we describe genetic tool development for P. putida M2, a soil isolate that can metabolize pentose sugars. The functionality of five inducible promoter systems and 12 ribosome binding sites was assessed to regulate gene expression. The utility of these expression systems was confirmed by the production of indigoidine from C6 and C5 sugars. Chromosomal integration and expression of non-native genes was achieved by using chassis-independent recombinase-assisted genome engineering (CRAGE) for single-step gene integration of biosynthetic pathways directly into the genome of P. putida M2. These genetic tools provide a foundation to develop hosts complementary to P. putida KT2440 and expand the ability of this versatile microbial group to convert biomass to bioproducts.
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Affiliation(s)
- Rahul Gauttam
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas Eng
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhiying Zhao
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Qurrat Ul Ain Rana
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yasuo Yoshikuni
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Role of Alternative Elicitor Transporters in the Onset of Plant Host Colonization by Streptomyces scabiei 87-22. BIOLOGY 2023; 12:biology12020234. [PMID: 36829511 PMCID: PMC9953190 DOI: 10.3390/biology12020234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Plant colonization by Streptomyces scabiei, the main cause of common scab disease on root and tuber crops, is triggered by cello-oligosaccharides, cellotriose being the most efficient elicitor. The import of cello-oligosaccharides via the ATP-binding cassette (ABC) transporter CebEFG-MsiK induces the production of thaxtomin phytotoxins, the central virulence determinants of this species, as well as many other metabolites that compose the 'virulome' of S. scabiei. Homology searches revealed paralogues of the CebEFG proteins, encoded by the cebEFG2 cluster, while another ABC-type transporter, PitEFG, is encoded on the pathogenicity island (PAI). We investigated the gene expression of these candidate alternative elicitor importers in S. scabiei 87-22 upon cello-oligosaccharide supply by transcriptomic analysis, which revealed that cebEFG2 expression is highly activated by both cellobiose and cellotriose, while pitEFG expression was barely induced. Accordingly, deletion of pitE had no impact on virulence and thaxtomin production under the conditions tested, while the deletion of cebEFG2 reduced virulence and thaxtomin production, though not as strong as the mutants of the main cello-oligosaccharide transporter cebEFG1. Our results thus suggest that both ceb clusters participate, at different levels, in importing the virulence elicitors, while PitEFG plays no role in this process under the conditions tested. Interestingly, under more complex culture conditions, the addition of cellobiose restored thaxtomin production when both ceb clusters were disabled, suggesting the existence of an additional mechanism that is involved in sensing or importing the elicitor of the onset of the pathogenic lifestyle of S. scabiei.
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Shinde R, Shahi DK, Mahapatra P, Naik SK, Thombare N, Singh AK. Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115843. [PMID: 36056484 DOI: 10.1016/j.jenvman.2022.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.
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Affiliation(s)
- Reshma Shinde
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India.
| | | | | | - Sushanta Kumar Naik
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
| | - Nandkishore Thombare
- ICAR- Indian Institute of Natural Resin and Gums, Ranchi, 834010, Jharkhand, India
| | - Arun Kumar Singh
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
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12
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Glycosyltransferase-Related Protein GtrA Is Essential for Localization of Type IX Secretion System Cargo Protein Cellulase Cel9A and Affects Cellulose Degradation in Cytophaga hutchinsonii. Appl Environ Microbiol 2022; 88:e0107622. [PMID: 36197104 PMCID: PMC9599414 DOI: 10.1128/aem.01076-22] [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: 11/20/2022] Open
Abstract
The Gram-negative bacterium Cytophaga hutchinsonii digests cellulose through a novel cellulose degradation mechanism. It possesses the lately characterized type IX secretion system (T9SS). We recently discovered that N-glycosylation of the C-terminal domain (CTD) of a hypothetical T9SS substrate protein in the periplasmic space of C. hutchinsonii affects protein secretion and localization. In this study, green fluorescent protein (GFP)-CTDCel9A recombinant protein was found with increased molecular weight in the periplasm of C. hutchinsonii. Site-directed mutagenesis studies on the CTD of cellulase Cel9A demonstrated that asparagine residue 900 in the D-X-N-X-S motif is important for the processing of the recombinant protein. We found that the glycosyltransferase-related protein GtrA (CHU_0012) located in the cytoplasm of C. hutchinsonii is essential for outer membrane localization of the recombinant protein. The deletion of gtrA decreased the abundance of the outer membrane proteins and affected cellulose degradation by C. hutchinsonii. This study provided a link between the glycosylation system and cellulose degradation in C. hutchinsonii. IMPORTANCE N-Glycosylation systems are generally limited to some pathogenic bacteria in prokaryotes. The disruption of the N-glycosylation pathway is related to adherence, invasion, colonization, and other phenotypic characteristics. We recently found that the cellulolytic bacterium Cytophaga hutchinsonii also has an N-glycosylation system. The cellulose degradation mechanism of C. hutchinsonii is novel and mysterious; cellulases and other proteins on the cell surface are involved in utilizing cellulose. In this study, we identified an asparagine residue in the C-terminal domain of cellulase Cel9A that is necessary for the processing of the T9SS cargo protein. Moreover, the glycosyltransferase-related protein GtrA is essential for the localization of the GFP-CTDCel9A recombinant protein. Deletion of gtrA affected cellulose degradation and the abundance of outer membrane proteins. This study enriched the understanding of the N-glycosylation system in C. hutchinsonii and provided a link between N-glycosylation and cellulose degradation, which also expanded the role of the N-glycosylation system in bacteria.
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13
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Kim DY, Kim J, Lee YM, Byeon SM, Gwak JH, Lee JS, Shin DH, Park HY. Novel, acidic, and cold-adapted glycoside hydrolase family 8 endo-β-1,4-glucanase from an Antarctic lichen-associated bacterium, Lichenicola cladoniae PAMC 26568. Front Microbiol 2022; 13:935497. [PMID: 35910630 PMCID: PMC9329076 DOI: 10.3389/fmicb.2022.935497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Endo-β-1,4-glucanase is a crucial glycoside hydrolase (GH) involved in the decomposition of cellulosic materials. In this study, to discover a novel cold-adapted β-1,4-D-glucan-degrading enzyme, the gene coding for an extracellular endo-β-1,4-glucanase (GluL) from Lichenicola cladoniae PAMC 26568, an Antarctic lichen (Cladonia borealis)-associated bacterium, was identified and recombinantly expressed in Escherichia coli BL21. The GluL gene (1044-bp) encoded a non-modular polypeptide consisting of a single catalytic GH8 domain, which shared the highest sequence identity of 55% with that of an uncharacterized protein from Gluconacetobacter takamatsuzukensis (WP_182950054). The recombinant endo-β-1,4-glucanase (rGluL: 38.0 kDa) most efficiently degraded sodium carboxymethylcellulose (CMC) at pH 4.0 and 45°C, and showed approximately 23% of its maximum degradation activity even at 3°C. The biocatalytic activity of rGluL was noticeably enhanced by >1.3-fold in the presence of 1 mM Mn2+ or NaCl at concentrations between 0.1 and 0.5 M, whereas the enzyme was considerably downregulated by 1 mM Hg2+ and Fe2+ together with 5 mM N-bromosuccinimide and 0.5% sodium dodecyl sulfate. rGluL is a true endo-β-1,4-glucanase, which could preferentially decompose D-cellooligosaccharides consisting of 3 to 6 D-glucose, CMC, and barley β-glucan, without other additional glycoside hydrolase activities. The specific activity (15.1 U mg-1) and k cat/K m value (6.35 mg-1 s-1mL) of rGluL toward barley β-glucan were approximately 1.8- and 2.2-fold higher, respectively, compared to its specific activity (8.3 U mg-1) and k cat/K m value (2.83 mg-1 s-1mL) toward CMC. The enzymatic hydrolysis of CMC, D-cellotetraose, and D-cellohexaose yielded primarily D-cellobiose, accompanied by D-glucose, D-cellotriose, and D-cellotetraose. However, the cleavage of D-cellopentaose by rGluL resulted in the production of only D-cellobiose and D-cellotriose. The findings of the present study imply that rGluL is a novel, acidic, and cold-adapted GH8 endo-β-1,4-glucanase with high specific activity, which can be exploited as a promising candidate in low-temperature processes including textile and food processes.
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Affiliation(s)
- Do Young Kim
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jonghoon Kim
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Soo Min Byeon
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biological Science, Daejeon University, Daejeon, South Korea
| | - Jeong Hae Gwak
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jong Suk Lee
- Biocenter, Gyeonggido Business and Science Accelerator (GBSA), Suwon, South Korea
| | | | - Ho-Yong Park
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
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14
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Tsudome M, Tachioka M, Miyazaki M, Uchimura K, Tsuda M, Takaki Y, Deguchi S. An ultrasensitive nanofiber-based assay for enzymatic hydrolysis and deep-sea microbial degradation of cellulose. iScience 2022; 25:104732. [PMID: 36039358 PMCID: PMC9418596 DOI: 10.1016/j.isci.2022.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/10/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mikiko Tsudome
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Mikako Tachioka
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kohsuke Uchimura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Miwako Tsuda
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Corresponding author
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15
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Sohail M, Barzkar N, Michaud P, Tamadoni Jahromi S, Babich O, Sukhikh S, Das R, Nahavandi R. Cellulolytic and Xylanolytic Enzymes from Yeasts: Properties and Industrial Applications. Molecules 2022; 27:3783. [PMID: 35744909 PMCID: PMC9229053 DOI: 10.3390/molecules27123783] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose, the main component of plant cell walls, comprises polyaromatic lignin and fermentable materials, cellulose and hemicellulose. It is a plentiful and renewable feedstock for chemicals and energy. It can serve as a raw material for the production of various value-added products, including cellulase and xylanase. Cellulase is essentially required in lignocellulose-based biorefineries and is applied in many commercial processes. Likewise, xylanases are industrially important enzymes applied in papermaking and in the manufacture of prebiotics and pharmaceuticals. Owing to the widespread application of these enzymes, many prokaryotes and eukaryotes have been exploited to produce cellulase and xylanases in good yields, yet yeasts have rarely been explored for their plant-cell-wall-degrading activities. This review is focused on summarizing reports about cellulolytic and xylanolytic yeasts, their properties, and their biotechnological applications.
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Affiliation(s)
- Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan;
| | - Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas 3995, Iran
| | - Philippe Michaud
- Institute Pascal, Université Clermont Auvergne, CNRS, Clermont Auvergne INP, F-63000 Clermont-Ferrand, France;
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecology Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas 3995, Iran
| | - Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
| | - Rakesh Das
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), 1433 Aas, Norway;
| | - Reza Nahavandi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj 8361, Iran;
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16
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Anye V, Kruger RF, Schubert WD. Structural and biophysical characterization of the multidomain xylanase Xyl. PLoS One 2022; 17:e0269188. [PMID: 35657930 PMCID: PMC9165906 DOI: 10.1371/journal.pone.0269188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
The depletion of fossil fuels, associated pollution, and resulting health hazards are of concern worldwide. Woody biomass constitutes an alternative source of cleaner and renewable energy. The efficient use of woody biomass depends on xylan depolymerisation as the endo-β-1,4-xylopyranosyl homopolymer is the main component of hemicellulose, the second most abundant component of wood. Xylan depolymerisation is achieved by hemicellulolytic xylanases of glycoside hydrolase (GH) families 5, 8, 10, 11, 30 and 43 of the CAZY database. We analysed a multidomain xylanase (Xyl) from the hindgut metagenome of the snouted harvester termite Trinervitermes trinervoides that releases xylobiose and xylotriose from beech and birch xylan and wheat arabinoxylan. The four domains of Xyl include an N-terminal GH11 xylanase domain, two family 36-like carbohydrate-binding domains CBM36-1 and 2, and a C-terminal CE4 esterase domain. Previous analyses indicated that CBM36-1 deletion slightly increased GH11 catalysis at low pH whereas removal of both CBMs decreased xylanase activity at 60°C from 90 to 56%. Possible cooperativity between the domains suggested by these observations was explored. A crystal structure of the two-domain construct, GH11-CBM36-1, confirmed the structure of the GH11 domain whereas the CBM36-1 domain lacked electron density, possibly indicating a random orientation of the CBM36-1 domain around the GH11 domain. Isothermal titration calorimetry (ITC) experiments similarly did not indicate specific interactions between the individual domains of Xyl supporting a "beads-on-a-string" model for Xyl domains.
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Affiliation(s)
- Valentine Anye
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Robert F. Kruger
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Wolf-Dieter Schubert
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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17
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Lewin GR, Davis NM, McDonald BR, Book AJ, Chevrette MG, Suh S, Boll A, Currie CR. Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods. mSystems 2022; 7:e0151921. [PMID: 35258341 PMCID: PMC9040578 DOI: 10.1128/msystems.01519-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022] Open
Abstract
The complexity of microbial communities hinders our understanding of how microbial diversity and microbe-microbe interactions impact community functions. Here, using six independent communities originating from the refuse dumps of leaf-cutter ants and enriched using the plant polymer cellulose as the sole source of carbon, we examine how changes in bacterial diversity and interactions impact plant biomass decomposition. Over up to 60 serial transfers (∼8 months) using Whatman cellulose filter paper, cellulolytic ability increased and then stabilized in four enrichment lines and was variable in two lines. Bacterial community characterization using 16S rRNA gene amplicon sequencing showed community succession differed between the highly cellulolytic enrichment lines and those that had slower and more variable cellulose degradation rates. Metagenomic and metatranscriptomic analyses revealed that Cellvibrio and/or Cellulomonas dominated each enrichment line and produced the majority of cellulase enzymes, while diverse taxa were retained within these communities over the duration of transfers. Interestingly, the less cellulolytic communities had a higher diversity of organisms competing for the cellulose breakdown product cellobiose, suggesting that cheating slowed cellulose degradation. In addition, we found competitive exclusion as an important factor shaping all of the communities, with a negative correlation of Cellvibrio and Cellulomonas abundance within individual enrichment lines and the expression of genes associated with the production of secondary metabolites, toxins, and other antagonistic compounds. Our results provide insights into how microbial diversity and competition affect the stability and function of cellulose-degrading communities. IMPORTANCE Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define. Here, we performed serial enrichment on cellulose using communities inoculated from leaf-cutter ant refuse dumps, a cellulose-rich environment. By concurrently tracking cellulolytic ability and community composition and through metagenomic and metatranscriptomic sequencing, we analyzed the ecological dynamics of the enrichment lines. Our data suggest that antagonism is prevalent in these communities and that competition for soluble sugars may slow degradation and lead to community instability. Together, these results help reveal the relationships between competition and polysaccharide decomposition, with implications in diverse areas ranging from microbial community ecology to cellulosic biofuels production.
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Affiliation(s)
- Gina R. Lewin
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Nicole M. Davis
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Bradon R. McDonald
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Adam J. Book
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Marc G. Chevrette
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Steven Suh
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Ardina Boll
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Cameron R. Currie
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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18
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Tan Y, Song W, Gao L, Zhang W, Lu X. Cytophaga hutchinsonii chu_2177, encoding the O-antigen ligase, is essential for cellulose degradation. J Microbiol 2022; 60:364-374. [DOI: 10.1007/s12275-022-1531-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022]
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19
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McGregor NGS, Overkleeft HS, Davies GJ. Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes. Methods Enzymol 2022; 664:103-134. [PMID: 35331370 DOI: 10.1016/bs.mie.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and selective for the enzyme(s) of interest. Deconvolution of the contributions of different enzymes to an observed catalytic ability further necessitates an often-challenging protein separation. The advent of broadly reactive activity-based probes (ABPs) for retaining glycoside hydrolases (GHs) has enabled an alternative, often complementary, assay for active GHs. Using activity-based protein profiling (ABPP) techniques, many retaining glycoside hydrolases can be separated, detected, and identified with high sensitivity and selectivity. This chapter outlines ABPP methods for the detection and identification of retaining glycoside hydrolases from microbial sources, including protein sample preparation from bacterial lysates and fungal secretomes, enzyme labeling and detection via fluorescence, and enzyme identification using affinity-based enrichment coupled to peptide sequencing following isobaric labeling.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom.
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20
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Goswami K, Deka Boruah HP, Saikia R. Purification and characterization of cellulase produced by
Novosphingobium
sp. Cm1 and its waste hydrolysis efficiency and bio‐stoning potential. J Appl Microbiol 2022; 132:3618-3628. [DOI: 10.1111/jam.15475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Kongkana Goswami
- CSIR‐North East Institute of Science and Technology Jorhat‐785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad‐201002 India
| | | | - Ratul Saikia
- CSIR‐North East Institute of Science and Technology Jorhat‐785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad‐201002 India
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21
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Perlman D, Martínez-Álvaro M, Moraïs S, Altshuler I, Hagen LH, Jami E, Roehe R, Pope PB, Mizrahi I. Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development. Annu Rev Anim Biosci 2021; 10:177-201. [PMID: 34941382 DOI: 10.1146/annurev-animal-013020-020412] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host-core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Daphne Perlman
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
| | - Marina Martínez-Álvaro
- Department of Agriculture, Horticulture and Engineering Sciences, SRUC (Scotland's Rural College), Edinburgh, Scotland, United Kingdom
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
| | - Ianina Altshuler
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway;
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Elie Jami
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Rainer Roehe
- Department of Agriculture, Horticulture and Engineering Sciences, SRUC (Scotland's Rural College), Edinburgh, Scotland, United Kingdom
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway; .,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
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22
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Dou Y, Yang Y, Mund NK, Wei Y, Liu Y, Wei L, Wang Y, Du P, Zhou Y, Liesche J, Huang L, Fang H, Zhao C, Li J, Wei Y, Chen S. Comparative Analysis of Herbaceous and Woody Cell Wall Digestibility by Pathogenic Fungi. Molecules 2021; 26:molecules26237220. [PMID: 34885803 PMCID: PMC8659149 DOI: 10.3390/molecules26237220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Fungal pathogens have evolved combinations of plant cell-wall-degrading enzymes (PCWDEs) to deconstruct host plant cell walls (PCWs). An understanding of this process is hoped to create a basis for improving plant biomass conversion efficiency into sustainable biofuels and bioproducts. Here, an approach integrating enzyme activity assay, biomass pretreatment, field emission scanning electron microscopy (FESEM), and genomic analysis of PCWDEs were applied to examine digestibility or degradability of selected woody and herbaceous biomass by pathogenic fungi. Preferred hydrolysis of apple tree branch, rapeseed straw, or wheat straw were observed by the apple-tree-specific pathogen Valsa mali, the rapeseed pathogen Sclerotinia sclerotiorum, and the wheat pathogen Rhizoctonia cerealis, respectively. Delignification by peracetic acid (PAA) pretreatment increased PCW digestibility, and the increase was generally more profound with non-host than host PCW substrates. Hemicellulase pretreatment slightly reduced or had no effect on hemicellulose content in the PCW substrates tested; however, the pretreatment significantly changed hydrolytic preferences of the selected pathogens, indicating a role of hemicellulose branching in PCW digestibility. Cellulose organization appears to also impact digestibility of host PCWs, as reflected by differences in cellulose microfibril organization in woody and herbaceous PCWs and variation in cellulose-binding domain organization in cellulases of pathogenic fungi, which is known to influence enzyme access to cellulose. Taken together, this study highlighted the importance of chemical structure of both hemicelluloses and cellulose in host PCW digestibility by fungal pathogens.
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Affiliation(s)
- Yanhua Dou
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yan Yang
- College of Chemistry and Chemical Engineering, Shanxi Datong University, Datong 037009, China;
| | - Nitesh Kumar Mund
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yanping Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yisong Liu
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Linfang Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yifan Wang
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Panpan Du
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yunheng Zhou
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Johannes Liesche
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Lili Huang
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Hao Fang
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chen Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jisheng Li
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yahong Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Xianyang 712100, China
- Correspondence: (Y.W.); (S.C.); Tel.: +86-029-87091021 (S.C.)
| | - Shaolin Chen
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Xianyang 712100, China
- Correspondence: (Y.W.); (S.C.); Tel.: +86-029-87091021 (S.C.)
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A T9SS Substrate Involved in Crystalline Cellulose Degradation by Affecting Crucial Cellulose Binding Proteins in Cytophaga hutchinsonii. Appl Environ Microbiol 2021; 88:e0183721. [PMID: 34731049 DOI: 10.1128/aem.01837-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytophaga hutchinsonii is an abundant soil cellulolytic bacterium that uses a unique cellulose degradation mechanism different from those that involve free cellulases or cellulosomes. Though several proteins were identified to be important for cellulose degradation, the mechanism used by C. hutchinsonii to digest crystalline cellulose remains a mystery. In this study, chu_0922 was identified by insertional mutation and gene deletion as an important gene locus indispensable for crystalline cellulose utilization. Deletion of chu_0922 resulted in defect in crystalline cellulose utilization. The Δ0922 mutant completely lost the ability to grow on crystalline cellulose even with extended incubation, and selectively utilized the amorphous region of cellulose leading to the increased crystallinity. As a protein secreted by the type Ⅸ secretion system (T9SS), CHU_0922 was found to be located on the outer membrane, and the outer membrane localization of CHU_0922 relied on the T9SS. Comparative analysis of the outer membrane proteins revealed that the abundance of several cellulose binding proteins, including CHU_1276, CHU_1277, and CHU_1279, was reduced in the Δ0922 mutant. Further study showed that CHU_0922 is crucial for the full expression of the gene cluster containing chu_1276, chu_1277, chu_1278, chu_1279, and chu_1280 (cel9C), which is essential for cellulose utilization. Moreover, CHU_0922 is required for the cell surface localization of CHU_3220, a cellulose binding protein that is essential for crystalline cellulose utilization. Our study provides insights into the complex system that C. hutchinsonii uses to degrade crystalline cellulose. IMPORTANCE The widespread aerobic cellulolytic bacterium Cytophaga hutchinsonii, belonging to the phylum Bacteroidetes, utilizes a novel mechanism to degrade crystalline cellulose. No genes encoding proteins specialized in loosening or disruption the crystalline structure of cellulose were identified in the genome of C. hutchinsonii, except for chu_3220 and chu_1557. The crystalline cellulose degradation mechanism remains enigmatic. This study identified a new gene locus, chu_0922, encoding a typical T9SS substrate that is essential for crystalline cellulose degradation. Notably, CHU_0922 is crucial for the normal transcription of chu_1276, chu_1277, chu_1278, chu_1279, and chu_1280 (cel9C), which play important roles in the degradation of cellulose. Moreover, CHU_0922 participates in the cell surface localization of CHU_3220. These results demonstrated that CHU_0922 plays a key role in the crystalline cellulose degradation network. Our study will promote the uncovering of the novel cellulose utilization mechanism of C. hutchinsonii.
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Goswami K, DekaBoruah HP, Saikia R. Production of cellulase by Novosphingobium sp. Cm1 and its potential application in lignocellulosic waste hydrolysis. Prep Biochem Biotechnol 2021; 52:724-735. [PMID: 34730478 DOI: 10.1080/10826068.2021.1989698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Management of lignocellulosic wastes in and around the municipality area requires special consideration. Continuous deposition of these wastes to the nearby areas led to gradual deterioration of the environment. The objective of this study was to produce cellulase from the bacteria isolated from the unexplored rainforest of NE-India for lignocellulosic waste hydrolysis. Based on carboxymethyl cellulose utilization and the congo red test, Novosphingobium sp. Cm1 was found to be the most promising strain out of 114 bacterial isolates and the strain was selected for further study. The optimization of the fermentative conditions for maximum enzyme activity was carried out using one factor-at-a-time strategy and the optimum pH, temperature and incubation time was recorded as pH 5, 37 °C and 96 h respectively. The maximum β-1,4-endoglucanase activity was observed with 1.5% CMC (5.1 ± 0.05 U/mL) and 0.25% yeast extract (7.6 ± 0.72 U/mL). The bacterial waste hydrolysis ability was investigated using three wastes where vegetable waste showed maximum activity of 3.4 ± 0.48 U/mL. Bacterial interaction and waste utilization were verified using Scanning Electron Microscope and Fourier-Transform infrared spectroscopy analysis. The present study confirmed the promising ability of Novosphingobium sp. to waste hydrolysis. Further investigations may lead to new possibilities for low-cost enzyme production that will help to meet the rising cellulase demand.
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Affiliation(s)
- Kongkana Goswami
- Biological Science & Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Hari Prasanna DekaBoruah
- Biological Science & Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India.,Govt. Model College, Kaziranga, Golaghat, Assam, India
| | - Ratul Saikia
- Biological Science & Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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25
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Wang Y, Wang C, Chen Y, Chen B, Guo P, Cui Z. Metagenomic Insight into Lignocellulose Degradation of the Thermophilic Microbial Consortium TMC7. J Microbiol Biotechnol 2021; 31:1123-1133. [PMID: 34226407 PMCID: PMC9706030 DOI: 10.4014/jmb.2106.06015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/15/2022]
Abstract
Biodegradation is the key process involved in natural lignocellulose biotransformation and utilization. Microbial consortia represent promising candidates for applications in lignocellulose conversion strategies for biofuel production; however, cooperation among the enzymes and the labor division of microbes in the microbial consortia remains unclear. In this study, metagenomic analysis was performed to reveal the community structure and extremozyme systems of a lignocellulolytic microbial consortium, TMC7. The taxonomic affiliation of TMC7 metagenome included members of the genera Ruminiclostridium (42.85%), Thermoanaerobacterium (18.41%), Geobacillus (10.44%), unclassified_f__Bacillaceae (7.48%), Aeribacillus (2.65%), Symbiobacterium (2.47%), Desulfotomaculum (2.33%), Caldibacillus (1.56%), Clostridium (1.26%), and others (10.55%). The carbohydrate-active enzyme annotation revealed that TMC7 encoded a broad array of enzymes responsible for cellulose and hemicellulose degradation. Ten glycoside hydrolases (GHs) endoglucanase, 4 GHs exoglucanase, and 6 GHs β-glucosidase were identified for cellulose degradation; 6 GHs endo-β-1,4-xylanase, 9 GHs β-xylosidase, and 3 GHs β-mannanase were identified for degradation of the hemicellulose main chain; 6 GHs arabinofuranosidase, 2 GHs α-mannosidase, 11 GHs galactosidase, 3 GHs α-rhamnosidase, and 4 GHs α-fucosidase were identified as xylan debranching enzymes. Furthermore, by introducing a factor named as the contribution coefficient, we found that Ruminiclostridium and Thermoanaerobacterium may be the dominant contributors, whereas Symbiobacterium and Desulfotomaculum may serve as "sugar cheaters" in lignocellulose degradation by TMC7. Our findings provide mechanistic profiles of an array of enzymes that degrade complex lignocellulosic biomass in the microbial consortium TMC7 and provide a promising approach for studying the potential contribution of microbes in microbial consortia.
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Affiliation(s)
- Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China
| | - Chen Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China.,College of Biology and Pharmacy, Three Gorges University, Yichang 443002, P.R. China
| | - Yonglun Chen
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China.,College of Biology and Pharmacy, Three Gorges University, Yichang 443002, P.R. China
| | - Beibei Chen
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, P.R. China.,College of Biology and Pharmacy, Three Gorges University, Yichang 443002, P.R. China
| | - Zongjun Cui
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P.R. China
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Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals. Microorganisms 2021; 9:microorganisms9051079. [PMID: 34069865 PMCID: PMC8157379 DOI: 10.3390/microorganisms9051079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/27/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
The long road from emerging biotechnologies to commercial “green” biosynthetic routes for chemical production relies in part on efficient microbial use of sustainable and renewable waste biomass feedstocks. One solution is to apply the consolidated bioprocessing approach, whereby microorganisms convert lignocellulose waste into advanced fuels and other chemicals. As lignocellulose is a highly complex network of polymers, enzymatic degradation or “saccharification” requires a range of cellulolytic enzymes acting synergistically to release the abundant sugars contained within. Complications arise from the need for extracellular localisation of cellulolytic enzymes, whether they be free or cell-associated. This review highlights the current progress in the consolidated bioprocessing approach, whereby microbial chassis are engineered to grow on lignocellulose as sole carbon sources whilst generating commercially useful chemicals. Future perspectives in the emerging biofoundry approach with bacterial hosts are discussed, where solutions to existing bottlenecks could potentially be overcome though the application of high throughput and iterative Design-Build-Test-Learn methodologies. These rapid automated pathway building infrastructures could be adapted for addressing the challenges of increasing cellulolytic capabilities of microorganisms to commercially viable levels.
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27
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Long term crop rotation effect on subsequent soybean yield explained by soil and root-associated microbiomes and soil health indicators. Sci Rep 2021; 11:9200. [PMID: 33911170 PMCID: PMC8080707 DOI: 10.1038/s41598-021-88784-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
Crop rotation is an important management tactic that farmers use to manage crop production and reduce pests and diseases. Long-term crop rotations may select groups of microbes that form beneficial or pathogenic associations with the following crops, which could explain observed crop yield differences with different crop sequences. To test this hypothesis, we used two locations each with four long-term (12–14-year), replicated, rotation treatments: continuous corn (CCC), corn/corn/soybean (SCC), corn/soybean (CSC), and soybean/corn (SCS). Afterwards, soybean was planted, and yield and soil health indicators, bulk soil microbiome, and soybean root-associated microbiome were assessed. Soybean yields, as well as soil protein, and POXC as soil health indicators were higher following CCC than in the other three treatments at both locations. A bacterial taxon in family JG30-KF-AS9 was enriched in CCC, whereas Microvirga, Rhodomicrobium, and Micromonosporaceae were enriched in SCS. Several ascomycetes explain lowered yield as soybean pathogens in SCS. Surprisingly, Tumularia, Pyrenochaetopsis and Schizothecium were enriched in soybean roots after CCC, suggesting corn pathogens colonizing soybean roots as nonpathogens. Our finding of associations between soil health indicators related to microbiomes and soybean yield has wide-ranging implications, opening the possibility of manipulating microbiomes to improve crop yield potential.
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Lu S, Mikkelsen D, Flanagan BM, Williams BA, Gidley MJ. Interaction of cellulose and xyloglucan influences in vitro fermentation outcomes. Carbohydr Polym 2021; 258:117698. [PMID: 33593569 DOI: 10.1016/j.carbpol.2021.117698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/12/2021] [Accepted: 01/22/2021] [Indexed: 01/08/2023]
Abstract
To investigate the effects of interactions between cellulose and xyloglucan (XG) on in vitro fermentation, a composite of bacterial cellulose (BC) incorporating XG during pellicle formation (BCXG), was fermented using a human faecal inoculum, and compared with BC, XG and a mixture (BC&XG) physically blended to have the same BC to XG ratio of BCXG. Compared to individual polysaccharides, the fermentation extent of BC and fermentation rate of XG were promoted in BC&XG. XG embedded in the BCXG composite was degraded less than in BC&XG, while more cellulose in BCXG was fermented than in BC&XG. This combination explains the similar amount of short chain fatty acid production noted throughout the fermentation process for BCXG and BC&XG. Microbial community dynamics for each substrate were consistent with the corresponding polysaccharide degradation. Thus, interactions between cellulose and XG are shown to influence their fermentability in multiple ways.
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Affiliation(s)
- Shiyi Lu
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Deirdre Mikkelsen
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia; School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Bernadine M Flanagan
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Barbara A Williams
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Michael J Gidley
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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29
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Visan AI, Popescu-Pelin G, Socol G. Degradation Behavior of Polymers Used as Coating Materials for Drug Delivery-A Basic Review. Polymers (Basel) 2021; 13:1272. [PMID: 33919820 PMCID: PMC8070827 DOI: 10.3390/polym13081272] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 12/21/2022] Open
Abstract
The purpose of the work was to emphasize the main differences and similarities in the degradation mechanisms in the case of polymeric coatings compared with the bulk ones. Combined with the current background, this work reviews the properties of commonly utilized degradable polymers in drug delivery, the factors affecting degradation mechanism, testing methods while offering a retrospective on the evolution of the controlled release of biodegradable polymeric coatings. A literature survey on stability and degradation of different polymeric coatings, which were thoroughly evaluated by different techniques, e.g., polymer mass loss measurements, surface, structural and chemical analysis, was completed. Moreover, we analyzed some shortcomings of the degradation behavior of biopolymers in form of coatings and briefly proposed some solving directions to the main existing problems (e.g., improving measuring techniques resolution, elucidation of complete mathematical analysis of the different degradation mechanisms). Deep studies are still necessary on the dynamic changes which occur to biodegradable polymeric coatings which can help to envisage the future performance of synthesized films designed to be used as medical devices with application in drug delivery.
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Affiliation(s)
- Anita Ioana Visan
- Lasers Department, National Institute for Lasers, Plasma and Radiation Physics, 077190 Magurele, Ilfov, Romania;
| | | | - Gabriel Socol
- Lasers Department, National Institute for Lasers, Plasma and Radiation Physics, 077190 Magurele, Ilfov, Romania;
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30
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Abstract
In recent years, the tree of life has expanded substantially. Despite this, many abundant yet uncultivated microbial groups remain to be explored. Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported. As such, their physiology, ecology, and evolutionary history remain unknown. The 16S rRNA gene survey reveals that Sumerlaeota is frequently detected in diverse environments globally, especially cold arid desert soils and deep-sea basin surface sediments, where it is one dominant microbial group. Here, we retrieved four Sumerlaeota metagenome-assembled genomes (MAGs) from two hot springs and one saline lake. Including another 12 publicly available MAGs, they represent six of the nine putative Sumerlaeota subgroups/orders, as indicated by 16S rRNA gene-based phylogeny. These elusive organisms likely obtain carbon mainly through utilization of refractory organics (e.g., chitin and cellulose) and proteinaceous compounds, suggesting that Sumerlaeota act as scavengers in nature. The presence of key bidirectional enzymes involved in acetate and hydrogen metabolisms in these MAGs suggests that they are acetogenic bacteria capable of both the production and consumption of hydrogen. The capabilities of dissimilatory nitrate and sulfate reduction, nitrogen fixation, phosphate solubilization, and organic phosphorus mineralization may confer these heterotrophs great advantages to thrive under diverse harsh conditions. Ancestral state reconstruction indicated that Sumerlaeota originated from chemotrophic and facultatively anaerobic ancestors, and their smaller and variably sized genomes evolved along dynamic pathways from a sizeable common ancestor (2,342 genes), leading to their physiological divergence. Notably, large gene gain and larger loss events occurred at the branch to the last common ancestor of the order subgroup 1, likely due to niche expansion and population size effects.
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31
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PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes. Int J Mol Sci 2021; 22:ijms22063077. [PMID: 33802923 PMCID: PMC8002723 DOI: 10.3390/ijms22063077] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 01/16/2023] Open
Abstract
Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.
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32
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Gao L, Tan Y, Zhang W, Qi Q, Lu X. Cytophaga hutchinsonii SprA and SprT Are Essential Components of the Type IX Secretion System Required for Ca 2+ Acquisition, Cellulose Degradation, and Cell Motility. Front Microbiol 2021; 12:628555. [PMID: 33643255 PMCID: PMC7906972 DOI: 10.3389/fmicb.2021.628555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/21/2021] [Indexed: 11/13/2022] Open
Abstract
The type IX secretion system (T9SS) is a novel protein secretion system, which is found in and confined to the phylum Bacteroidetes. T9SS is involved in the secretion of virulence factors, cell surface adhesins, and complex biopolymer degrading enzymes to the cell surface or extracellular medium. Cytophaga hutchinsonii is a widely distributed bacterium, which is able to efficiently digest cellulose and rapidly glide along the solid surfaces. C. hutchinsonii has a full set of orthologs of T9SS components. However, the functions of most homologous proteins have not been verified. In C. hutchinsonii, CHU_0029 and CHU_2709 are similar in sequence to Flavobacterium johnsoniae T9SS components SprA and SprT, respectively. In this study, the single deletion mutants of chu_0029 (sprA) and chu_2709 (sprT) were obtained using a complex medium with the addition of Ca2+ and Mg2+. Single deletion of sprA or sprT resulted in defects in cellulose utilization and gliding motility. Moreover, the ΔsprA and ΔsprT mutants showed growth defects in Ca2+- and Mg2+-deficient media. The results of ICP-MS test showed that both the whole cell and intracellular concentrations of Ca2+ were dramatically reduced in the ΔsprA and ΔsprT mutants, indicating that SprA and SprT are both important for the assimilation of trace amount of Ca2+. While the assimilation of Mg2+ was not obviously influenced in the ΔsprA and ΔsprT mutants. Through proteomics analysis of the cell surface proteins of the wild type and mutants, we found that the ΔsprA and ΔsprT mutants were defective in secretion of the majority of T9SS substrates. Together, these results indicate that SprA and SprT are both essential components of C. hutchinsonii T9SS, which is required for protein secretion, Ca2+ acquisition, cellulose degradation, and gliding motility in C. hutchinsonii. Our study shed more light on the functions of SprA and SprT in T9SS, and further proved the link between the T9SS and Ca2+ uptake system.
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Affiliation(s)
- Lijuan Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yahong Tan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Ghosh S, Godoy L, Anchang KY, Achilonu CC, Gryzenhout M. Fungal Cellulases: Current Research and Future Challenges. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome. Microorganisms 2020; 9:microorganisms9010020. [PMID: 33374587 PMCID: PMC7822412 DOI: 10.3390/microorganisms9010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 11/17/2022] Open
Abstract
The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F. velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54-95 AAs, 145-188 GHs, 55-73 GTs, 6-19 PLs, 13-59 CEs, and 7-67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.
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Screening of cellulose degradation bacteria from Min pigs and optimization of its cellulase production. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Shi Z, Han C, Zhang X, Tian L, Wang L. Novel Synergistic Mechanism for Lignocellulose Degradation by a Thermophilic Filamentous Fungus and a Thermophilic Actinobacterium Based on Functional Proteomics. Front Microbiol 2020; 11:539438. [PMID: 33042052 PMCID: PMC7518101 DOI: 10.3389/fmicb.2020.539438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Effective artificial microbial consortia containing microorganisms with desired biological functions have the potential to optimize the lignocellulose-based bioindustry. Thermobifida fusca was a dominant actinobacterium in high-temperature corn stalk composts, but it was unable to grow alone in corn stalk solid medium. Interestingly, T. fusca showed good growth and secreted enzymes when cocultured with Thermomyces lanuginosus. T. lanuginosus grew firstly during the initial stage, whereas T. fusca dominated the system subsequently during cocultivation. The secretome indicated that T. lanuginosus mainly degraded xylan by expressing a GH11 xylanase (g4601.t1, GenBank AAB94633.1; with relative secretion of 4.95 ± 0.65%). T. fusca was induced by xylan mainly to secrete a xylanase from GH11 family (W8GGR4, GenBank AHK22788.1; with relative secretion of 8.71 ± 3.83%) which could rapidly degrade xylan to xylo-oligosaccharide (XOS) and xylose within 2 min, while high concentrations (>0.5%, w/v) of XOS or xylose suppressed the growth of T. fusca; which may be the reason why T. fusca unable to grow alone in corn stalk solid medium. However, T. lanuginosus could utilize the XOS and xylose produced by xylanases secreted by T. fusca. During the synergistic degradation of lignocellulose by T. lanuginosus and T. fusca, xylan was rapidly consumed by T. lanuginosus, the residual cellulose could specifically induced T. fusca to express a GH10 xylanase with a CBM2 domain (Q47KR6, GenBank AAZ56956.1; with relative secretion of 5.03 ± 1.33%) and 6 cellulases (2 exocellulases and 4 endocellulases). Moreover, T. lanuginosus increased the secretion of cellulases from T. fusca by 19-25%. The order of T. lanuginosus and T. fusca was consistent with the multilayered structures of lignocellulose and could be regulated by different concentrations of XOS and xylose. The novel synergism of T. lanuginosus and T. fusca gave a new sight for revealing more synergetic relationships in natural environments and exploring efficient microbial inoculants and enzyme cocktails for lignocellulose degradation.
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Affiliation(s)
- Zelu Shi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Chao Han
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xiujun Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Li Tian
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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Guerrero EB, de Villegas RMD, Soria MA, Santangelo MP, Campos E, Talia PM. Characterization of two GH5 endoglucanases from termite microbiome using synthetic metagenomics. Appl Microbiol Biotechnol 2020; 104:8351-8366. [DOI: 10.1007/s00253-020-10831-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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Ganesan M, Mathivani Vinayakamoorthy R, Thankappan S, Muniraj I, Uthandi S. Thermotolerant glycosyl hydrolases-producing Bacillus aerius CMCPS1 and its saccharification efficiency on HCR-laccase (LccH)-pretreated corncob biomass. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:124. [PMID: 32684977 PMCID: PMC7362481 DOI: 10.1186/s13068-020-01764-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The current production of bioethanol based on lignocellulosic biomass (LCB) highly depends on thermostable enzymes and extremophiles owing to less risk of contamination. Thermophilic bacterial cellulases are preferred over fungi due to their higher growth rate, presence of complex multi-enzymes, stability, and enhanced bioconversion efficiency. Corncob, underutilized biomass, ensures energy conservation due to high lignocellulosic and more fermentable sugar content. In the present study, the thermophilic bacterium Bacillus aerius CMCPS1, isolated from the thermal springs of Manikaran, Himachal Pradesh, India, was characterized in terms of its activity, stability, and hydrolytic capacity. A two-step process comprising: (i) a combined strategy of hydrodynamic cavitation reaction (HCR)-coupled enzymatic (LccH at 6.5 U) pretreatment for delignification and (ii) subsequent hydrolysis of pre-treated (HCR-LccH) corncob biomass (CCB) using a thermostable cocktail of CMCPS1 was adopted to validate the efficiency of the process. Some of the parameters studied include lignin reduction, cellulose increase, and saccharification efficiency. RESULT Among the five isolates obtained by in situ enrichment on various substrates, B. aerius CMCPS1, isolated from hot springs, exhibited the maximum hydrolytic activity of 4.11. The GH activity of the CMCPS1 strain under submerged fermentation revealed maximum filter paper activity (FPA) and endoglucanase activity of 4.36 IU mL-1 and 2.98 IU mL-1, respectively, at 44 h. Similarly, the isolate produced exoglucanase and β-glucosidase with an activity of 1.76 IU mL-1 and 1.23 IU mL-1 at 48 h, respectively. More specifically, the enzyme endo-1,4-β-d glucanase E.C.3.2.1.4 (CMCase) produced by B. aerius CMCPS1 displayed wider stability to pH (3-9) and temperature (30-90 °C) than most fungal cellulases. Similarly, the activity of CMCase increased in the presence of organic solvents (118% at 30% acetone v/v). The partially purified CMCase from the culture supernatant of CMCPS1 registered 64% yield with twofold purification. The zymogram and SDS-PAGE analyses further confirmed the CMCase activity with an apparent molecular mass of 70 kDa. The presence of genes specific to cellulases, such as cellulose-binding domain CelB, confirmed the presence of GH family 46 and β-glucosidase activity (GH3). The multifunctional cellulases of CMCPS1 were evaluated for their saccharification efficiency on laccase (LccH, a fungal laccase from Hexagonia hirta MSF2)-pretreated corncob in a HCR. The lignin and hemicelluloses removal efficiency of HCR-LccH was 54.1 and 6.57%, respectively, with an increase in cellulose fraction (42.25%). The saccharification efficiency of 55% was achieved with CMCPS1 multifunctional cellulases at 50 °C and pH 5.0. CONCLUSION The multifunctional cellulase complex of B. aerius CMCPS1 is a potential biocatalyst for application in lignocellulosic biomass-based biorefineries. The saccharification ability of HCR-LccH-pretreated corncob at elevated temperatures would be an advantage for biofuel production from lignocellulosic biomass.
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Affiliation(s)
- Meena Ganesan
- Biocatalysts Lab., Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | | | - Sugitha Thankappan
- Biocatalysts Lab., Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - Iniyakumar Muniraj
- Department of Crop Management, Kumaraguru Institute of Agriculture, Sakthi Nagar, Erode, 638315 India
| | - Sivakumar Uthandi
- Biocatalysts Lab., Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003 India
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Harindintwali JD, Zhou J, Yu X. Lignocellulosic crop residue composting by cellulolytic nitrogen-fixing bacteria: A novel tool for environmental sustainability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136912. [PMID: 32014770 DOI: 10.1016/j.scitotenv.2020.136912] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/19/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Lignocellulosic crop residue (LCCR) composting is a cost-effective and sustainable approach for addressing environmental pollution associated with open biomass burning and application of chemical fertilizers in agriculture. The value-added bio-product of the composting process contributes to the improvement of the soil properties and plant growth in an environment-friendly way. However, the conventional process employed for composting LCCRs is slow and becomes an impediment for farmers who plant two or three crops a year. This concern has led to the development of different techniques for rapid composting of LCCRs. The use of cellulolytic nitrogen-fixing microorganisms for composting has emerged as a promising method for enhancing LCCR composting and quality of the compost. Therefore, this review addresses the recent progress on the potential use of cellulolytic nitrogen-fixing bacteria (CNFB) for LCCR composting and discusses various applications of nutrient-rich compost for sustainable agriculture to increase crop yields in a nature-friendly way. This knowledge of bacteria with both cellulose-degrading and nitrogen-fixing activities is significant with respect to rapid composting, soil fertility, plant growth and sustainable management of the lignocellulosic agricultural waste and it provides a means for the development of new technology for sustainability.
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Affiliation(s)
- Jean Damascene Harindintwali
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi 214122, China
| | - Jianli Zhou
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi 214122, China
| | - Xiaobin Yu
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi 214122, China.
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Zheng W, Anzaldua M, Arora A, Jiang Y, McIntyre K, Doerfert M, Winter T, Mishra A, Ma H, Liang H. Environmentally Benign Nanoantibiotics with a Built-in Deactivation Switch Responsive to Natural Habitats. Biomacromolecules 2020; 21:2187-2198. [PMID: 32202760 DOI: 10.1021/acs.biomac.0c00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The massive use of antibiotics in healthcare and agriculture has led to their artificial accumulation in natural habitats, which risks the structure and function of the microbial communities in ecosystems, threatens food and water security, and accelerates the development of resistome. Ideally, antibiotics should remain fully active in clinical services while becoming deactivated rapidly once released into the environment, but none of the current antibiotics meet this criterion. Here, we show a nanoantibiotic design that epitomizes the concept of carrying a built-in "OFF" switch responsive to natural stimuli. The environmentally benign nanoantibiotics consist of cellulose backbones covalently grafted with hydrophilic polymer brushes that by themselves are antimicrobially inactive. In their nanostructured forms in services, these cellulose-based polymer molecular brushes are potent killers for both Gram-positive and Gram-negative bacteria, including clinical multidrug-resistant strains; after services and being discharged into the environment, they are shredded into antimicrobially inactive pieces by cellulases that do not exist in the human body but are abundant in natural habitats. This study illuminates a new concept of mitigating the environmental footprints of antibiotics with rationally designed nanoantibiotics that can be dismantled and disabled by bioorthogonal chemistry occurring exclusively in natural habitats.
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Affiliation(s)
- Wan Zheng
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Miguel Anzaldua
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ankita Arora
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Department of Materials Science and Engineering, Indian Institute of Technology Gandhinagar, Gujarat 382355, India
| | - Yunjiang Jiang
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Kelly McIntyre
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Michael Doerfert
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Theodora Winter
- The Honors College, Texas Tech University, Lubbock, Texas 79409, United States
| | - Abhijit Mishra
- Department of Materials Science and Engineering, Indian Institute of Technology Gandhinagar, Gujarat 382355, India
| | - Hairong Ma
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hongjun Liang
- Department of Cell Physiology & Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States.,Department of Chemistry, Texas Tech University, Lubbock, Texas 79409, United States
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Quistad SD, Doulcier G, Rainey PB. Experimental manipulation of selfish genetic elements links genes to microbial community function. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190681. [PMID: 32200751 PMCID: PMC7133536 DOI: 10.1098/rstb.2019.0681] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
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Affiliation(s)
- Steven D Quistad
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Guilhem Doulcier
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Paul B Rainey
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
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Li F, Dong J, Lv X, Wen Y, Chen S. Recombinant expression and characterization of two glycoside hydrolases from extreme alklinphilic bacterium Cellulomonas bogoriensis 69B4 T. AMB Express 2020; 10:44. [PMID: 32157462 PMCID: PMC7064699 DOI: 10.1186/s13568-020-00979-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 02/26/2020] [Indexed: 01/05/2023] Open
Abstract
Two novel glycoside hydrolases were cloned from the genomic DNA of alklinphilic bacterium Cellulomonas bogoriensis 69B4T and functionally expressed in Escherichia coli. The two enzymes shared less than 73% of identities with other known glycosidases and belonged to glycoside hydrolase families 5 and 9. Recombinant Cel5A exhibited optimum activity at pH 5.0 and at a temperature of 70 °C, and Cel9A showed optimum activity at pH 7.0 and at a temperature of 60 °C. The two enzymes exhibited activity at alkaline pH 11 and were stable over a wide range of pH. The maximum activities of Cel5A and Cel9A were observed in 0.5 M NaCl and 1 M KCl, respectively. In addition, these two enzymes exhibited excellent halostability with residual activities of more than 70% after pre-incubation for 6 days in 5 M NaCl or 4 M KCl. Substrate specificity analysis revealed that Cel5A and Cel9A specifically cleaved the β-1,4-glycosidic linkage in cellulose with the highest activity on carboxymethyl cellulose sodium (78.3 and 145.3 U/mg, respectively). Cel5A is an endoglucanase, whereas Cel9A exhibits endo and exo activities. As alkali-activated, thermo-tolerant, and salt-tolerant cellulases, Cel5A and Cel9A are promising candidates for further research and industrial applications.
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Tasirnafas M, Karimi K, Asgari Jafarabadi G, Seidavi A, Noorbakhsh F. Extraction and purification of β-glucanase from bovine rumen fungus Trichoderma reesei and its effect on performance, carcass characteristics, microbial flora, plasma biochemical parameters, and immunity in a local broiler hybrid Golpayegan-Ross. Trop Anim Health Prod 2020; 52:1833-1843. [PMID: 31938956 DOI: 10.1007/s11250-019-02186-5] [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: 02/12/2019] [Accepted: 12/22/2019] [Indexed: 10/25/2022]
Abstract
The enzyme β-glucanase was extracted from Trichoderma reesei in bovine rumen fluid samples collected from a slaughterhouse and its effect was investigated in broilers. Data collected was broiler performance, carcass characteristics, duodenum microbial flora, hematological, and immunological parameters. β-glucanase activity was assayed through spectrometry and was approximately 0.434 IU per gram culture medium. In the current study, endoglucanase enzymes were extracted from Trichoderma reesei. A total of 160 local broilers (Golpayegan-Ross hybrid) were allocated to 4 treatments with 4 replicates per treatment. Over a 49-day experimental period, broilers were fed a basal diet (T1), basal diet plus 20% barley (T2), basal diet with 10 IU extracted β-glucanase and 20% barley (T3), and basal diet with 10 IU commercial β-glucanase and 20% barley (T4). The T3 treatment resulted in the greatest body weight gain at the end of experiment (P < 0.01). No significant differences were for feed conversion (FCR; P > 0.05). The highest cholesterol, high density lipoprotein (HDL), low density lipoprotein (LDL), and LDL cholesterol ratio was observed in the T3 treatment. The highest concentrations of immunoglobulin G1 (IgG1), immunoglobulin G2 (IgG2), and immunoglobulin M1 (IgM1) were observed in the T4 treatment. The T3 treatment resulted in the best response for all measured carcass characteristics. The highest levels of aerobic bacteria, lactobacilli, anaerobic bacteria, and E. coli were associated with the T4, T3, T4, and T1 treatments, respectively. It is concluded that β-glucanase supplementation can be used to overcome the anti-nutritive effects of water soluble barley non-starch polysaccharides (NSPs) and consequently enhance broiler performance without any adverse effects on humoral immunity parameters.
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Affiliation(s)
- Mohammadebrahim Tasirnafas
- Department of Animal Science, Faculty of Agriculture, Varamin-Pishva Branch, Islamic Azad University, Varamin-Pishva, Iran
| | - Kazem Karimi
- Department of Animal Science, Faculty of Agriculture, Varamin-Pishva Branch, Islamic Azad University, Varamin-Pishva, Iran.
| | - Ghobad Asgari Jafarabadi
- Department of Animal Science, Faculty of Agriculture, Varamin-Pishva Branch, Islamic Azad University, Varamin-Pishva, Iran
| | - Alireza Seidavi
- Department of Animal Science, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Fatemeh Noorbakhsh
- Department of Microbiology, Biological Science College, Varamin-Pishva Branch, Islamic Azad University, Varamin-Pishva, Iran
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Sarsaiya S, Jain A, Kumar Awasthi S, Duan Y, Kumar Awasthi M, Shi J. Microbial dynamics for lignocellulosic waste bioconversion and its importance with modern circular economy, challenges and future perspectives. BIORESOURCE TECHNOLOGY 2019; 291:121905. [PMID: 31387838 DOI: 10.1016/j.biortech.2019.121905] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 05/15/2023]
Abstract
An extensive use of microbial dynamics for utilizing the lignocellulosic wastes has been attributed to their efficiency in bioenergy and bioproducts development as a cost effective high nutritional value. The integration of lignocellulosic waste into the circular economy can scaleup the sustainable bioproducts and bioenergy development. In this review paper, the aim is to describe the existing research efforts on organic lignocellulosic waste, cellulase producing microbes, their potential enzyme, modern circular economy with associated challenges and future perspectives. Presently, it has been reviewed that microbial cellulases have provided treasure bioproducts visions into industrial bioproducts marvels unveiled through lignocellulosic waste cutting-edge microbial explorations. Furthermore, the review focused on new insights of the growing circular economy of lignocellulosic waste used for many bioproducts and bioenergy dealings and explored the emergent lignocellulosic biorefinery approaches which could then be applied to review industrial-scale sustainable economic models for upgraded bioproducts and other production associated problems.
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Affiliation(s)
- Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563003, China; Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi 563003, China
| | - Archana Jain
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563003, China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Yumin Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563003, China
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Park YJ, Lee CS, Kong WS. Genomic Insights into the Fungal Lignocellulolytic Machinery of Flammulina rossica. Microorganisms 2019; 7:microorganisms7100421. [PMID: 31597238 PMCID: PMC6843371 DOI: 10.3390/microorganisms7100421] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) of the Flammulina rossica (wood-rotting basidiomycete) genome was performed to identify its carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) revealed a total length of 35,646,506 bp (49.79% GC content). In total, 12,588 gene models of F. rossica were predicted using an ab initio gene prediction tool (AUGUSTUS). Orthologous analysis with other fungal species revealed that 7433 groups contained at least one F. rossica gene. Additionally, 12,033 (95.6%) of 12,588 genes for F. rossica proteins had orthologs among the Dikarya, and F. rossica contained 12 species-specific genes. CAZyme annotation in the F. rossica genome revealed 511 genes predicted to encode CAZymes including 102 auxiliary activities, 236 glycoside hydrolases, 94 glycosyltransferases, 19 polysaccharide lyases, 56 carbohydrate esterases, and 21 carbohydrate binding-modules. Among the 511 genes, several genes were predicted to simultaneously encode two different CAZymes such as glycoside hydrolases (GH) as well as carbohydrate-binding module (CBM). The genome information of F. rossica offers opportunities to understand the wood-degrading machinery of this fungus and will be useful for biotechnological and industrial applications.
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Affiliation(s)
- Young-Jin Park
- Department of Biomedical Chemistry, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, 268 Chungwon-daero, Chungju-si 27478, Korea.
| | - Chang-Soo Lee
- Department of Biomedical Chemistry, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, 268 Chungwon-daero, Chungju-si 27478, Korea.
| | - Won-Sik Kong
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, 92, Bisan-ro, Eumseong-gun 27709, Korea.
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A highly thermostable crude endoglucanase produced by a newly isolated Thermobifida fusca strain UPMC 901. Sci Rep 2019; 9:13526. [PMID: 31537863 PMCID: PMC6753106 DOI: 10.1038/s41598-019-50126-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/06/2019] [Indexed: 01/22/2023] Open
Abstract
A thermophilic Thermobifida fusca strain UPMC 901, harboring highly thermostable cellulolytic activity, was successfully isolated from oil palm empty fruit bunch compost. Its endoglucanase had the highest activity at 24 hours of incubation in carboxymethyl-cellulose (CMC) and filter paper. A maximum endoglucanase activity of 0.9 U/mL was achieved at pH 5 and 60 °C using CMC as a carbon source. The endoglucanase properties were further characterized using crude enzyme preparations from the culture supernatant. Thermal stability indicated that the endoglucanase activity was highly stable at 70 °C for 24 hours. Furthermore, the activity was found to be completely maintained without any loss at 50 °C and 60 °C for 144 hours, making it the most stable than other endoglucanases reported in the literature. The high stability of the endoglucanase at an elevated temperature for a prolonged period of time makes it a suitable candidate for the biorefinery application.
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Li Y, Hu Y, Zhu Z, Zhao K, Liu G, Wang L, Qu Y, Zhao J, Qin Y. Normal transcription of cellulolytic enzyme genes relies on the balance between the methylation of H3K36 and H3K4 in Penicillium oxalicum. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:198. [PMID: 31452679 PMCID: PMC6700826 DOI: 10.1186/s13068-019-1539-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/06/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Enzymatic hydrolysis of lignocellulose by fungi is a key step in global carbon cycle and biomass utilization. Cellulolytic enzyme production is tightly controlled at a transcriptional level. Here, we investigated the roles of different histone lysine methylation modifications in regulating cellulolytic enzyme gene expression, as histone lysine methylation is an important process of chromatin regulation associated with gene transcription. RESULTS PoSet1 and PoSet2 in Penicillium oxalicum, orthologs of Set1 and Set2 in budding yeast, were associated with the methylation of histone H3 lysine 4 (H3K4) and lysine 36 (H3K36). Cellulolytic enzyme production was extensively upregulated by the disruption of PoSet2, but was significantly downregulated by the disruption of PoSet1. We revealed that the activation of cellulolytic enzyme genes was accompanied by the increase of H3K4me3 signal, as well as the decrease of H3K36me1 and H3K36me3 signal on specific gene loci. The repression of cellulolytic enzyme genes was accompanied by the absence of global H3K4me1 and H3K4me2. An increase in the H3K4me3 signal by Poset2 disruption was eliminated by the further disruption of Poset1 and accompanied by the repressed cellulolytic enzyme genes. The active or repressed genes were not always associated with transcription factors. CONCLUSION H3K4 methylation is an active marker of cellulolytic enzyme production, whereas H3K36 methylation is a marker of repression. A crosstalk occurs between H3K36 and H3K4 methylation, and PoSet2 negatively regulates cellulolytic enzyme production by antagonizing the PoSet1-H3K4me3 pathway. The balance of H3K4 and H3K36 methylation is required for the normal transcription of cellulolytic enzyme genes. These results extend our previous understanding that cellulolytic enzyme gene transcription is primarily controlled by transcription factors.
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Affiliation(s)
- Yanan Li
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
- State Key Lab of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Yueyan Hu
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
- State Key Lab of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Zhu Zhu
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
- State Key Lab of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Kaili Zhao
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
- State Key Lab of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Guodong Liu
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
- State Key Lab of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Lushan Wang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
| | - Yinbo Qu
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
- State Key Lab of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Jian Zhao
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237 China
- State Key Lab of Microbial Technology, Shandong University, Qingdao, 266237 China
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Pratama R, Schneider D, Böer T, Daniel R. First Insights Into Bacterial Gastrointestinal Tract Communities of the Eurasian Beaver ( Castor fiber). Front Microbiol 2019; 10:1646. [PMID: 31428060 PMCID: PMC6690062 DOI: 10.3389/fmicb.2019.01646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023] Open
Abstract
The Eurasian or European beaver (Castor fiber) is the second-largest living rodent after the capybara. It is a semi-aquatic animal known for building dams and lodges. They strictly feed on lignocellulose-rich plants and correspondingly harbor cellulolytic microbial communities in their digestive tract. In this study, the bacterial community composition, diversity, and functional profile of different gut compartments ranging from stomach to colon have been explored. A total of 277 bacterial operational taxonomic units (OTUs) at species level were obtained from the gut systems of two males (juvenile and subadult) and one subadult female beaver. In general, cecum and colon are dominated by Firmicutes and Actinobacteria. High abundance of Bacteroidetes was observed only in male juvenile beaver cecum and colon, suggesting that the bacterial composition changes with age. Within the cecum and colon, members of known cellulase-producing bacterial taxa including the families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae 1 were detected. The presence of putative genes encoding cellulolytic and carbohydrate-degrading enzymes indicated also the degradation of recalcitrant plant material in both gut compartments. The bacterial community in the gut systems of the Eurasian beaver differed from that of the North American beaver. Higher abundance of Actinobacteria and lower abundances of Bacteroidetes were recorded in the Eurasian beaver. Similar differences were obtained to bacterial communities of termites and herbivorous animals such as bovine. The data presented in this study provides the first insight into bacterial communities in the gut system of the Eurasian beaver.
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Affiliation(s)
- Rahadian Pratama
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Bogor, Indonesia
| | - Dominik Schneider
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Tim Böer
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
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Nguyen SN, Flores A, Talamantes D, Dar F, Valdez A, Schwans J, Berlemont R. GeneHunt for rapid domain-specific annotation of glycoside hydrolases. Sci Rep 2019; 9:10137. [PMID: 31300677 PMCID: PMC6626019 DOI: 10.1038/s41598-019-46290-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
The identification of glycoside hydrolases (GHs) for efficient polysaccharide deconstruction is essential for the development of biofuels. Here, we investigate the potential of sequential HMM-profile identification for the rapid and precise identification of the multi-domain architecture of GHs from various datasets. First, as a validation, we successfully reannotated >98% of the biochemically characterized enzymes listed on the CAZy database. Next, we analyzed the 43 million non-redundant sequences from the M5nr data and identified 322,068 unique GHs. Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs and identified 160,790 additional enzymes. Although most identified sequences corresponded to single domain enzymes, many contained several domains, including known accessory domains and some domains never identified in association with GH. Several sequences displayed multiple catalytic domains and few of these potential multi-activity proteins combined potentially synergistic domains. Finally, we produced and confirmed the biochemical activities of a GH5-GH10 cellulase-xylanase and a GH11-CE4 xylanase-esterase. Globally, this "gene to enzyme pipeline" provides a rationale for mining large datasets in order to identify new catalysts combining unique properties for the efficient deconstruction of polysaccharides.
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Affiliation(s)
- S N Nguyen
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Flores
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - D Talamantes
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - F Dar
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Valdez
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - J Schwans
- Department of Chemistry and Biochemistry, California State University Long Beach, Long Beach, California, USA
| | - R Berlemont
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA.
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The multivariate statistical selection of fungal strains isolated from Neoteredo reynei, with the high hydrolytic potential to deconstruct cellulose. Food Res Int 2019; 122:402-410. [PMID: 31229094 DOI: 10.1016/j.foodres.2019.04.019] [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: 11/18/2018] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
Abstract
The aim of this study was to select isolated filamentous fungi, naturally occurring in the digestive tract of Neoteredo reynei, with high potential to hydrolyze cellulolytic biomass. The selection of the fungi strains, which produce cellulases, was performed by adding carboxymethylcellulose (CMC), microcrystalline cellulose (MCC) or glucose in the media containing peptone and yeast-extract. In this case, the glucose was used as a reference standard for the growth of the mycelia. The abilities of the fungal strains, to hydrolyze cellulose, on the solid media (MCC or CMC), were evaluated. Two methods were used: the congo-red and the speed of mycelial growth. The measurements of the diameters were performed at 24 h intervals, and the speed of the mycelial growth was calculated after 72 h of cultivation. The molecular and morphological identification of the fungi were applied to the isolated strains. Statistical analysis, including ANOVA and Tukey test, and multivariate analysis were applied as tools to select the strains. Twelve strains were isolated and the results of the identification were 2 strains of Hypocrea lutea, 2 strains of Trichoderma reesei, 2 strains of Aspergillus niger; 2 genera of Aspergillus sp., 2 genera of Trichoderma sp., 1 genus of Fusarium sp. and 1 genus of Gliocadium sp. The discrimination analysis methods such as HCA (Hierarchical Cluster Analysis) and PCA (Principal Component Analysis) indicated three strains with the highest potential to hydrolyze cellulose. In this study, the selection strategy was successful, resulting in the classification of strains from the genera Trichoderma and Hypocrea. This is the first time that this kind of studying was applied to select the potential of the cellulolytic fungal strains, isolated from N. reynei, using the methods of the growth of the mycelial diameter and the statistical discrimination.
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