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Ercole TG, Kava VM, Petters-Vandresen DAL, Nassif Gomes ME, Aluizio R, Ribeiro RA, Hungria M, Galli LV. Unlocking the growth-promoting and antagonistic power: A comprehensive whole genome study on Bacillus velezensis strains. Gene 2024; 927:148669. [PMID: 38866259 DOI: 10.1016/j.gene.2024.148669] [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: 02/29/2024] [Revised: 05/14/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Bacillus species are extensively documented as plant growth-promoting rhizobacteria, contributing significantly to the enhancement of soil fertility, nutrient recycling, and the control of phytopathogens. Utilizing them as biocontrol agents represents an environmentally friendly strategy, particularly within the rhizospheric community. This study presents the comprehensive genome sequences of three B. velezensis strains (LGMB12, LGMB319, and LGMB426) which were previously isolated from root samples of maize (Zea mays L.), along with a type strain FZB42. The research assesses the capability of the three strains for antagonizing fungi, specifically Fusarium graminearum, Fusarium verticillioides, Colletotrichum graminicola, and Stenocarpella sp. In paired cultures involving maize fungi, treatments containing bacteria B. velezensis exhibited statistically significant differences compared to both negative and positive treatments in terms of antagonism. Furthermore, genome mining techniques were employed to explore their inherent antagonistic potential. The assembly revealed that strains LGMB12, LGMB319, LGMB426, and FZB42 exhibit genome sizes of 4,187,541 bp, 4,244,954 bp, 3,976,537 bp, and 3,990,518 respectively. Their respective G + C content stands at 46.42 %, 46.50 %, 46.51 %, and 46.38 %. Moreover, the genomes present multiple gene clusters responsible for the synthesis of secondary metabolites and carbohydrate-active enzymes (CAZymes). These clusters highlight a diverse array of antibacterial and antifungal properties, complemented by numerous plant growth-promoting genes. These results highlight the potential of B. velezensis LGMB12, LGMB319, and LGMB426 strains as biocontrol and plant growth promotion agents, being promising candidates for further studies in agricultural production, including field trials.
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Affiliation(s)
- Tairine Graziella Ercole
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Vanessa Merlo Kava
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Desirrê Alexia Lourenço Petters-Vandresen
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Maria Eduarda Nassif Gomes
- Pontifical Catholic University of Paraná, Imaculada Conceição St., 1155, 80215-901 Curitiba, PR, Brazil.
| | - Rodrigo Aluizio
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil.
| | | | - Lygia Vitoria Galli
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
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Wang J, Wang Z, Liu C, Song M, Xu Q, Liu Y, Yan H. Genome analysis of a newly isolated Bacillus velezensis-YW01 for biodegrading acetaldehyde. Biodegradation 2024; 35:539-549. [PMID: 38573500 DOI: 10.1007/s10532-024-10075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/16/2024] [Indexed: 04/05/2024]
Abstract
Acetaldehyde (AL), a primary carcinogen, not only pollutes the environment, but also endangers human health after drinking alcohol. Here a promising bacterial strain was successfully isolated from a white wine cellar pool in the province of Shandong, China, and identified as Bacillus velezensis-YW01 with 16 S rDNA sequence. Using AL as sole carbon source, initial AL of 1 g/L could be completely biodegraded by YW01 within 84 h and the cell-free extracts of YW01 has also been detected to biodegrade the AL, which indicate that YW01 is a high-potential strain for the biodegradation of AL. The optimal culture conditions and the biodegradation of AL of YW01 are at pH 7.0 and 38 °C, respectively. To further analyze the biodegradation mechanism of AL, the whole genome of YW01 was sequenced. Genes ORF1040, ORF1814 and ORF0127 were revealed in KEGG, which encode for acetaldehyde dehydrogenase. Furthermore, ORF0881 and ORF052 encode for ethanol dehydrogenase. This work provides valuable information for exploring metabolic pathway of converting ethanol to AL and subsequently converting AL to carboxylic acid compounds, which opened up potential pathways for the development of microbial catalyst against AL.
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Affiliation(s)
- Jingjing Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Zhihao Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Chao Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Meijie Song
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Qianqian Xu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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Palit K, Das S. Cellulolytic potential of mangrove bacteria Bacillus haynesii DS7010 and the effect of anthropogenic and environmental stressors on bacterial survivability and cellulose metabolism. ENVIRONMENTAL RESEARCH 2024; 252:118774. [PMID: 38552827 DOI: 10.1016/j.envres.2024.118774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
Cellulose degrading bacterial diversity of Bhitarkanika mangrove ecosystem, India, was uncovered and the cellulose degradation mechanism in Bacillus haynesii DS7010 under the modifiers such as pH (pCO2), salinity and lead (Pb) was elucidated in the present study. The abundance of cellulose degrading heterotrophic bacteria was found to be higher in mangrove sediment than in water. The most potential strain, B. haynesii DS7010 showed the presence of endoglucanase, exoglucanase and β-glucosidase with the maximum degradation recorded at 48 h of incubation, with 1% substrate concentration at 41 °C incubation temperature. Two glycoside hydrolase genes, celA and celB were confirmed in this bacterium. 3D structure prediction of the translated CelA and CelB proteins showed maximum similarities with glycoside hydrolase 48 (GH48) and glycoside hydrolase 5 (GH5) respectively. Native PAGE followed by zymogram assay unveiled the presence of eight isoforms of cellulase ranged from 78 kDa to 245 kDa. Among the stressors, most adverse effect was observed under Pb stress at 1400 ppm concentration, followed by pH at pH 4. This was indicated by prolonged lag phase growth, higher reactive oxygen species (ROS) production, lower enzyme activity and downregulation of celA and celB gene expressions. Salinity augmented bacterial metabolism up to 3% NaCl concentration. Mangrove leaf litter degradation by B. haynesii DS7010 indicated a substantial reduction in cellulolytic potential of the bacterium in response to the synergistic effect of the stressors. Microcosm set up with the stressors exhibited 0.97% decrease in total carbon (C%) and 0.02% increase in total nitrogen (N%) after 35 d of degradation while under natural conditions, the reduction in C and the increase in N were 4.05% and 0.2%, respectively. The findings of the study suggest the cellulose degradation mechanism of a mangrove bacterium and its resilience to the future consequences of environmental pollution and climate change.
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Affiliation(s)
- Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Gong Y, Shang DD, Sun CL, Du ZJ, Chen GJ. Direct Degradation of Fresh and Dried Macroalgae by Agarivorans albus B2Z047. Mar Drugs 2024; 22:203. [PMID: 38786594 PMCID: PMC11122777 DOI: 10.3390/md22050203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Marine macroalgae are increasingly recognized for their significant biological and economic potential. The key to unlocking this potential lies in the efficient degradation of all carbohydrates from the macroalgae biomass. However, a variety of polysaccharides (alginate, cellulose, fucoidan, and laminarin), are difficult to degrade simultaneously in a short time. In this study, the brown alga Saccharina japonica was found to be rapidly and thoroughly degraded by the marine bacterium Agarivorans albus B2Z047. This strain harbors a broad spectrum of carbohydrate-active enzymes capable of degrading various polysaccharides, making it uniquely equipped to efficiently break down both fresh and dried kelp, achieving a hydrolysis rate of up to 52%. A transcriptomic analysis elucidated the presence of pivotal enzyme genes implicated in the degradation pathways of alginate, cellulose, fucoidan, and laminarin. This discovery highlights the bacterium's capability for the efficient and comprehensive conversion of kelp biomass, indicating its significant potential in biotechnological applications for macroalgae resource utilization.
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Affiliation(s)
- Ya Gong
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai 264209, China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
| | - Cheng-Lin Sun
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai 264209, China
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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Lu K, Wang X, Zhou Y, Zhu Q. Genomic characterization and probiotic potential assessment of an exopolysaccharide-producing strain Pediococcus pentosaceus LL-07 isolated from fermented meat. BMC Microbiol 2024; 24:142. [PMID: 38664612 PMCID: PMC11044368 DOI: 10.1186/s12866-024-03304-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND The genomic information available for Pediococcus pentosaceus is primarily derived from fermented fruits and vegetables, with less information available from fermented meat. P. pentosaceus LL-07, a strain isolated from fermented meat, has the capability of producing exopolysaccharides (EPS). To assess the probiotic attributes of P. pentosaceus LL-07, we conducted whole-genome sequencing (WGS) using the PacBio SequelIIe and Illumina MiSeq platforms, followed by in vitro experiments to explore its probiotic potential. RESULTS The genome size of P. pentosaceus LL-07 is 1,782,685 bp, comprising a circular chromosome and a circular plasmid. Our investigation revealed the absence of a CRISPR/Cas system. Sugar fermentation experiments demonstrated the characteristics of carbohydrate metabolism. P. pentosaceus LL-07 contains an EPS synthesis gene cluster consisting of 13 genes, which is different from the currently known gene cluster structure. NO genes associated with hemolysis or toxin synthesis were detected. Additionally, eighty-six genes related to antibiotic resistance were identified but not present in the prophage, transposon or plasmid. In vitro experiments demonstrated that P. pentosaceus LL-07 was comparable to the reference strain P. pentosaceus ATCC25745 in terms of tolerance to artificial digestive juice and bile, autoaggregation and antioxidation, and provided corresponding genomic evidence. CONCLUSION This study confirmed the safety and probiotic properties of P. pentosaceus LL-07 via complete genome and phenotype analysis, supporting its characterization as a potential probiotic candidate.
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Affiliation(s)
- Kuan Lu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Xueya Wang
- Chili Pepper Research Institute, Guizhou Provincial Academy of Agricultural Sciences, Guizhou, Guiyang, 550006, China
| | - Ying Zhou
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China
| | - Qiujin Zhu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guizhou Province, Guiyang, 550025, China.
- Guizhou Province Key Laboratory of Agricultural and Animal Products Storage and Processing, School of Liquor and Food Engineering, Guizhou University, Guizhou, Guiyang, 550025, China.
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Zhang X, He X, Chen J, Li J, Wu Y, Chen Y, Yang Y. Whole-Genome Analysis of Termite-Derived Bacillus velezensis BV-10 and Its Application in King Grass Silage. Microorganisms 2023; 11:2697. [PMID: 38004709 PMCID: PMC10672971 DOI: 10.3390/microorganisms11112697] [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: 09/26/2023] [Revised: 10/28/2023] [Accepted: 10/29/2023] [Indexed: 11/26/2023] Open
Abstract
Bacillus velezensis (B. velezensis) is a cellulose-degrading strain that has the potential as an additive in fermented feed. B. velezensis BV-10 was isolated and screened from the termite gut. We sequenced the whole genome of this new source of B. velezensis to reveal its potential for use in cellulose degradation. Whole-genome sequencing of B. velezensis BV-10 showed that it has a circular chromosome of 3929792 bp containing 3873 coding genes with a GC content of 45.51% and many genes related to cellulose, hemicellulose, and lignin degradation. King grass silage was inoculated with B. velezensis BV-10 and mixed with other feed additives to assess the effect of B. velezensis BV-10 on the fermentation quality of silage. Six treatment groups were established: the control, B. velezensis BV-10, molasses, cellulase, B. velezensis BV-10 plus molasses, and B. velezensis BV-10 plus cellulase groups. After 30 days of silage-fermentation testing, B. velezensis BV-10 was found to rapidly reduce the silage pH value and significantly reduce the acid-detergent fiber (ADF) content (p < 0.05). The addition of B. velezensis BV-10 plus molasses and cellulase in fermented feed significantly reduced the silage neutral-detergent fiber and ADF content and promoted organic-acid accumulation (p < 0.05). The above results demonstrate that B. velezensis BV-10 promotes the fermentation quality of silage and that this effect is greater when other silage-fermentation additives are included. In conclusion, genes involved in cellulose degradation in B. velezensis BV-10 were identified by whole-genome sequencing and further experiments explored the effects of B. velezensis BV-10 and different feed additives on the fermentation quality of king grass silage, revealing the potential of Bacillus velezensis as a new silage additive.
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Affiliation(s)
| | | | | | | | | | | | - Yuhui Yang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (X.Z.); (X.H.); (J.C.); (J.L.); (Y.W.); (Y.C.)
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Zhang Y, Zhang S, Xu L. The pivotal roles of gut microbiota in insect plant interactions for sustainable pest management. NPJ Biofilms Microbiomes 2023; 9:66. [PMID: 37735530 PMCID: PMC10514296 DOI: 10.1038/s41522-023-00435-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
The gut microbiota serves as a critical "organ" in the life cycle of animals, particularly in the intricate interplay between herbivorous pests and plants. This review summarizes the pivotal functions of the gut microbiota in mediating the insect-plant interactions, encompassing their influence on host insects, modulation of plant physiology, and regulation of the third trophic level species within the ecological network. Given these significant functions, it is plausible to harness these interactions and their underlying mechanisms to develop novel eco-friendly pest control strategies. In this context, we also outline some emerging pest control methods based on the intestinal microbiota or bacteria-mediated interactions, such as symbiont-mediated RNAi and paratransgenesis, albeit these are still in their nascent stages and confront numerous challenges. Overall, both opportunities and challenges coexist in the exploration of the intestinal microbiota-mediated interactions between insect pests and plants, which will not only enrich the fundamental knowledge of plant-insect interactions but also facilitate the development of sustainable pest control strategies.
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Affiliation(s)
- Yuxin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Shouke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, 311300, Hangzhou, China.
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China.
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Liu G, Zhang K, Gong H, Yang K, Wang X, Zhou G, Cui W, Chen Y, Yang Y. Whole genome sequencing and the lignocellulose degradation potential of Bacillus subtilis RLI2019 isolated from the intestine of termites. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:130. [PMID: 37598218 PMCID: PMC10439612 DOI: 10.1186/s13068-023-02375-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/25/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Lignocellulosic biomass is the most abundant and renewable terrestrial raw material for conversion into bioproducts and biofuels. However, the low utilization efficiency of lignocellulose causes environmental pollution and resource waste, which limits the large-scale application of bioconversion. The degradation of lignocellulose by microorganisms is an efficient and cost-effective way to overcome the challenge of utilizing plant biomass resources. This work aimed to screen valuable cellulolytic bacteria, explore its molecular mechanism from genomic insights, and investigate the ability of the strain to biodegrade wheat straw. RESULTS Bacillus subtilis (B. subtilis) RLI2019 was isolated from the intestine of Reticulitermes labralis. The strain showed comprehensive enzyme activities related to lignocellulose degradation, which were estimated as 4.06, 1.97, 4.12, 0.74, and 17.61 U/mL for endoglucanase, β-glucosidase, PASC enzyme, filter paper enzyme, and xylanase, respectively. Whole genome sequencing was performed to better understand the genetic mechanism of cellulose degradation. The genome size of B. subtilis RLI2019 was 4,195,306 bp with an average GC content of 43.54%, and the sequence characteristics illustrated an extremely high probability (99.41%) as a probiotic. The genome contained 4,381 protein coding genes with an average GC content of 44.20%, of which 145 genes were classified into six carbohydrate-active enzyme (CAZyme) families and 57 subfamilies. Eight cellulose metabolism enzyme-related genes and nine hemicellulose metabolism enzyme-related genes were annotated by the CAZyme database. The starch and sucrose metabolic pathway (ko00500) was the most enriched with 46 genes in carbohydrate metabolism. B. subtilis RLI2019 was co-cultured with wheat straw for 7 days of fermentation, the contents of neutral detergent fiber, acid detergent fiber, hemicellulose, and lignin were significantly reduced by 5.8%, 10.3%, 1.0%, and 4.7%, respectively. Moreover, the wheat straw substrate exhibited 664.9 μg/mL of reducing sugars, 1.22 U/mL and 6.68 U/mL of endoglucanase and xylanase activities, respectively. Furthermore, the fiber structures were effectively disrupted, and the cellulose crystallinity was significantly reduced from 40.2% to 36.9%. CONCLUSIONS The complex diversity of CAZyme composition mainly contributed to the strong cellulolytic attribute of B. subtilis RLI2019. These findings suggest that B. subtilis RLI2019 has favorable potential for biodegradation applications, thus it can be regarded as a promising candidate bacterium for lignocellulosic biomass degradation.
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Affiliation(s)
- Gongwei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hanxuan Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kaiyao Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoyu Wang
- Qinling Giant Panda Breeding Research Center, Shaanxi Academy of Forestry Sciences, Zhouzhi, 710402, Shaanxi, China
| | - Guangchen Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenyuan Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yuxin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Zhang T, Wei S, Liu Y, Cheng C, Ma J, Yue L, Gao Y, Cheng Y, Ren Y, Su S, Zhao X, Lu Z. Screening and genome-wide analysis of lignocellulose-degrading bacteria from humic soil. Front Microbiol 2023; 14:1167293. [PMID: 37637133 PMCID: PMC10450921 DOI: 10.3389/fmicb.2023.1167293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Crop straw contains huge amounts of exploitable energy, and efficient biomass degradation measures have attracted worldwide attention. Mining strains with high yields of cellulose-degrading enzymes is of great significance for developing clean energy and industrial production of related enzymes. In this study, we reported a high-quality genome sequence of Bacillus velezensis SSF6 strain using high-throughput sequencing technology (Illumina PE150 and PacBio) and assessed its lignocellulose degradation potential. The results demonstrated that the genome of B. velezensis SSF6 was 3.89 Mb and contained 4,015 genes, of which 2,972, 3,831 and 158 genes were annotated in the COGs (Clusters of Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes) and CAZyme (Carbohydrate-Active enZymes) databases, respectively, and contained a large number of genes related to carbohydrate metabolism. Furthermore, B. velezensis SSF6 has a high cellulose degradation capacity, with a filter paper assay (FPA) and an exoglucanase activity of 64.48 ± 0.28 and 78.59 ± 0.42 U/mL, respectively. Comparative genomic analysis depicted that B. velezensis SSF6 was richer in carbohydrate hydrolase gene. In conclusion, the cellulose-degrading ability of B. velezensis SSF6 was revealed by genome sequencing and the determination of cellulase activity, which laid a foundation for further cellulose degradation and bioconversion.
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Affiliation(s)
- Tianjiao Zhang
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Shuli Wei
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yajie Liu
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Chao Cheng
- School of Life Science, Jining Normal University, Ulanqab, China
| | - Jie Ma
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Linfang Yue
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Yanrong Gao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yongfeng Ren
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Shaofeng Su
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Xiaoqing Zhao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Zhanyuan Lu
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
- Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
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Li G, Yuan Y, Jin B, Zhang Z, Murtaza B, Zhao H, Li X, Wang L, Xu Y. Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides. Front Microbiol 2023; 14:1205767. [PMID: 37608941 PMCID: PMC10440823 DOI: 10.3389/fmicb.2023.1205767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.
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Affiliation(s)
- Gen Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yue Yuan
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Bowen Jin
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhiqiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Hong Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
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11
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Vittoria M, Saggese A, Isticato R, Baccigalupi L, Ricca E. Probiotics as an Alternative to Antibiotics: Genomic and Physiological Characterization of Aerobic Spore Formers from the Human Intestine. Microorganisms 2023; 11:1978. [PMID: 37630538 PMCID: PMC10458579 DOI: 10.3390/microorganisms11081978] [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: 07/07/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
A total of thirty-two aerobic spore former strains were isolated from intestinal samples of healthy children and analyzed for their hemolytic and antibiotic-resistant activities. Four strains selected as non-hemolytic and sensitive to all antibiotics recommended as relevant by regulatory agencies were short-listed and evaluated for their in silico and in vitro probiotic potentials. The four selected strains were assigned to the Bacillus velezensis (MV4 and MV11), B. subtilis (MV24), and Priestia megaterium (formerly Bacillus megaterium) (MV30) species. A genomic analysis indicated that MV4, MV11, and MV24 contained a homolog of the gene coding for the fibrinolytic enzyme nattokinase while only MV30 encoded a glutamic acid decarboxylase essential to synthesize the neurotransmitter GABA. All four strains contained gene clusters potentially coding for new antimicrobials, showed strong antioxidant activity, formed biofilm, and produced/secreted quorum-sensing peptides able to induce a cytoprotective stress response in a model of human intestinal (HT-29) cells. Altogether, genomic and physiological data indicate that the analyzed strains do not pose safety concerns and have in vitro probiotic potentials allowing us to propose their use as an alternative to antibiotics.
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Affiliation(s)
- Maria Vittoria
- Department of Biology, Federico II University of Naples, 80125 Naples, Italy; (M.V.); (A.S.); (R.I.)
| | - Anella Saggese
- Department of Biology, Federico II University of Naples, 80125 Naples, Italy; (M.V.); (A.S.); (R.I.)
| | - Rachele Isticato
- Department of Biology, Federico II University of Naples, 80125 Naples, Italy; (M.V.); (A.S.); (R.I.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy;
| | - Loredana Baccigalupi
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy;
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, 80131 Naples, Italy
| | - Ezio Ricca
- Department of Biology, Federico II University of Naples, 80125 Naples, Italy; (M.V.); (A.S.); (R.I.)
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12
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Chen L, Qu Z, Yu W, Zheng L, Qiao H, Wang D, Wei B, Zhao Z. Comparative genomic and transcriptome analysis of Bacillus velezensis CL-4 fermented corn germ meal. AMB Express 2023; 13:10. [PMID: 36683079 PMCID: PMC9868226 DOI: 10.1186/s13568-023-01510-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023] Open
Abstract
Bacillus, an excellent organic-degrading agent, can degrade lignocellulose. Notably, some B. velezensis strains encode lignocellulases. However, their ability to degrade lignocellulose in fermented feed is not much appreciated. This study performed a comparative genomic analysis of twenty-three B. velezensis strains to find common carbohydrate-active enzymes (CAZymes) encoding genes and evaluated their potential to degrade lignocellulose. The comparative genomic and CAZyme database-based analyses identified several potential CAZymes genes that degrade cellulose (GH1, GH4, GH5, GH13, GH16, GH32, PL1, and PL9), hemicellulose (GH11, GH26, GH43, GH51, and CE3) and lignin (AA4, AA6, AA7, and AA10). Furthermore, Illumina RNA-seq transcriptome analysis revealed the expression of more than 1794 genes in B. velezensis CL-4 fermented corn germ meal at 48 h (FCGM 48 h). Gene ontology analysis of expressed genes revealed their enrichment in hydrolase activity (breaking the glycosyl bonds during carbohydrate metabolism), indicating the upregulation of CAZymes. In total, 58 differentially upregulated CAZymes-encoding genes were identified in FCGM 48 h compared to FCGM 0 h. The upregulated CAZymes-encoding genes were related to cellulose (6-phospho-β-galactosidase and 6-phospho-α-glucosidase), starch (α-glucosidase and α-amylase), pectin (pectin lyase), and hemicellulose (arabinan endo-1,5-α-L-arabinosidase, xylan 1,4-beta-xylosidase, α-N-arabinofuranosidase, and acetyl xylan esterase). Importantly, arabinoxylan degradation mainly occurred in FCGM 48 h, followed by partial degradation of cellulose, pectin, and starch. This study can support the development of enzymatic cocktails for the solid-state fermented feed (SFF).
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Affiliation(s)
- Long Chen
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Zihui Qu
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Wei Yu
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Lin Zheng
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Haixin Qiao
- Information Application Department, Jilin Intellectual Property Protection Center, Changchun, 130000 China
| | - Dan Wang
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Bingdong Wei
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Zijian Zhao
- grid.464388.50000 0004 1756 0215Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, No. 1366 Cai Yu Street, Changchun, 130033 Jilin Province China
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13
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Wu Z, Peng K, Zhang Y, Wang M, Yong C, Chen L, Qu P, Huang H, Sun E, Pan M. Lignocellulose dissociation with biological pretreatment towards the biochemical platform: A review. Mater Today Bio 2022; 16:100445. [PMID: 36212906 PMCID: PMC9535326 DOI: 10.1016/j.mtbio.2022.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/30/2022]
Abstract
Lignocellulose utilization has been gaining great attention worldwide due to its abundance, accessibility, renewability and recyclability. Destruction and dissociation of the cross-linked, hierarchical structure within cellulose hemicellulose and lignin is the key procedure during chemical utilization of lignocellulose. Of the pretreatments, biological treatment, which can effectively target the complex structures, is attractive due to its mild reaction conditions and environmentally friendly characteristics. Herein, we report a comprehensive review of the current biological pretreatments for lignocellulose dissociation and their corresponding degradation mechanisms. Firstly, we analyze the layered, hierarchical structure of cell wall, and the cross-linked network between cellulose, hemicellulose and lignin, then highlight that the cracking of β-aryl ether is considered the key to lignin degradation because of its dominant position. Secondly, we explore the effect of biological pretreatments, such as fungi, bacteria, microbial consortium, and enzymes, on substrate structure and degradation efficiency. Additionally, combining biological pretreatment with other methods (chemical methods and catalytic materials) may reduce the time necessary for the whole process, which also help to strengthen the lignocellulose dissociation efficiency. Thirdly, we summarize the related applications of lignocellulose, such as fuel production, chemicals platform, and bio-pulping, which could effectively alleviate the energy pressure through bioconversion into high value-added products. Based on reviewing of current progress of lignocellulose pretreatment, the challenges and future prospects are emphasized. Genetic engineering and other technologies to modify strains or enzymes for improved biotransformation efficiency will be the focus of future research.
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Affiliation(s)
- Zengyou Wu
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Kun Peng
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yin Zhang
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Mei Wang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Cheng Yong
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ling Chen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ping Qu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Hongying Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Enhui Sun
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
- College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville, 3209, South Africa
- Corresponding author. Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Mingzhu Pan
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Corresponding author.
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14
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Chettri D, Nad S, Konar U, Verma AK. CAZyme from gut microbiome for efficient lignocellulose degradation and biofuel production. FRONTIERS IN CHEMICAL ENGINEERING 2022. [DOI: 10.3389/fceng.2022.1054242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Over-exploitation and energy security concerns of the diminishing fossil fuels is a challenge to the present global economy. Further, the negative impact of greenhouse gases released using conventional fuels has led to the need for searching for alternative biofuel sources with biomass in the form of lignocellulose coming up as among the potent candidates. The entrapped carbon source of the lignocellulose has multiple applications other than biofuel generation under the biorefinery approach. However, the major bottleneck in using lignocellulose for biofuel production is its recalcitrant nature. Carbohydrate Active Enzymes (CAZymes) are enzymes that are employed for the disintegration and consumption of lignocellulose biomass as the carbon source for the production of biofuels and bio-derivatives. However, the cost of enzyme production and their stability and catalytic efficiency under stressed conditions is a concern that hinders large-scale biofuel production and utilization. Search for novel CAZymes with superior activity and stability under industrial condition has become a major research focus in this area considering the fact that the most conventional CAZymes has low commercial viability. The gut of plant-eating herbivores and other organisms is a potential source of CAZyme with high efficiency. The review explores the potential of the gut microbiome of various organisms in the production of an efficient CAZyme system and the challenges in using the biofuels produced through this approach as an alternative to conventional biofuels.
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15
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Chen L, Chen W, Zheng B, Yu W, Zheng L, Qu Z, Yan X, Wei B, Zhao Z. Fermentation of NaHCO 3-treated corn germ meal by Bacillus velezensis CL-4 promotes lignocellulose degradation and nutrient utilization. Appl Microbiol Biotechnol 2022; 106:6077-6094. [PMID: 35976426 DOI: 10.1007/s00253-022-12130-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
Abstract
Sodium bicarbonate pretreatment and solid-state fermentation (SSF) were used to maximize the nutritional value of corn germ meal (CGM) by inoculating it with Bacillus velezensis CL-4 (isolated from chicken cecal contents and capable of degrading lignocellulose). Based on genome sequencing, B. velezensis CL-4 has a 4,063,558 bp ring chromosome and 46.27% GC content. Furthermore, genes associated with degradation of lignocellulose degradation were detected. Pretreatment of CGM (PCGM) with sodium bicarbonate (optimized to 0.06 g/mL) neutralized low pH. Fermented and pretreated CGM (FPCGM) contained more crude protein (CP), soluble protein of trichloroacetic acid (TCA-SP), and total amino acids (aa) than CGM and PCGM. Degradation rates of cellulose and hemicellulose were reduced by 21.33 and 71.35%, respectively, after 48 h fermentation. Based on electron microscopy, FPCGM destroys the surface structure and adds small debris of the CGM substrate, due to lignocellulose breakdown. Furthermore, 2-oxoadipic acid and dimethyl sulfone were the most important metabolites during pretreatment. Concentrations of adenosine, cytidine, guanosine, S-methyl-5'-thioadenosine, and adenine decreased significantly after 48 h fermentation, whereas concentrations of probiotics, enzymes, and fatty acids (including palmitic, 16-hydroxypalmitic, and linoleic acids) were significantly improved after fermentation. In conclusion, the novel pretreatment of CGM provided a proof of concept for using B. velezensis CL-4 to degrade lignocellulose components, improve nutritional characteristics of CGM, and expand CGM lignocellulosic biological feed production. KEY POINTS: • Sodium bicarbonate (baking soda) can be used as an economical and green additive to pretreat corn germ meal; • Fermentation with B. velezensis degrades the cellulose and hemicellulose component of corn germ meal and improves its feed quality; • As a novel qualified presumption of safety (QPS) strain, B. velezensis should have broad potential applications in food and feed industries.
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Affiliation(s)
- Long Chen
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Wanying Chen
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Boyu Zheng
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Wei Yu
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Lin Zheng
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Zihui Qu
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Xiaogang Yan
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Bingdong Wei
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China.
| | - Zijian Zhao
- Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, No. 1366 Cai Yu Street, Changchun, Jilin Province, 130033, People's Republic of China.
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16
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Li J, Wang S, Zhao J, Dong Z, Shao T. Gut Microbiota of Ostrinia nubilalis Larvae Degrade Maize Cellulose. Front Microbiol 2022; 13:816954. [PMID: 35495661 PMCID: PMC9039043 DOI: 10.3389/fmicb.2022.816954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/25/2022] [Indexed: 12/04/2022] Open
Abstract
Most arthropod guts harbor diverse microbiota for symbiotic digestion. The European corn borer (ECB), Ostrinia nubilalis (Hübner), is a devastating pest that feeds the lignocellulose-rich tissues of maize plants. However, the potential role of ECB gut microbes in degrading maize cellulose remains largely unexplored. Here, we investigated the gut microbiota of ECB fed with different diets and their potential function in maize lignocellulose degradation. The diversity and composition of gut bacterial communities varied dramatically between the ECB larva fed with artificial diets (ECB-D) and maize plants (ECB-M). Draft genomes of the microbial consortia from ECB-D and ECB-M showed that the principal degraders of cellulose mainly belonged to Firmicutes or Proteobacteria and they were primarily found in the midgut. The cellulolytic microbial consortia contained genes encoding various carbohydrate-active enzymes (CAZyme). Furthermore, scanning electron microscopy revealed significant breakdown of lignocellulose in maize treated by the two microbial consortia for 9 days in vitro. Metabolomic analyses show that maize particles treated by two microbial consortia generate distinctive metabolomic profiles, with enrichment for different monosaccharides (i.e., Glucose, Rhamnofuranose, Isomaltose, and Cellobiose) and amino acids (i.e., Threonine, Histidine, and Lysine). The results indicated that the diet of the host impacted the composition and function of its gut microbiota and ECB exploited specific gut microbes to digest maize lignocellulose with distinctive products. Our study provides valuable microbiota resources for lignocellulose bioconversion.
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Affiliation(s)
| | | | | | | | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
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17
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Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects. Microbiol Spectr 2022; 10:e0216921. [PMID: 35107331 PMCID: PMC8809340 DOI: 10.1128/spectrum.02169-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined Bacillus strains in the evolutionary tree. A comparative genomic analysis among Bacillus velezensis HNA3, Bacillus velezensis FZB42, Bacillus amyloliquefaciens DSM7, and Bacillus subtilis 168 showed that only HNA3 has one predicated secretory protein feruloyl esterase that catalyzes the hydrolysis of plant cell wall polysaccharides. The analysis of gene clusters revealed that whole biosynthetic gene clusters type Lanthipeptide was exclusively identified in HNA3 and might lead to the synthesis of new bioactive compounds. Twelve gene clusters were detected in HNA3 responsible for the synthesis of 14 secondary metabolites including Bacillaene, Fengycin, Bacillomycin D, Surfactin, Plipastatin, Mycosubtilin, Paenilarvins, Macrolactin, Difficidin, Amylocyclicin, Bacilysin, Iturin, Bacillibactin, Paenibactin, and others. HNA3 has 77 genes encoding for possible antifungal and antibacterial secreting carbohydrate active enzymes. It also contains genes involved in plant growth promotion, such as 11 putative indole acetic acid (IAA)-producing genes, spermidine and polyamine synthase genes, volatile compound producing genes, and multiple biofilm related genes. HNA3 also has 19 phosphatase genes involved in phosphorus solubilization. Our results provide insights into the genetic characteristics responsible for the bioactivities and potential application of HNA3 as plant growth-promoting strain in ecological agriculture. IMPORTANCE This study is the primary initiative to identify Bacillus velezensis HNA3 whole genome sequence and reveal its genomic properties as an effective biocontrol agent against plant pathogens and a plant growth stimulator. HNA3 genetic profile can be used as a reference for future studies that can be applied as a highly effective biofertilizer and biofungicide inoculum to improve agriculture productivity. HNA3 reclassified in the phylogenetic tree which may be helpful for highly effective strain engineering and taxonomy. The genetic comparison among HNA3 and closely similar species B. velezensis FZB42, B. amyloliquefaciens DSM7, and B. subtilis 168 demonstrates some distinctive genetic properties of HNA3 and provides a basis for the genetic diversity of the Bacillus genus, which allows developing more effective eco-friendly resources for agriculture and separation of Bacillus velezensis as distinct species in the phylogenetic tree.
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Guo H, He T, Lee DJ. Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review. BIORESOURCE TECHNOLOGY 2022; 344:126263. [PMID: 34728359 DOI: 10.1016/j.biortech.2021.126263] [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: 10/03/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This review overviewed the current researches on the isolation of novel strains, the development of novel identification protocols, the key enzymes and their synergistic interactions with other functional enzyme systems, and the strategies for enhancing enzymolysis efficiencies. The main obstacle for realizing biorefinery of lignocellulosic biomass to biofuels or biochemicals is the high cost of enzymolysis stage. Therefore, research prospects to reduce the costs for lignocellulose hydrolysis were outlined.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China; College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Tongyuan He
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong.
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19
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Li J, Wu Y, Zhao J, Wang S, Dong Z, Shao T. Bioaugmented degradation of rice straw combining two novel microbial consortia and lactic acid bacteria for enhancing the methane production. BIORESOURCE TECHNOLOGY 2022; 344:126148. [PMID: 34673188 DOI: 10.1016/j.biortech.2021.126148] [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: 08/03/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Two consortia of lignocellulolytic microbes (CL and YL) were isolated from the rumen of ruminants. Their ability to facilitate the degradation of rice straw and enhance methane (CH4) production were evaluated, both individually and combined with lactic acid bacteria (LAB). After 30 days of degradation, rice straw powders (RSPs) were observed to change in physical structure and also displayed a significant reduction in lignocellulose content. Combined application of microbial consortia with LAB efficiently improved enzymatic hydrolysis of RSPs, increasing organic acid as well as mono- and disaccharide contents. Synergistic action between microbial consortia and LAB enhanced CH4 yield, and rice straw treated with YL + LAB had the highest CH4 production (357.53 mL CH4/g VS), more than fivefold of the control. The newly identified microbial consortia are capable of efficiently degrading lignocellulosic biomass. Functioning synergistically with LAB, they provide a feasible way biodegrade rice straw and enhance methane production from agricultural wastes.
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Affiliation(s)
- Junfeng Li
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongjie Wu
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Siran Wang
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zihao Dong
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
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20
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Li J, Tang X, Chen S, Zhao J, Shao T. Ensiling pretreatment with two novel microbial consortia enhances bioethanol production in sterile rice straw. BIORESOURCE TECHNOLOGY 2021; 339:125507. [PMID: 34303101 DOI: 10.1016/j.biortech.2021.125507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
The present study extracts and enriches cellulolytic microbial consortia from yak (Bos grunniens) and evaluates their effects on the fermentation profile and bioethanol yield in rice straw silage. Two microbial consortia (CF and PY) with high cellulolytic activity were isolated and observed to be prone to utilize natural carbon sources. Two consortia were introduced with and without combined lactic acid bacteria (CLAB) to rice straw for up to 60 days of ensiling, and their application notably decreased the levels of structural carbohydrates and pH values of rice straw silages. Treatments that combining microbial consortia and CLAB resulted in the highest levels of lactic acid, water soluble carbohydrates, mono- and disaccharides, and lignocellulose degradation, with PY + CLAB group yielding the highest bioethanol production. The microbial consortia identified herein exhibit great potential for degrading fibrous substrates, and their combination with CLAB provides a feasible way to efficiently use rice straw for bioethanol production.
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Affiliation(s)
- Junfeng Li
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyue Tang
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Sifan Chen
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
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21
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Vu NTH, Quach TN, Dao XTT, Le HT, Le CP, Nguyen LT, Le LT, Ngo CC, Hoang H, Chu HH, Phi QT. A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides. PeerJ 2021; 9:e11839. [PMID: 34395081 PMCID: PMC8325422 DOI: 10.7717/peerj.11839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
Background Lignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date. Methods The cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities. Results Among 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in strain MP1 genome, but not with closely related C. cellulans strains, proving this strain to be a potential candidate for further studies. Endoglucanases, exoglucanases, and xylanase were achieved by using cheaply available agro-residues such as rice bran and sugar cane bagasse. The maximum levan production by C. cellulans MP1 was 14.8 ± 1.2 g/l after 20 h of cultivation in media containing 200 g/l sucrose. To the best of our knowledge, the present study is the first genome-based analysis of a Cellulosimicrobium species which focuses on lignocellulosic enzymes and levan biosynthesis, illustrating that the C. cellulans MP1 has a great potential to be an efficient platform for basic research and industrial exploitation.
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Affiliation(s)
- Nguyen Thi-Hanh Vu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Tung Ngoc Quach
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Xuan Thi-Thanh Dao
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam.,Vinh University, Vinh, Vietnam
| | - Ha Thanh Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Chi Phuong Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Hanoi, Vietnam
| | - Lam Tung Nguyen
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Lam Tung Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Hanoi, Vietnam
| | | | - Ha Hoang
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Hanoi, Vietnam
| | - Ha Hoang Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Quyet-Tien Phi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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22
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Qi Y, Jiang Y, Zhang X, Lee YK, Liu X, Zhao J, Zhang H, Chen W. Diversity in genetic and peptidase activity of Lactobacillus helveticus strains biodiversity of Lactobacillus helveticus. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.100915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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23
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Comparative genomic and secretomic characterisation of endophytic Bacillus velezensis LC1 producing bioethanol from bamboo lignocellulose. Arch Microbiol 2021; 203:3089-3099. [PMID: 33792738 DOI: 10.1007/s00203-021-02306-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/30/2022]
Abstract
Bacillus is an excellent organic matter degrader, and it has exhibited various abilities required for lignocellulose degradation. Several B. velezensis strains encode lignocellulosases, however their ability to efficiently transform biomass has not been appreciated. In the present study, through the comparative genomic analysis of the whole genome sequences of 21 B. velezensis strains, CAZyome related to lignocellulose degradation was identified and their similarities and differences were compared. Subsequently, the secretome of B. velezensis LC1 by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were identified and confirmed that a considerable number of proteins were involved in lignocellulose degradation. Moreover, after 6-day treatment, the degradation efficiency of the B. velezensis LC1 toward cellulose, hemicellulose and lignin were 59.90%, 75.44% and 23.41%, respectively, the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielded 10.44 g/L ethanol after 96 h. These results indicate that B. velezensis LC1 has the ability to effectively degrade bamboo lignocellulose and has the potential to be used in bioethanol production.
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24
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Zhang Z, Li Y, Zhang J, Peng N, Liang Y, Zhao S. High-Titer Lactic Acid Production by Pediococcus acidilactici PA204 from Corn Stover through Fed-Batch Simultaneous Saccharification and Fermentation. Microorganisms 2020; 8:microorganisms8101491. [PMID: 32998448 PMCID: PMC7600695 DOI: 10.3390/microorganisms8101491] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/21/2022] Open
Abstract
Lignocellulose comprised of cellulose and hemicellulose is one of the most abundant renewable feedstocks. Lactic acid bacteria have the ability to ferment sugar derived from lignocellulose. In this study, Pediococcus acidilactici PA204 is a lactic acid bacterium with a high tolerance of temperature and high-efficiency utilization of xylose. We developed a fed-batch simultaneous saccharification and fermentation (SSF) process at 37 °C (pH 6.0) using the 30 FPU (filter paper units)/g cellulase and 20 g/L corn steep powder in a 5 L bioreactor to produce lactic acid (LA). The titer, yield, and productivity of LA produced from 12% (w/w) NaOH-pretreated and washed stover were 92.01 g/L, 0.77 g/g stover, and 1.28 g/L/h, respectively, and those from 15% NaOH-pretreated and washed stover were 104.11 g/L, 0.69 g/g stover, and 1.24 g/L/h, respectively. This study develops a feasible fed-batch SSF process for LA production from corn stover and provides a promising candidate strain for high-titer and -yield lignocellulose-derived LA production.
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Affiliation(s)
- Zhenting Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Z.); (Y.L.); (J.Z.); (N.P.); (Y.L.)
| | - Yanan Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Z.); (Y.L.); (J.Z.); (N.P.); (Y.L.)
| | - Jianguo Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Z.); (Y.L.); (J.Z.); (N.P.); (Y.L.)
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Z.); (Y.L.); (J.Z.); (N.P.); (Y.L.)
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Z.); (Y.L.); (J.Z.); (N.P.); (Y.L.)
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Z.); (Y.L.); (J.Z.); (N.P.); (Y.L.)
- Correspondence: ; Tel.: +86-27-8728-1267; Fax: +86-27-8728-0670
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Szczerba H, Dudziak K, Krawczyk M, Targoński Z. A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production. Int J Mol Sci 2020; 21:ijms21144835. [PMID: 32650546 PMCID: PMC7402333 DOI: 10.3390/ijms21144835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/31/2022] Open
Abstract
Enterobacter sp. LU1, a wild-type bacterium originating from goat rumen, proved to be a potential succinic acid producer in previous studies. Here, the first complete genome of this strain was obtained and analyzed from a biotechnological perspective. A hybrid sequencing approach combining short (Illumina MiSeq) and long (ONT MinION) reads allowed us to obtain a single continuous chromosome 4,636,526 bp in size, with an average 55.6% GC content that lacked plasmids. A total of 4425 genes, including 4283 protein-coding genes, 25 ribosomal RNA (rRNA)-, 84 transfer RNA (tRNA)-, and 5 non-coding RNA (ncRNA)-encoding genes and 49 pseudogenes, were predicted. It has been shown that genes involved in transport and metabolism of carbohydrates and amino acids and the transcription process constitute the major group of genes, according to the Clusters of Orthologous Groups of proteins (COGs) database. The genetic ability of the LU1 strain to metabolize a wide range of industrially relevant carbon sources has been confirmed. The genome exploration indicated that Enterobacter sp. LU1 possesses all genes that encode the enzymes involved in the glycerol metabolism pathway. It has also been shown that succinate can be produced as an end product of fermentation via the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. The transport system involved in succinate excretion into the growth medium and the genes involved in the response to osmotic and oxidative stress have also been recognized. Furthermore, three intact prophage regions ~70.3 kb, ~20.9 kb, and ~49.8 kb in length, 45 genomic islands (GIs), and two clustered regularly interspaced short palindromic repeats (CRISPR) were recognized in the genome. Sequencing and genome analysis of Enterobacter sp. LU1 confirms many earlier results based on physiological experiments and provides insight into their genetic background. All of these findings illustrate that the LU1 strain has great potential to be an efficient platform for bio-based succinate production.
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Affiliation(s)
- Hubert Szczerba
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 20-704 Lublin, Poland;
- Correspondence: ; Tel.: +48-81-462-3402
| | - Karolina Dudziak
- Chair and Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland;
| | | | - Zdzisław Targoński
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 20-704 Lublin, Poland;
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