Genomically Defined Paenibacillus polymyxa ND24 for Efficient Cellulase Production Utilizing Sugarcane Bagasse as a Substrate

Bohra, Varsha; Tikariha, Hitesh; Dafale, Nishant A.

doi:10.1007/s12010-018-2820-5

Cited by 29 publications

(5 citation statements)

References 43 publications

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“…When a Pfam HMM for a given GH either did not exist or did not correspond to the catalytic module, BLAST searches against the data set were performed using regions of sequences listed at the Carbohydrate-Active Enzymes database. In addition, the coding sequences predicted as GHs were further characterized bysimilarity search against NCBI's protein data bank and non-redundant (nr) database using the BLASTP algorithm [42]. The output obtained were analyzed manually for determining the diversity and abundance of the various CAZymes classes: GHs, CBMs, carbohydrate esterases (CEs), glycosyl transferases (GTs), and polysaccharide lyases (PLs) in the rumen metagenomes.…”

Section: Mining Of Carbohydrate-active Enzymes For Muskoxen Fed Triticale Strawmentioning

confidence: 99%

Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

et al. 2021

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Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

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Section: Mining Of Carbohydrate-active Enzymes For Muskoxen Fed Triticale Strawmentioning

confidence: 99%

Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

et al. 2021

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“…The larger the enzyme repertoire is, the greater the potential to discover new enzymes with robust activities. As herbivores, ruminant animals harbour a highly diverse ecosystem of microorganisms in their gut, especially the rumen, which contains numerous unknown cellulases [13, 14]. Although some researchers have predicted many biomass-degrading gene candidates from the rumen using metagenomics [8, 15], only a few studies have evaluated their expression profiling or experimentally verified the activities of the enzymes encoded by these genes [15, 16].…”

Section: Introductionmentioning

confidence: 99%

Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases

Jin

Cao

et al. 2019

Biotechnol Biofuels

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Background Cellulosic biomass has great potential as a renewable biofuel resource. Robust, high-performance enzymes are needed to effectively utilize this valuable resource. In this study, metatranscriptomics was used to explore the carbohydrate-active enzymes (CAZymes), especially glycoside hydrolases (GHs), present in the rumen microbiome of Hu sheep. Select CAZymes were experimentally verified and characterized after cloning and expression in E. coli . Results The metatranscriptomes of six Hu sheep rumen microbiomes yielded 42.3 Gbp of quality-checked sequence data that represented in total 2,380,783 unigenes after de novo assembling using Trinity and clustered with CD-HIT-EST. Annotation using the CAZy database revealed that 2.65% of the unigenes encoded GHs, which were assigned to 111 different CAZymes families. Firmicutes (18.7%) and Bacteroidetes (13.8%) were the major phyla to which the unigenes were taxonomically assigned. In total, 14,489 unigenes were annotated to 15 cellulase-containing GH families, with GH3, GH5 and GH9 being the predominant. From these putative cellulase-encoding unigenes, 4225 open reading frames (ORFs) were predicted to contain 2151 potential cellulase catalytic modules. Additionally, 147 ORFs were found to encode proteins that contain carbohydrate-binding modules (CBMs). Heterogeneous expression of 30 candidate cDNAs from the GH5 family in E. coli BL21 showed that 17 of the tested proteins had endoglucanase activity, while 7 exhibited exoglucanase activity. Interestingly, two of the GH5 proteins (Cel5A-h28 and Cel5A-h11) showed high specific activity against carboxymethylcellulose (CMC) and p -nitrophenyl-β- d -cellobioside (pNPC) (222.2 and 142.8 U/mg), respectively. The optimal pH value for activity of Cel5A-h11 and Cel5A-h28 was 6.0 for both enzymes, and optimal temperatures were 40 and 50 °C, respectively. Both enzymes retained over 70 and 60%, respectively, of their original activities after incubation at 40 °C for 60 min. However, their activities were rapidly diminished upon exposure to higher temperatures. Cel5A-h11 and Cel5A-h28 retained more than 80 and 60% of their maximal enzymatic activities after incubation for 16 h in buffered solutions in the pH range from 4.0 to 9.0. Conclusion The metatranscriptomic results revealed that the rumen microbiome of Hu sheep encoded a repertoire of new enzymes capable of cellulose degradation and metatranscriptomics was an effective method to discover novel cellulases for biotechnological applications. Electronic supplementary material The online version of this article (10.1186/s13068-019-1498-4) contains supplementary material, which is available to authorized users.

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“…For instance, the activity of P. polymyxa ND24 was studied in a 5-L laboratory bioreactor where the cellulosic substrate in the medium was sugarcane bagasse; the strain showed the highest endoglucanase activity after 72 h of incubation. The sugarcane hydrolysate was then used for biogas production; the authors suggest that the obtained results support the use of P. polymyxa ND24 for cost-effective bioprocessing of lignocellulosic biomass [137]. In turn, other authors have used strains from the genus Bacillus to treat rice straw in order to increase the biomethane fermentation efficiency.…”

Section: Cellulase Activitymentioning

confidence: 76%

Taxonomy, Ecology, and Cellulolytic Properties of the Genus Bacillus and Related Genera

Dobrzyński,

Wróbel,

Górska

2023

Agriculture

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Bacteria of the genus Bacillus and related genera (e.g., Paenibacillus, Alicyclobacillus or Brevibacillus) belong to the phylum Firmicutes. Taxonomically, it is a diverse group of bacteria that, to date, has not been well described phylogenetically. The group consists of aerobic and relatively anaerobic bacteria, capable of spore-forming. Bacillus spp. and related genera are widely distributed in the environment, with a particular role in soil. Their abundance in the agricultural environment depends mainly on fertilization, but can also depend on soil cultivated methods, meaning whether the plants are grown in monoculture or rotation systems. The highest abundance of the phylum Firmicutes is usually recorded in soil fertilized with manure. Due to the great abundance of cellulose in the environment, one of the most important physiological groups among these spore-forming bacteria are cellulolytic bacteria. Three key cellulases produced by Bacillus spp. and related genera are required for complete cellulose degradation and include endoglucanases, exoglucanases, and β-glucosidases. Due to probable independent evolution, cellulases are encoded by hundreds of genes, which results in a large structural diversity of these enzymes. The microbial degradation of cellulose depends on its type and environmental conditions such as pH, temperature, and various substances including metal ions. In addition, Bacillus spp. are among a few bacteria capable of producing multi-enzymatic protein complexes called cellulosomes. In conclusion, the taxonomy of Bacillus spp. and related bacteria needs to be reorganized based on, among other things, additional genetic markers. Also, the ecology of soil bacteria of the genus Bacillus requires additions, especially in the identification of physical and chemical parameters affecting the occurrence of the group of bacteria. Finally, it is worth adding that despite many spore-forming strains well-studied for cellulolytic activity, still few are used in industry, for instance for biodegradation or bioconversion of lignocellulosic waste into biogas or biofuel. Therefore, research aimed at optimizing the cellulolytic properties of spore-forming bacteria is needed for more efficient commercialization.

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Genomically Defined Paenibacillus polymyxa ND24 for Efficient Cellulase Production Utilizing Sugarcane Bagasse as a Substrate

Cited by 29 publications

References 43 publications

Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases

Taxonomy, Ecology, and Cellulolytic Properties of the Genus Bacillus and Related Genera

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