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Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes
Han Na Oh,Doyoung Park,Hoon Je Seong,Dockyu Kim,Woo Jun Sul 한국미생물학회 2019 The journal of microbiology Vol.57 No.10
Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil’s metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.
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Kumar, Himansu,Park, Woncheoul,Lim, Dajeong,Srikanth, Krishnamoorthy,Kim, Jun-Mo,Jia, Xin-Zheng,Han, Jian-Lin,Hanotte, Olivier,Park, Jong-Eun,Oyola, Samuel O. Elsevier 2020 Genomics Vol.112 No.2
<P><B>Abstract</B></P> <P>We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by <I>Bacteroidetes</I> and <I>Firmicutes.</I> We identified 2210 common genes in the two groups. LEfSe showed that the distribution of <I>Coprobacter, Geobacter, Cronobacter, Alloprevotella,</I> and <I>Dysgonomonas</I> were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Microbial comparison of scavenging chicken's cecum content between high land and low land region of Ethiopia. </LI> <LI> Differential functional annotations of identified microbiota from both regions. </LI> <LI> Antibiotic resistant genes identification and their differential abundance. </LI> </UL> </P>
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( Han Na Oh ),( Tae Kwon Lee ),( Jae Wan Park ),( Jee Hyun No ),( Dockyu Kim ),( Woo Jun Sul ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.9
Lignocellulose, composed mostly of cellulose, hemicellulose, and lignin generated through secondary growth of woody plant, is considered as promising resources for biofuel. In order to use lignocellulose as a biofuel, biodegradation besides high-cost chemical treatments were applied, but knowledge on the decomposition of lignocellulose occurring in a natural environment is insufficient. We analyzed the 16S rRNA gene and metagenome to understand how the lignocellulose is decomposed naturally in decayed Torreya nucifera (L) of Bija forest (Bijarim) in Gotjawal, an ecologically distinct environment. A total of 464,360 reads were obtained from 16S rRNA gene sequencing, representing diverse phyla; Proteobacteria (51%), Bacteroidetes (11%) and Actinobacteria (10%). The metagenome analysis using single molecules real-time sequencing revealed that the assembled contigs determined originated from Proteobacteria (58%) and Actinobacteria (10.3%). Carbohydrate Active enZYmes (CAZy)- and Protein families (Pfam)-based analysis showed that Proteobacteria was involved in degrading whole lignocellulose, and Actinobacteria played a role only in a part of hemicellulose degradation. Combining these results, it suggested that Proteobacteria and Actinobacteria had selective biodegradation potential for different lignocellulose substrates. Thus, it is considered that understanding of the systemic microbial degradation pathways may be a useful strategy for recycle of lignocellulosic biomass, and the microbial enzymes in Bija forest can be useful natural resources in industrial processes.
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