Metagenomic SMRT Sequencing-Based Exploration of Novel Lignocellulose-Degrading Capability in Wood Detritus from Torreya nucifera in Bija Forest on Jeju Island

Abstract

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.

Metagenomic Insight into Lignocellulose Degradation of the Thermophilic Microbial Consortium TMC7

“…Active enzymes related to the breakdown of carbohydrates are classified into six groups: glycoside hydrolase (GH), glycosyl transferase (GT), auxiliary activity (AA), carbohydrate esterase (CE), polysaccharide lyases (PL), and carbohydrate-binding domains (CBM). The cooperation of multiple CAZymes in lignocellulose degradation was studied in microbial consortia originating from compost [ 4 ], woodlice gut [ 9 ], forest [ 10 ], and biogas-producing digesters [ 11 ].…”

Study on dynamic changes of microbial community and lignocellulose transformation mechanism during green waste composting

“…The phylum Actinobacteria was the most abundant bacteria phylum identified and followed by Proteobacteria. The phyla, Actinobacteria, and Proteobacteria, were also found in tree decayed process [32]. Zhou et al.…”

“…The phylum Actinobacteria was the most abundant bacteria phylum identified and followed by Proteobacteria. The phyla, Actinobacteria, and Proteobacteria, were also found in tree decayed process [32]. Zhou et al reported that Firmicutes, Actinobacteria and Proteobacteria were the dominant phyla in rice straw composing with pig manure [9].…”

Bacteria associated with wood tissues of Esca‐diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components

“…This is in accordance with prior findings in decaying wood of pine (Kielak et al ., 2016 ), beech (Valásková et al ., 2009 ), and in microcosms containing beech sawdust inoculated with Phanerochaete chrysosporium (Hervé et al ., 2014 , 2016 ). It has also been reported that Xanthomonadaceae were able to degrade the lignocellulose (cellulose, hemicellulose and lignin) of different lignocellulose substrates under controlled conditions (Zimmermann, 1990 ; Behera et al ., 2014 ; Ceballos et al ., 2017 ; Oh et al ., 2017 ). At genus level, the isolated bacterial community was composed primarily of Pseudomonas , which aligns with previous results demonstrating this genus as the most abundant in many organs as well as sap of grapevine (West et al ., 2010 ; Martins et al ., 2012 , 2013 ; Faist et al ., 2016 ; Deyett et al ., 2017 ; Compant et al ., 2019 ; Deyett and Rolshausen, 2019 ).…”