The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications

Abstract

Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw. The 4.7 Mbp genome encodes 4,194 proteins, including 36 glycoside hydrolases (GH), supporting the hypothesis that this bacterium may contribute to lignocellulose decomposition. Comparative analysis among fully sequenced Dyella species indicate that the genome synteny is not conserved, and that D. jiangningensis FCAV SCS01 carries 372 unique genes, including an alpha-glucosidase and maltodextrin glucosidase coding genes, and other potential biomass degradation related genes. Additional genomic features, such as prophage-like, genomic islands and putative new biosynthetic clusters were also uncovered. Overall, D. jiangningensis FCAV SCS01 represents the first South American Dyella genome sequenced and shows an exclusive feature among its genus, related to biomass degradation.

Isolation and Genome Analysis of an Amoeba-Associated Bacterium Dyella terrae Strain Ely Copper Mine From Acid Rock Drainage in Vermont, United States

“…Several genes are putatively involved in lignin degradation, including 26 RAST-annotated hydrolases ( Supplementary Table 8 ), a dye-decolorizing (DyP) peroxidase, and four laccases containing copper-binding domains (HMMER annotation using LccED; Supplementary Table 9 ; Janusz et al, 2017 ). Hydrolases, a DyP-type peroxidase, and laccases were also found in the closely related D. terrae KACC 12748 genome and strains of D. jiangningensis ( Supplementary Tables 8–10 ) characterized as having lignin-degrading capabilities ( Desiderato et al, 2018 ; Constancio et al, 2020 ). In addition to having lignin-degrading genes, the D. terrae strain Ely Copper Mine genome also contained a total of six putative biosynthetic gene clusters (BGCs) dedicated to secondary metabolism (antiSMASH annotation; Supplementary Table 11 ).…”

“…Its hydrolysis, oxidation, and depolymerization plays a critical role in carbon recycling ( Kamimura et al, 2017 ). Several genes encoding peroxidases, hydrolases, and multicopper oxidases (e.g., laccases) involved in this process have been identified in D. terrae strain Ely Copper Mine in comparable numbers to those in other lignin-degrading Dyella ( Supplementary Tables 8–10 ; De Gonzalo et al, 2016 ; Desiderato et al, 2018 ). While the lignin-degrading capabilities of D. jiangningensis FCSAV SCS01 were based on several of its genes encoding hydrolases ( Desiderato et al, 2018 ), a D. jiangningensis isolate was observed to exhibit extracellular cellulase and amylase enzyme activities involved in lignin degradation ( Constancio et al, 2020 ).…”

“…The size of the bacterial genome is similar to those of Dyella strains with genomes ranging from 4.0 to 5.49 Mbp ( He et al, 2017 ; Ou et al, 2019 ). Dyella terrae strain Ely Copper Mine does not have a reduced genome, has similar GC content (59.1%–65.2%) to that of other Dyella strains ( Desiderato et al, 2018 ; Ou et al, 2019 ), and can exist outside amoebal cells ( Figure 5 ), indicating that it is likely a facultative symbiont of Stemonitis sp. ( McCutcheon and Moran, 2012 ).…”

“…KOs (or K numbers) were then assigned to KEGG pathways and biomolecular reaction pathways for information transfer and expression (BRITE) hierarchies. ORFs were also annotated via the RAST web annotation tool version 2.0 ( Aziz et al, 2008 ) using the RasTtk annotation pipeline to identify lignocellulose decomposition-related enzymes for comparison with other publicly available Dyella genomes, including D. terrae KACC 12748 (BioProject: PRJNA523522), D. jiangningensis SBZ 3-12 (BioProject: PRJEB16000), and D. jiangningensis FCAV SCS01 (BioProject PRJNA386033), a species speculated to be involved in lignin degradation ( Desiderato et al, 2018 ; Constancio et al, 2020 ). While only the D. jiangningensis SBZ 3-12 genome was complete, the other genomes had a completeness of 100%, according to the checkM metrics database ( Parks et al, 2015 ).…”

Bagasse minority pathway expression: Real time study of GH2 β-mannosidases from bacteroidetes

“…Thus, the low content of mannan in this substrate can lead to a simplistic view that the pathways involved in the degradation of mannan in sugar cane biomass can be neglected, though oligosaccharides of different complexities can be obtained through biomass biorefinery. Nevertheless, these minority compounds seem to be of importance from a physiological point of view, since microorganisms isolated by our team from communities associated with the degradation of substrates that are poor in mannan often have several mannanases in their genetic arsenal [ 9 , 28 , 29 ].…”