Potential of semiarid soil from Caatinga biome as a novel source for mining lignocellulose-degrading enzymes

Abstract

The litterfall is the major organic material deposited in soil of Brazilian Caatinga biome, thus providing the ideal conditions for plant biomass-degrading microorganisms to thrive. Herein, the phylogenetic composition and lignocellulose-degrading capacity have been explored for the first time from a fosmid library dataset of Caatinga soil by sequence-based screening. A complex bacterial community dominated by Proteobacteria and Actinobacteria was unraveled. SEED subsystems-based annotations revealed a broad range of genes assigned to carbohydrate and aromatic compounds metabolism, indicating microbial ability to utilize plant-derived material. CAZy-based annotation identified 7275 genes encoding 37 glycoside hydrolases (GHs) families related to hydrolysis of cellulose, hemicellulose, oligosaccharides and other lignin-modifying enzymes. Taxonomic affiliation of genes showed high genetic potential of the phylum Acidobacteria for hemicellulose degradation, whereas Actinobacteria members appear to play an important role in celullose hydrolysis. Additionally, comparative analyses revealed greater GHs profile similarity among soils as compared to the digestive tract of animals capable of digesting plant biomass, particularly in the hemicellulases content. Combined results suggest a complex synergistic interaction of community members required for biomass degradation into fermentable sugars. This large repertoire of lignocellulolytic enzymes opens perspectives for mining potential candidates of biochemical catalysts for biofuels production from renewable resources and other environmental applications.

Isolation, Identification, and Biocontrol Potential of Entomopathogenic Nematodes and Associated Bacteria against Virachola livia (Lepidoptera: Lycaenidae) and Ectomyelois ceratoniae (Lepidoptera: Pyralidae)

“…For example, Stenotrophomonas , Ochrobactrum , and Pseudomonas have often been identified in the soil-dwelling Caenorhabditis elegans nematodes [ 51 ]. Likewise, Proteobacteria is the most abundant phylum in bacterial communities associated with plant roots [ 52 ], as well as in plant-covered soils, such as the rhizosphere [ 53 ].…”

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest

“…Wafula et al (2015) also reported a positive correlation of total N, organic matter and moisture with Acidobacteria communities from treated wastewater-irrigated soils. In fact, bacterial isolates of this phylum are able to grow in high concentrations of C sources (Eichorst et al, 2007; Castro et al, 2014; García-Fraile et al, 2016), and genetic evidence have revealed the presence of genes required to decompose complex substrates (García-Fraile et al, 2016; Kielak et al, 2016; Lacerda Júnior et al, 2017). Genomic insights also presume a role of ‘ Candidatus Koribacter’ and ‘ Candidatus Solibacter’ in N 2 cycling by the reduction of nitrate, nitrite, and possibly nitric oxide (Ward et al, 2009).…”

“…On the other hand, moist soils showed an increase of polysaccharide degradation pathways, including xyloglucans (plant polysaccharides) and glycogen. In fact, a vast repertoire of lignocellulolytic enzymes was mined by sequence-based screening from a metagenomic library of a Caatinga soil in the rainy season (Lacerda Júnior et al, 2017). This is expected since the litterfall is the major organic source deposited in the soil of Caatinga forest (Salgado et al, 2015).…”

“…Increased attention has recently been paid to the cultivation, characterization and biotechnological potential of Caatinga microbes due to their unique biological features that allow them to survive under severe climate conditions (high temperature, high ultraviolet exposure, and water shortage) (Monteiro et al, 2009; Marcon et al, 2010; Castro et al, 2014; Fernandes-Júnior et al, 2015). Metagenomics-based approaches and 16S rRNA amplicon sequencing have sought to assess the great microbial diversity and shed light on the metabolic strategies that enable the Caatinga microbes to survive under harsh conditions (Lançoni et al, 2013; Nessner Kavamura et al, 2013; Pacchioni et al, 2014; Lacerda Júnior et al, 2017; Leite et al, 2017). Although some studies have shown that soil microbial communities are shaped by seasonality, it is still not clear how microbes adapt to the conversion of intact Caatinga dry forest into cultivation fields, in addition to the underlying impact on the ecosystem functioning.…”

The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types

“…Other aspects of metagenomic studies involve large-insert metagenomic library analysis [4], shotgun targeted metagenomic sequencing [5,6], or proteomics [7] and aim to study not only the taxonomic structure of the cellulolytic community but also the biodiversity of genes involved in decomposition. However, it is not necessary to dwell on them here, because their goals are beyond the scope of the current study.…”