Genome Sequence of Lysinibacillus sphaericus, a Lignin-Degrading Bacterium Isolated from Municipal Solid Waste Soil

ABSTRACT We report here the draft genome sequence of Lysinibacillus sphaericus strain A1, a potential lignin-degrading bacterium isolated from municipal solid waste (MSW) soil and capable of enhancing gas release from lignocellulose-containing soil. </jats:p

Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization

BACKGROUND: Lignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bio-derived products for the chemical industry. However, the inherent structural complexity and recalcitrance of lignin makes its conversion into valuable chemicals a challenge. Natural microbial communities produce biocatalysts derived from a large number of microorganisms, including those considered unculturable, which operate synergistically to perform a variety of bioconversion processes. Thus, metagenomic approaches are a powerful tool to reveal novel optimized metabolic pathways for lignin conversion and valorization. RESULTS: The lignin-degrading consortium (LigMet) was obtained from a sugarcane plantation soil sample. The LigMet taxonomical analyses (based on 16S rRNA) indicated prevalence of Proteobacteria, Actinobacteria and Firmicutes members, including the Alcaligenaceae and Micrococcaceae families, which were enriched in the LigMet compared to sugarcane soil. Analysis of global DNA sequencing revealed around 240,000 gene models, and 65 draft bacterial genomes were predicted. Along with depicting several peroxidases, dye-decolorizing peroxidases, laccases, carbohydrate esterases, and lignocellulosic auxiliary (redox) activities, the major pathways related to aromatic degradation were identified, including benzoate (or methylbenzoate) degradation to catechol (or methylcatechol), catechol ortho-cleavage, catechol meta-cleavage, and phthalate degradation. A novel Paenarthrobacter strain harboring eight gene clusters related to aromatic degradation was isolated from LigMet and was able to grow on lignin as major carbon source. Furthermore, a recombinant pathway for vanillin production was designed based on novel gene sequences coding for a feruloyl-CoA synthetase and an enoyl-CoA hydratase/aldolase retrieved from the metagenomic data set. CONCLUSION: The enrichment protocol described in the present study was successful for a microbial consortium establishment towards the lignin and aromatic metabolism, providing pathways and enzyme sets for synthetic biology engineering approaches. This work represents a pioneering study on lignin conversion and valorization strategies based on metagenomics, revealing several novel lignin conversion enzymes, aromatic-degrading bacterial genomes, and a novel bacterial strain of potential biotechnological interest. The validation of a biosynthetic route for vanillin synthesis confirmed the applicability of the targeted metagenome discovery approach for lignin valorization strategies

Otocinclus batmani, a new species of hypoptopomatine catfish (Siluriformes: Loricariidae) from Colombia and Peru

A new species of the hypoptopomatine catfish genus Otocinclus is described from two localities in the upper Río Amazonas basin: a tributary of the Río Puré in Colombia and two tributaries to the Río Amazonas near Iquitos in Peru. The new taxon can be easily distinguished from all congeners, except Otocinclus cocama, by having a single, intensely pigmented, vertical W-shaped caudal fin spot and by having three discrete dark bands on dorsum, between the dorsal-fin base and the caudal fin. Otocinclus batmani differs from O. cocama by the absence of vertically elongated blotches from the dorsal midline to the ventral border of flanks, and by lacking a posterior extension of black pigmentation on the base of two central caudal-fin rays. Phylogenetic relationships of the new species are investigated and it is possibly more closely related to a clade formed by O. huaorani, O. mariae, O. bororo, O. mura, and O. cocama

Effect of hemicellulolytic enzymes to improve sugarcane bagasse saccharification and xylooligosaccharides production

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Enzymatic hydrolysis of lignocellulosic biomass is limited by economic considerations arising from enzyme production costs and specific activities. The effect of six hemicellulases on raw sugarcane bagasse and two types of pretreated sugarcane bagasse was investigated using experimental designs. Our strategy was successful for developing more efficient and less expensive enzymatic mixture, and also revealed that hemicellulase mixtures with multiple activities could be less effective than expected. In this study, only two hemicelulases, the endo-1,4-xylanases (GH11) from Penicillium funiculosum (XynC11/CAC15487) and the feruloyl esterase (CE1) from Clostridium thermocellum (CtFAEIATCC27405), effectively broke down hemicellulose from pretreated sugarcane bagasse (up to 65%), along with the production of xylooligosaccharides (XOS). Our results also demonstrated that GH11 and CE1 can improve biomass saccharification by cellulases. Treatment with these two enzymes followed by a commercial cellulase cocktail (Accellerase (R) 1500) increased saccharifi cation of pretreated lignocellulose by 24%. Collectively, our data contributes to the rational design of more efficient and less expensive enzyme mixtures, targeting the viable production of bioethanol and other biorefinery products. (C) 2016 Elsevier B.V. All rights reserved.Enzymatic hydrolysis of lignocellulosic biomass is limited by economic considerations arising from enzyme production costs and specific activities. The effect of six hemicellulases on raw sugarcane bagasse and two types of pretreated sugarcane bagasse was1313646FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNQP - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)2012/18859-52012/20549-4SEM INFORMAÇÃOWe are grateful to FAPESP (The State of São Paulo Research Foundation) for the pos-doctoral scholarship and financial support (2012/18859-5 to RG2012/20549-4 to ARLD, respectively).This work was also financially supported by the CNPq (National Counci

Structure and Function of a Novel Cellulase 5 from Sugarcane Soil Metagenome

<div><p>Cellulases play a key role in enzymatic routes for degradation of plant cell-wall polysaccharides into simple and economically-relevant sugars. However, their low performance on complex substrates and reduced stability under industrial conditions remain the main obstacle for the large-scale production of cellulose-derived products and biofuels. Thus, in this study a novel cellulase with unusual catalytic properties from sugarcane soil metagenome (CelE1) was isolated and characterized. The polypeptide deduced from the <i>celE1</i> gene encodes a unique glycoside hydrolase domain belonging to GH5 family. The recombinant enzyme was active on both carboxymethyl cellulose and β-glucan with an endo-acting mode according to capillary electrophoretic analysis of cleavage products. CelE1 showed optimum hydrolytic activity at pH 7.0 and 50 °C with remarkable activity at alkaline conditions that is attractive for industrial applications in which conventional acidic cellulases are not suitable. Moreover, its three-dimensional structure was determined at 1.8 Å resolution that allowed the identification of an insertion of eight residues in the β8-α8 loop of the catalytic domain of CelE1, which is not conserved in its psychrophilic orthologs. This 8-residue-long segment is a prominent and distinguishing feature of thermotolerant cellulases 5 suggesting that it might be involved with thermal stability. Based on its unconventional characteristics, CelE1 could be potentially employed in biotechnological processes that require thermotolerant and alkaline cellulases.</p> </div

Development and Biotechnological Application of a Novel Endoxylanase Family GH10 Identified from Sugarcane Soil Metagenome

Metagenomics has been widely employed for discovery of new enzymes and pathways to conversion of lignocellulosic biomass to fuels and chemicals. In this context, the present study reports the isolation, recombinant expression, biochemical and structural characterization of a novel endoxylanase family GH10 (SCXyl) identified from sugarcane soil metagenome. The recombinant SCXyl was highly active against xylan from beechwood and showed optimal enzyme activity at pH 6,0 and 45°C. The crystal structure was solved at 2.75 Å resolution, revealing the classical (β/α)8-barrel fold with a conserved active-site pocket and an inherent flexibility of the Trp281-Arg291 loop that can adopt distinct conformational states depending on substrate binding. The capillary electrophoresis analysis of degradation products evidenced that the enzyme displays unusual capacity to degrade small xylooligosaccharides, such as xylotriose, which is consistent to the hydrophobic contacts at the +1 subsite and low-binding energies of subsites that are distant from the site of hydrolysis. The main reaction products from xylan polymers and phosphoric acid-pretreated sugarcane bagasse (PASB) were xylooligosaccharides, but, after a longer incubation time, xylobiose and xylose were also formed. Moreover, the use of SCXyl as pre-treatment step of PASB, prior to the addition of commercial cellulolytic cocktail, significantly enhanced the saccharification process. All these characteristics demonstrate the advantageous application of this enzyme in several biotechnological processes in food and feed industry and also in the enzymatic pretreatment of biomass for feedstock and ethanol production. © 2013 Alvarez et al

Comparative structural analysis of CelE1 (4M1R) with other structurally similar cellulases 5.

<p>(A) Representation of the extended α₈/β₈ loop conserved in thermostable enzymes (BsCel5A, <i>Bacillus subtilis</i>, 3PZU; BaCel5A, <i>Bacillus agaradhaerens</i>, 1QHZ) in comparison to meso- and psychrophilic cellulases (EcCel5, <i>Erwinia chrysanthemi</i>, 1EGZ; Cel5G, <i>Pseudoalteromonas haloplanktis</i>, 1TVN). The helix α1 that makes new interactions with the extended α₈/β₈ loop is colored in light pink. (B) Surface complementarity between the extended α₈/β₈ loop (yellow mesh) and the neighboring structural elements (green) indicating the additional intramolecular contacts favored by this motif. </p