Broad thermal spectrum metagenomic laccase with action for dye decolorization and fentin hydroxide treatment.

Laccases are multicopper oxidases that act on various phenolic and non-phenolic compounds, enabling numerous applications including xenobiotic bioremediation, biofuel production, drug development, and cosmetic production, and they can be used as additives in the textile and food industries. This wide range of uses makes these enzymes extremely attractive for novel biotechnology applications. Here, we undertook the kinetic characterization of LacMeta, a predicted as homotrimeric (~ 107,93 kDa) small laccase, and demonstrated that this enzyme performs best at an acidic pH (pH 3-5) towards ABTS as substrate and has a broad thermal spectrum (10-60 °C), which can promote high plastic action potential through dynamic environmental temperature fluctuations. This enzyme showed following kinetic parameters: kcat = 6.377 s-1 ± 0.303, Km = 4.219 mM, and Vmax = 24.43 µM/min (against ABTS as substrate). LacMeta almost completely degraded malachite green (50 mg/mL) in only 2 h. Moreover, the enzyme was able to degrade seven dyes from four distinct classes and it respectively achieved 85% and 83% decolorization of methylene blue and trypan blue with ABTS as the mediator. In addition, LacMeta showed potential for the degradation of two thirds of an agricultural fungicide: fentin hydroxide, thus demonstrating its biotechnological aptitude for bioremediation. The results of this study suggest that LacMeta has potential in textile wastewater treatment and that it could help in the bioremediation of other human/environmental toxins such as pesticides and antibiotic compounds belonging to the same chemical classes as the degraded dyes.

Bioremediation of heavy metal-polluted environments by non-living cells from rhizobial isolates.

Rhizosphere bacteria, for example, rhizobia, can play several roles, and one of the most important, the protection of plant roots against toxic conditions and other environmental stresses. In this work, the action of Cu2+ and Cr6+ on cell growth and EPS production of four strains of rhizobia, Rhizobium tropici (LBMP-C01), Ensifer sp. (LBMP-C02 and LBMP-C03), and Rhizobium sp. LBMP-C04, were tested. The results confirmed the strong effect of Cu2+ and Cr6+ on bacterial exopolysaccharides (EPS) synthesis, and how cells can adsorb these metals, which may be a key factor in the interactions between rhizosphere bacteria and host plants in heavy metal-contaminated soils. Here, we emphasize the importance of proving the potential of treating bacterial cells and their extracellular EPS to promote the bio-detoxification of terrestrial and aquatic systems contaminated by heavy metals in a highly sustainable, economic, and ecological way.

Metagenome-assembled genome of a Chitinophaga sp. and its potential in plant biomass degradation, as well of affiliated Pandoraea and Labrys species.

The prospection of new degrading enzymes of the plant cell wall has been the subject of many studies and is fundamental for industries, due to the great biotechnological importance of achieving a more efficient depolymerization conversion from plant polysaccharides to fermentable sugars, which are useful not only for biofuel production but also for various bioproducts. Thus, we explored the shotgun metagenome data of a bacterial community (CB10) isolated from sugarcane bagasse and recovered three metagenome-assembled genomes (MAGs). The genomic distance analyses, along with phylogenetic analysis, revealed the presence of a putative novel Chitinophaga species, a Pandoraea nosoerga, and Labrys sp. isolate. The isolation process for each one of these bacterial lineages from the community was carried out in order to relate them with the MAGs. The recovered draft genomes have reasonable completeness (72.67-100%) and contamination (0.26-2.66%) considering the respective marker lineage for Chitinophaga (Bacteroidetes), Pandoraea (Burkholderiales), and Labrys (Rhizobiales). The in-vitro assay detected cellulolytic activity (endoglucanases) only for the isolate Chitinophaga, and its genome analysis revealed 319 CAZymes, of which 115 are classified as plant cell wall degrading enzymes, which can act in fractions of hemicellulose and pectin. Our study highlights the potential of this Chitinophaga isolate provides several plant-polysaccharide-degrading enzymes.

Exploring the Potential of Two Bacterial Consortia to Degrade Cellulosic Biomass for Biotechnological Applications.

This paper outlines two cellulolytic bacterial consortia named SCS and SCB, isolated from soil samples of sugarcane (Saccharum officinarum) crop field, and a sugarcane bagasse deposit in an ethanol mill. Both consortia were able to grow on different carbon sources, such as sugarcane bagasse, corn husk, peanut hulls, and carboxymethylcellulose, releasing up to 11.90 µmol/mL and 15.23 µmol/mL of glucose for SCS and SCB, respectively. In addition, SCS and SCB have several strains capable of producing cellulase, amylase, lipase, and protease. Whole genome sequencing of the SCS consortium revealed that Burkholderia was the most prevalent genus, encompassing approximately 80% of the consortia. In addition, metagenome analysis allowed the identification of genes encoding enzymes related to starch and cellulose degradation, as well as enzymes related to lipases and proteases, confirming our initial findings. The results showed that SCS and SCB had the capability to degrade cellulose, and that they were an efficient source of enzyme production, which would provide a new choice for use in different biotechnological applications.

Rhizobium spp exopolysaccharides production and xanthan lyase use on its structural modification.

Enzymes can be very useful on exopolysaccharides (EPS) research, can be used at elucidation and also to modify the polysaccharides' structure in order to alter their physical properties. Thus, the reduction of the molecular mass could increase applications of these biopolymers. Therefore, the EPS production of different rhizobia and the action of xanthan lyase on its structures were evaluated. The strains produced significant amounts of EPS, and it was noticed that are heteropolysaccharides, composed galactose and glucose. Both EPS and xanthan were modified on ß-glycosidic bonds, the mannose was removed of xanthan had but the EPS was affected in the CO stretching vibration, where the glucuronic acid removed from of your structure. The ester/carboxylic acid portions affected functional groups of the acetate/succinate, methyl carbons of the O-acetyl and pyruvate methyl groups in addition to affect the carbons the main pyranoid. The Resistance to temperature increase of the EPS was observed, made possible by the activity of the lyase. EPS has the ability to form stable gels at higher temperatures and anionic feature can be used on solubilization and controlled release of substances. Modified EPS knowledge will presently facilitate future investigations relating the structure of the rhizobia polysaccharide against rheological properties.

Characterization of new exopolysaccharide production by Rhizobium tropici during growth on hydrocarbon substrate.

Exopolysaccharide (EPS) are produced by a diverse of rhizobia species and has been demonstrated to be a bioemulsifier with potential applications in the degradation of hydrocarbons. In the present study, attempts were made to obtain the new exopolysaccharide production by Rhizobium tropici (SEMIA 4080 and MUTZC3) strains during growth on hydrocarbon substrate. Under the different cultivation conditions, the high molecular weight exopolysaccharides from Rhizobium tropici strains cultivated for 96h mainly consisted of carbohydrates (79-85%) and a low percentage of protein. The EPSC3-D differed from the others, with only 60% of carbohydrate. However, all strains produced polymers with distinct rheology properties, such as viscosity of each EPS sample, suitable for different applications. In addition, RP-HPLC, FTIR and NMR studies revealed EPS produced by rhizobia strains were similar indicating minimal difference between EPS compositions.

Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools.

BACKGROUND: Evidence based on genomic sequences is extremely important to confirm the phylogenetic relationships within the Rhizobium group. SEMIA3007 was analyzed within the Mesorhizobium groups to define the underlying causes of taxonomic identification. We previously used biochemical tests and phenotypic taxonomic methods to identify bacteria, which can lead to erroneous classification. An improved understanding of bacterial strains such as the Mesorhizobium genus would increase our knowledge of classification and evolution of these species. RESULTS: In this study, we sequenced the complete genome of SEMIA3007 and compared it with five other Mesorhizobium and two Rhizobium genomes. The genomes of isolated SEMIA3007 showed several orthologs with M. huakuii, M. erdmanii and M. loti. We identified SEMIA3007 as a Mesorhizobium by comparing the 16S rRNA gene and the complete genome. CONCLUSION: Our ortholog, 16S rRNA gene and average nucleotide identity values (ANI) analysis all demonstrate SEMIA3007 is not Rhizobium leguminosarum bv. viceae. The results of the phylogenetic analysis clearly show SEMIA3007 is part of the Mesorhizobium group and suggest a reclassification is warranted.

Optimized medium culture for Acidobacteria subdivision 1 strains.

Members of subdivision 1 of the phylum Acidobacteria were grown at different pH values in a new medium formulation named PSYL 5, which includes sucrose as a carbon source and other compounds (such as KH2PO4 and MgSO4.7H2O). Growth rate was nearly constant at pH 5.0 and declined at pH 3-4 and 6-7. However, it was found that effects involving good carbon/nitrogen ratios and pH on the growth of the members of Acidobacteria subdivision 1 were significant, and the strongest effect of these conditions was at pH 5.0. In addition, incubation time of 48, 72, 96 and 120 h was shorter than that described previously for members of Acidobacteria subdivision 1 on solid laboratory media.

Production of exopolysaccharide from rhizobia with potential biotechnological and bioremediation applications.

The potential use of rhizobia under controlled fermentation conditions may result in the production of new extracellular polymeric substances (EPS) having novel and superior properties that will open up new areas of industrial applications and thus increase their demand. The production of EPS and the stability of emulsions formed with soybean oil, diesel oil and toluene using different concentrations of purified EPS derived from wild-type and mutant strains of Rhizobium tropici SEMIA 4077 was investigated. The EPS was defined as a heteropolysaccharide composed of six constituent monosaccharides that displayed higher intrinsic viscosity and pseudoplastic non-Newtonian fluid behavior in an aqueous solution. The ratio between the total EPS production and the cellular biomass was 76.70 for the 4077::Z04 mutant strain and only 8.10 for the wild-type strain. The EPS produced by the wild-type R. tropici SEMIA 4077 resulted in more stable emulsions with the tested toluene than xanthan gum, and the emulsification indexes with hydrocarbons and soybean oil were higher than 50%, indicating strong emulsion-stabilizing capacity. These results demonstrate that the EPS of R. tropici strains could be attractive for use in industrial and environmental applications, as it had higher intrinsic viscosity and good emulsification activity.

Genomics-based design of defined growth media for the plant pathogen Xylella fastidiosa.

Based on the genetic analysis of the phytopathogen Xylella fastidiosa genome, five media with defined composition were developed and the growth abilities of this fastidious prokaryote were evaluated in liquid media and on solid plates. All media had a common salt composition and included the same amounts of glucose and vitamins but differed in their amino acid content. XDM(1) medium contained amino acids threonine, serine, glycine, alanine, aspartic acid and glutamic acid, for which complete degradation pathways occur in X. fastidiosa; XDM(2) included serine and methionine, amino acids for which biosynthetic enzymes are absent, plus asparagine and glutamine, which are abundant in the xylem sap; XDM(3) had the same composition as XDM(2) but with asparagine replaced by aspartic acid due to the presence of complete degradation pathway for aspartic acid; XDM(4) was a minimal medium with glutamine as a sole nitrogen source; XDM(5) had the same composition as XDM(4), plus methionine. The liquid and solidified XDM(2) and XDM(3) media were the most effective for the growth of X. fastidiosa. This work opens the opportunity for the in silico design of bacterial defined media once their genome is sequenced.

Growth optimization procedures for the phytopathogen Xylella fastidiosa.

For the first time, growth curves are shown for the phytopathogen Xylella fastidiosa on traditional growth media such as PW (periwinkle wilt), BCYE (buffered charcoal yeast extract), and on new ones such as GYE (glutamate yeast extract) and PYE (phosphate yeast extract) that were developed in this work. The optimal growth conditions on solid and liquid media as well as their measurements are presented, by using total protein content and turbidity determinations. The results demonstrated that yeast extract provided sufficient nutrients for X. fastidiosa, since the cells grew well on PYE medium.