Genomic and enzymatic results show Bacillus cellulosilyticus uses a novel set of LPXTA carbohydrases to hydrolyze polysaccharides

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.

Solid-State Fermentation of Cassava Roots Using Cellulolytic-Type Alkaliphilic Bacillus spp. Cultures to Modify the Cell Walls and Assist Starch Release

To improve cassava starch extraction by wet milling, solid-state fermentation of ground roots using cellulolytic-type alkaliphilic Bacilli spp., Bacillus akibai, B. cellulosilyticus and B. hemicellulosilyticus was investigated. Enzyme assay and scanning electron microscopy indicated that Bacillus spp. production of extracellular cellulase and polygalacturonase caused the formation of micropores through the root parenchyma cell walls and exposed the embedded cellulosic network. Gas chromatography data of the cell wall constituent sugars remaining after fermentation and Fourier transform infrared data indicated that the Bacillus treatments reduced the levels of pectin and, hemicellulose and to lesser extent cellulose. Wide-angle X-ray scattering data indicated that the Bacillus spp. cell wall degrading enzymes had partially hydrolysed the amorphous fractions of the cell wall polysaccharides. All the Bacillus spp. treatments improved starch extraction by 17-23% compared to fermentation with endogenous microflora. B. cellulosilyticus was most effective in disintegration of large root particles and as result, released marginally the most starch, probably due to it having the highest cellulase activity. Solid-state fermentation using cellulolytic-type Bacillus spp. is, therefore, promising to technology to improve the efficiency of cassava wet milling cell wall disintegration and consequent starch yield without use of commercial cell wall degrading enzymes or polluting chemicals.

Climate and Soil Properties Influence Species Diversity of Soil Bacillus Community in India

Bacillus is an important genus as it is a source for antibiotics, enzymes, and probiotics. Therefore, several studies are targeted on this genus in order to understand its diversity abundance in different soil environments. In present study, we investigated the diversity of Bacillus at species level using culturable approach in soils collected at different climatic zones of India and identified 20 prominent members of genus Bacillus species that are able to grow in different media types under same culture conditions. Results also showed that the species diversity of Bacillus changes according to the soil microenvironment under the influence of different climatic conditions. As a pilot study using culturable approach, we made an attempt to investigate the shift in Bacillus species diversity present in the Indian soils experiencing a climatic gradient over a large geographic area.

Regulation of acidogenic metabolism towards enhanced short chain fatty acid biosynthesis from waste: metagenomic profiling

To enhance short chain carboxylic (volatile fatty) acids production from food waste, the present study evaluates a strategy for selective enrichment of the biocatalyst by exposing it to acid-shock.

Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies

In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.

Sortagging: a robust and efficient chemoenzymatic ligation strategy

Bioorthogonal, chemoselective ligation methods are an essential part of the tools utilized to investigate biochemical pathways. Specifically enzymatic approaches are valuable methods in this context due to the inherent specificity of the deployed enzymes and the mild conditions of the modification reactions. One of the most common strategies is based on the transpeptidation catalyzed by sortase A derived from Staphylococcus aureus. The procedure is well established and a wide variety of applications have been published to date. Here, implementations of sortase A, which range from protein labeling using fluorescence dyes and the preparation of cyclic proteins to the modification of entire cells, are summarized. Furthermore, there is a focus on the optimization approaches established to solve the drawbacks of sortase-mediated transpeptidation.