Functional genomics assessment of lytic polysaccharide mono-oxygenase with glycoside hydrolases in Paenibacillus dendritiformis CRN18

Tailored microbial consortium producing hydrolytic enzyme cocktail for maximum saccharification of wheat straw

The potential of hydrolytic enzyme cocktail obtained from designed bacterial consortium WSh-1 comprising Bacillus subtilis CRN 16, Paenibacillus dendritiformis CRN 18, Niallia circulans CRN 24, Serratia marscens CRN 29, and Streptomyces sp. CRN 30, was investigated for maximum saccharification. Activity was further enhanced to 1.01 U/ml from 0.82 U/ml by supplementing growth medium with biotin and cellobiose as a cofactor and inducer. Through kinetic analysis, the enzyme cocktail showed a high wheat straw affinity with Michaelis-Menten constant (Km) of 0.68 µmol/L and a deconstruction rate (Vmax) of 4.5 U/ml/min. The statistical optimization of critical parameters increased saccharification to 89 %. The optimized process in a 5-L lab-scale bioreactor yielded 501 mg/g of reducing sugar from NaOH-pretreated wheat straw. Lastly, genomic insights revealed unique abundant oligosaccharide deconstruction enzymes with the most diverse CAZyme profile. The consortium-mediated enzyme cocktails offer broader versatility with efficiency for the economical and sustainable valorization of lignocellulosic waste.

Genomic dissection of Niallia sp. for potential application in lignocellulose hydrolysis and bioremediation

Genus Niallia has recently been separated taxonomic group from the Bacillus based on conserved signature indels in the genome. Unlike bioremediation, its role in plant biomass hydrolysis has not garnered considerable attention. The present study investigates the genomic potential of a novel Niallia sp. CRN 25 for applications in lignocellulose hydrolysis, significant enzyme production, and bioremediation. The CRN 25 strain exhibits xylosidase, cellobiosidase, α-arabinosidase, and α-D-galactosidase activity as 0.03 U/ml whereas β-D-glucosidase and glucuronidase as 0.06 U/ml and 0.01 U/ml, respectively. Further genome sequencing reveals nine copies of GH43 gene coding for hemicellulose-specific xylanase enzyme attached to the CBM 6 domain for increased processivity. The presence of β-glucosidase and β-galactosidase indicates the possible application of CRN 25 in facilitating the valorization of plant biomass into value-added products. Apart from this, genes of FMN-dependent NADH-azoreductase, cytochrome P450, and nitrate reductase, playing a crucial role in bioremediation processes, were annotated. Biosynthetic gene clusters (BGCs), responsible for synthesizing specialized metabolites of terpenes and lasso peptides, were also found in the genome. Conclusively genomic sketch of Niallia sp. CRN 25 reveals versatile metabolic potential for diverse environmental applications.

Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides

The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.

Potential of camel rumen derived Bacillus subtilis and Bacillus velezensis strains for application in plant biomass hydrolysis

Rumen inhabiting Bacillus species possesses a high genetic potential for plant biomass hydrolysis and conversion to value-added products. In view of the same, five camel rumen-derived Bacillus strains, namely B. subtilis CRN 1, B. velezensis CRN 2, B. subtilis CRN 7, B. subtilis CRN 11, and B. velezensis CRN 23 were initially assayed for diverse hydrolytic activities, followed by genome mining to unravel the potential applications. CRN 1 and CRN 7 showed the highest endoglucanase activity with 0.4 U/ml, while CRN 23 showed high β-xylosidase activity of 0.36 U/ml. The comprehensive genomic insights of strains resolve taxonomic identity, clusters of an orthologous gene, pan-genome dynamics, and metabolic features. Annotation of Carbohydrate active enzymes (CAZymes) reveals the presence of diverse glycoside hydrolases (GH) GH1, GH5, GH43, and GH30, which are solely responsible for the effective breakdown of complex bonds in plant polysaccharides. Further, protein modeling and ligand docking of annotated endoglucanases showed an affinity for cellotrioside, cellobioside, and β-glucoside. The finding indicates the flexibility of Bacillus-derived endoglucanase activity on diverse cellulosic substrates. The presence of the butyrate synthesis gene in the CRN 1 strain depicts its key role in the production of important short-chain fatty acids essential for healthy rumen development. Similarly, antimicrobial peptides such as bacilysin and non-ribosomal peptides (NRPS) synthesized by the Bacillus strains were also annotated in the genome. The findings clearly define the role of Bacillus sp. inside the camel rumen and its potential application in various plant biomass utilizing industry and animal health research sectors.

Early Weaning and Milk Substitutes Affect the Gut Microbiome, Metabolomics, and Antibody Profile in Goat Kids Suffering From Diarrhea

Early weaning and milk substitutes increase the incidence of diarrhea in young ruminants, which may modify their gut microbiota, metabolism, immunity, and health. The aim of the study was to determine if early weaning and milk substitutes affect the gut microbiota, metabolism, and immunological status of goat kids suffering from diarrhea. The 16S rRNA gene and metagenomic sequencing in feces and serum metabolomics of early-weaned and artificially reared goat kids suffering from diarrhea (DK group) and healthy goat kids reared by their mothers (HK group) were analyzed. The serum biochemistry and immunoglobulin concentration were also determined. Several probiotics, such as Streptococcus and Lactobacillus, were higher in the feces of the DK group than in feces of the HK group. Ruminococcus sp. was elevated in the feces of HKs, likely being a biomarker for goat health. Taking all the carbohydrate-active enzyme (CAZyme) families into consideration, 20 CAZyme families were different between the groups. Compared with the DK group, the relative quantity of glycoside hydrolases (GH) and glycosyltransferase (GT) families in the HK group decreased. GT70 was only identified in HK kids participating in the activity of β-glucuronosyltransferase during the carbohydrate metabolism. Overall, 24 metabolites were different between the groups, which were mainly involved in protein digestion and absorption, cyanoamino acid metabolism, and cholesterol metabolism. The concentrations of immunoglobulins G and M were significantly lower in the DK than in the HK group. In conclusion, our study characterized the fecal microbiota, metabolism, and immunological status of early-weaned and artificially reared goat kids suffering from diarrhea.

Unique pool of carbohydrate-degrading enzymes in novel bacteria assembled from cow and buffalo rumen metagenomes

Reconstruction of genomes from environmental metagenomes offers an excellent prospect for studying the metabolic potential of organisms resilient to isolation in laboratory conditions. Here, we assembled 12 high-quality metagenome-assembled genomes (MAGs) with an estimated completion of ≥ 90% from cow and buffalo rumen metagenomes. Average nucleotide identity (ANI) score-based screening with an existing database suggests the novelty of these genomes. Gene prediction led to the identification of 30,359 protein-encoding genes (PEGs) across 12 genomes, of which only 44.8% were annotated against a specific functional attribute. Further analysis revealed the presence of 985 carbohydrate-active enzymes (CAZymes) from more than 50 glycoside hydrolase families, of which 90% do not have a proper match in the CAZy database. Genome mining revealed the presence of a high frequency of plant biomass deconstructing genes in Bacteroidetes MAGs compared to Firmicutes. The results strongly indicate that the rumen chamber harbors high numbers of deeply branched and as-yet uncultured microbes that encode novel CAZymes, candidates for prospective usage in plant biomass-hydrolyzing and biofuels industries. KEY POINTS: • Genome binning plays a crucial role in revealing the metabolic potential of uncultivable microbes. • Assembled 12 novel genomes from cow and buffalo rumen metagenome datasets. • High frequency of plant biomass deconstructing genes identified in Bacteroidetes MAGs.

Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem

Theionarchaea is a recently described archaeal class within the Euryarchaeota. While it is widely distributed in sediment ecosystems, little is known about its metabolic potential and ecological features. Here, we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes, which were further divided into two subgroups, from coastal mangrove sediments of China and seawater columns of the Yap Trench. Genomic analysis revealed that apart from the canonical sulfhydrogenase, Theionarchaea harbor genes encoding heliorhodopsin, group 4 [NiFe]-hydrogenase, and flagellin, in which genes for heliorhodopsin and group 4 [NiFe]-hydrogenase were transcribed in mangrove sediment. Further, the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics, and the potential carbon substrates include detrital proteins, hemicellulose, ethanol, and CO2. The genes for organic substrate metabolism (mainly detrital protein and amino acid metabolism genes) have relatively higher transcripts in the top sediment layers in mangrove wetlands. In addition, co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters (e.g., Chloroflexi) and methanogens. Collectively, these observations expand the current knowledge of the metabolic potential of Theionarchaea, and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.

Revealing the potential of Klebsiella pneumoniae PVN-1 for plant beneficial attributes by genome sequencing and analysis

Genome sequencing of Klebsiella pneumoniae PVN-1, isolated from effluent treatment plant (ETP), generates a 5.064 Mb draft genome with 57.6% GC content. The draft genome assembled into 19 contigs comprises 4783 proteins, 3 rRNA, 44 tRNA, 8 other RNA, 4911 genes, and 73 pseudogenes. Genome information revealed the presence of phosphate metabolism/solubilizing, potassium solubilizing, auxin production, and other plant benefiting attributes like enterobactin and pyrroloquinoline quinone biosynthesis genes. Presence of gcd and pqq genes in K. pneumoniae PVN-1 genome validates the inorganic phosphate solubilizing potential (528.5 mg/L). Pangenome analysis identified a unique 5'-Nucleotidase that further assists in enhanced phosphate acquisition. Additionally, the genetic potential for complete benzoate, catechol, and phenylacetate degradation with stress response and heavy metal (Cu, Zn, Ni, Co) resistance was identified in K. pneumoniae PVN-1. Functioning of annotated plant benefiting genes validates by the metabolic activity of auxin production (7.40 µg/mL), nitrogen fixation, catalase activity, potassium solubilization (solubilization index-3.47), and protease activity (proteolytic index-2.27). In conclusion, the K. pneumoniae PVN-1 genome has numerous beneficial qualities that can be employed to enhance plant growth as well as for phytoremediation.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03020-2.

Genomic insight for algicidal activity in Rhizobium strain AQ_MP

Occurrence of Harmful Algal Blooms (HABs) creates a threat to aquatic ecosystem affecting the existing flora and fauna. Hence, the mitigation of HABs through an eco-friendly approach remains a challenge for environmentalists. The present study provides the genomic insights of Rhizobium strain AQ_MP, an environmental isolate that showed the capability of degrading Microcystis aeruginosa (Cyanobacteria) through lytic mechanisms. Genome sequence analysis of Rhizobium strain AQ_MP unraveled the algal lytic features and toxin degradative pathways in it. Functional genes of CAZymes such as glycosyltransferases (GT), glycoside hydrolases (GH), polysaccharide lyases (PL) which supports algal polysaccharide degradation (lysis) were present in Rhizobium strain AQ_MP. Genome analysis also clarified the presence of the glutathione metabolic pathway, which is the biological detoxification pathway responsible for toxin degradation. The conserved region mlrC, a microcystin toxin-degrading gene was also annotated in the genome. The study illustrated that Rhizobium strain AQ_MP harbored a wide range of mechanisms for the lysis of Microcystis aeruginosa cells and its toxin degradation. In future, this study finds promiscuity for employing Rhizobium strain AQ_MP species for bioremediation, based on its physiological and genomic analysis.

Hybrid Genome Assembly for Predicting Functional Potential of a Novel Streptomyces Strain as Plant Biomass Valorisation Agent

Environmental bioremediation relies heavily on the realized potential of efficient bioremediation agents or microbial strains of interest. Identifying suitable microbial agents for plant biomass waste valorization requires (i) high-quality genome assemblies to predict the full metabolic and functional potential, (ii) accurate mapping of lignocellulose metabolizing enzymes. However, fragmented nature of the sequenced genomes often limits the prediction ability due to breaks occurring in coding sequences. To address these challenges and as part of our ongoing agri-culturomics efforts, we have performed a hybrid genome assembly using Illumina and Nanopore reads with modified assembly protocol, for a novel Streptomyces strain isolated from the rhizosphere niche of green leafy vegetables grown in a commercial urban farm. High-quality genome was assembled with the size of 8.6 Mb in just two contigs with N50 of 8,542,030 and coverage of 383X. This facilitated identification and complete arrangement of approximately 248 CAZymes and 38 biosynthetic gene clusters in the genome. Multiple gene clusters consisting of cellulases and hemicellulases associated with substrate recognition domain were identified in the genome. Genes for lignin, chitin, and even some aromatic compounds degradation were found in the Streptomyces sp. genome which makes it a promising candidate for lignocellulosic waste valorization.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-021-00935-5.