Identification and functional characterization of an α-amylase with broad temperature and pH stability from Paenibacillus sp

Detergent-stable amylase production by Paenibacillus lactis strain OPSA3 isolated from soil; optimization by response surface methodology

This study aimed to isolate thermostable, alkaliphilic, and detergent-tolerant amylase-producing bacteria. Pure isolates from environmental samples were screened on a starch-based medium (pH 11), and selected isolates were identified using cultural and molecular techniques. Product optimization studies were conducted, and secreted amylase was partially purified using 40% (w/v) saturation ammonium sulfate at 4 °C. The wash performance of concentrated amylase was analyzed. A novel isolate, Paenibacillus lactis OPSA3, was selected for further studies. The isolate produced amylase optimally when grown on banana peels and soybean extracts, which are agro-wastes. Optimization by Response surface Methodology resulted in a 2.1-fold increase in alkaliphilic amylase production. A 2.46-fold purification was achieved, with an enzyme activity yield of 79.53% and specific activity of 26.19 Umg^-1. Wash performance analysis using the amylase supplemented with boiled commercial detergent (kiln®) showed good cleaning efficiency. The amylase has the potential for application as a component of green detergent.

Characterization and in-depth genome analysis of a halotolerant probiotic bacterium Paenibacillus sp. S-12, a multifarious bacterium isolated from Rauvolfia serpentina

BACKGROUND

Members of Paenibacillus genus from diverse habitats have attracted great attention due to their multifarious properties. Considering that members of this genus are mostly free-living in soil, we characterized the genome of a halotolerant environmental isolate belonging to the genus Paenibacillus. The genome mining unravelled the presence of CAZymes, probiotic, and stress-protected genes that suggested strain S-12 for industrial and agricultural purposes.

RESULTS

Molecular identification by 16 S rRNA gene sequencing showed its closest match to other Paenibacillus species. The complete genome size of S-12 was 5.69 Mb, with a GC-content 46.5%. The genome analysis of S-12 unravelled the presence of an open reading frame (ORF) encoding the functions related to environmental stress tolerance, adhesion processes, multidrug efflux systems, and heavy metal resistance. Genome annotation identified the various genes for chemotaxis, flagellar motility, and biofilm production, illustrating its strong colonization ability.

CONCLUSION

The current findings provides the in-depth investigation of a probiotic Paenibacillus bacterium that possessed various genome features that enable the bacterium to survive under diverse conditions. The strain shows the strong ability for probiotic application purposes.

Isolation of Saccharibacillus WB17 strain from wheat bran phyllosphere and genomic insight into the cellulolytic and hemicellulolytic complex of the Saccharibacillus genus

The microorganisms living on the phyllosphere (the aerial part of the plants) are in contact with the lignocellulosic plant cell wall and might have a lignocellulolytic potential. We isolated a Saccharibacillus strain (Saccharibacillus WB17) from wheat bran phyllosphere and its cellulolytic and hemicellulolytic potential was investigated during growth onto wheat bran. Five other type strains from that genus selected from databases were also cultivated onto wheat bran and glucose. Studying the chemical composition of wheat bran residues by FTIR after growth of the six strains showed an important attack of the stretching C-O vibrations assigned to polysaccharides for all the strains, whereas the C = O bond/esterified carboxyl groups were not impacted. The genomic content of the strains showed that they harbored several CAZymes (comprised between 196 and 276) and possessed four of the fifth modules reflecting the presence of a high diversity of enzymes families. Xylanase and amylase activities were the most active enzymes with values reaching more than 4746 ± 1400 mIU/mg protein for the xylanase activity in case of Saccharibacillus deserti KCTC 33693 T and 452 ± 110 mIU/mg protein for the amylase activity of Saccharibacillus WB17. The total enzymatic activities obtained was not correlated to the total abundance of CAZyme along that genus. The Saccharibacillus strains harbor also some promising proteins in the GH30 and GH109 modules with potential arabinofuranosidase and oxidoreductase activities. Overall, the genus Saccharibacillus and more specifically the Saccharibacillus WB17 strain represent biological tools of interest for further biotechnological applications.

Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups

The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and D-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus. KEY POINTS: • Paenibacillus clustered into 10 subgroups. • Genomic content variation and metabolic diversity in the subgroup A, E, and G were described. • Carbohydrate transport and metabolism is important for Paenibacillus survival.

Plant growth promotion and suppression of bacterial leaf blight in rice by Paenibacillus polymyxa Sx3

The effects and mechanisms of Paenibacillus polymyxa Sx3 on growth promotion and the suppression of bacterial leaf blight in rice were evaluated in this study. The results from a plate assay indicated that Sx3 inhibited the growth of 20 strains of Xanthomonas oryzae pv. oryzae (Xoo). Rice seedling experiments indicated that Sx3 promoted plant growth and suppressed bacterial leaf blight. In addition, bacteriological tests showed that Sx3 was able to fix nitrogen, solubilize phosphate and produce indole acetic acid, indicating that various mechanisms may be involved in the growth promotion by Sx3. The culture filtrate of P. polymyxa Sx3 reduced bacterial growth, biofilm formation and disrupted the cell morphology of Xoo strain GZ 0005, as indicated by the transmission and scanning electron microscopic observations. In addition, MALDI-TOF MS analysis revealed that Sx3 could biosynthesize two types of secondary metabolites fusaricidins and polymyxin P. In summary, this study clearly indicated that P. polymyxa Sx3 has strong in vitro and in vivo antagonistic activity against Xoo, which may be at least partially attributed to its production of secondary metabolites. SIGNIFICANCE AND IMPACT OF THE STUDY: Antagonistic bacteria can grow well in their originating environment. However, it is unclear whether antagonistic bacteria were able to survive in different ecological environments. This study revealed that Paenibacillus polymyxa Sx3 isolated from rhizosphere soil of cotton significantly promoted the plant growth and suppressed bacterial leaf blight in rice. Therefore, it could be inferred that P. polymyxa Sx3 has the potential to be used as biocontrol agents in plants grown in different ecological environments.

Comparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation

The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus. Furthermore, a large number of genes gained are associated with carbohydrate transport and metabolism. It indicates that the evolution of glycometabolism is a key factor for the environmental adaptability of Paenibacillus species. Interestingly, through horizontal gene transfer, Paenibacillus sp. SSG-1 acquired an approximately 150 kb DNA fragment and shows an agar-degrading characteristic distinct from most other non-marine bacteria. This region may be transported in bacteria as a complete unit responsible for agar degradation. Taken together, these results provide insights into the evolutionary pattern of Paenibacillus and have implications for studies on the taxonomy and functional genomics of this genus.

Stepwise bioprocess for exopolysaccharide production using potato starch as carbon source

Xanthan gum is a biopolymer produced by Xanthomonas sp. XC6. In this study, xanthan gum is produced from potato starch using a stepwise bioprocess design. Potato starch is hydrolyzed using Bacillus sp. having amylase activity and 30.2 g/L reducing sugar was released, while Xanthomonas sp. XC6 can release only 14.5 g/L. Bacillus sp. hydrolyzed potato starch extract was further used as a carbon source for xanthan gum biosynthesis using Xanthomonas sp. XC6. Yeast extract acts as the best nitrogen source, and 10.0 g/L xanthan gum was recovered. Downstreaming process after stepwise bioprocess resulted in 17.4 g/L xanthan gum production, which is 2.8 times higher as compared to single step process.

β-Amylase production from packaging-industry wastewater using a novel strain Paenibacillus chitinolyticus CKS 1

Transforming waste into valuable biotechnology products – the treatment of transport packaging wastewater withPaenibacillus chitinolyticusCKS1 for β-amylase and maltose production.

An exceptionally cold-adapted alpha-amylase from a metagenomic library of a cold and alkaline environment

A cold-active α-amylase, AmyI3C6, identified by a functional metagenomics approach was expressed in Escherichia coli and purified to homogeneity. Sequence analysis showed that the AmyI3C6 amylase was similar to α-amylases from the class Clostridia and revealed classical characteristics of cold-adapted enzymes, as did comparison of the kinetic parameters K m and k cat to a mesophilic α-amylase. AmyI3C6 was shown to be heat-labile. Temperature optimum was at 10-15 °C, and more than 70 % of the relative activity was retained at 1 °C. The pH optimum of AmyI3C6 was at pH 8-9, and the enzyme displayed activity in two commercial detergents tested, suggesting that the AmyI3C6 α-amylase may be useful as a detergent enzyme in environmentally friendly, low-temperature laundry processes.

Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing

Background

The use of cold-active enzymes has many advantages, including reduced energy consumption and easy inactivation. The ikaite columns of SW Greenland are permanently cold (4-6°C) and alkaline (above pH 10), and the microorganisms living there and their enzymes are adapted to these conditions. Since only a small fraction of the total microbial diversity can be cultured in the laboratory, a combined approach involving functional screening of a strain collection and a metagenomic library was undertaken for discovery of novel enzymes from the ikaite columns.

Results

A strain collection with 322 cultured isolates was screened for enzymatic activities identifying a large number of enzyme producers, with a high re-discovery rate to previously characterized strains. A functional expression library established in Escherichia coli identified a number of novel cold-active enzymes. Both α-amylases and β-galactosidases were characterized in more detail with respect to temperature and pH profiles and one of the β-galactosidases, BGal_I17E2, was able to hydrolyze lactose at 5°C. A metagenome sequence of the expression library indicated that the majority of enzymatic activities were not detected by functional expression. Phylogenetic analysis showed that different bacterial communities were targeted with the culture dependent and independent approaches and revealed the bias of multiple displacement amplification (MDA) of DNA isolated from complex microbial communities.

Conclusions

Many cold- and/or alkaline-active enzymes of industrial relevance were identified in the culture based approach and the majority of the enzyme-producing isolates were closely related to previously characterized strains. The function-based metagenomic approach, on the other hand, identified several enzymes (β-galactosidases, α-amylases and a phosphatase) with low homology to known sequences that were easily expressed in the production host E. coli. The β-galactosidase BGal_I17E2 was able to hydrolyze lactose at low temperature, suggesting a possibly use in the dairy industry for this enzyme. The two different approaches complemented each other by targeting different microbial communities, highlighting the usefulness of combining methods for bioprospecting. Finally, we document here that ikaite columns constitute an important source of cold- and/or alkaline-active enzymes with industrial application potential.

Monitoring of the bacterial and fungal biodiversity and dynamics during Massa Medicata Fermentata fermentation

The microbial community dynamics play an important role during Massa Medicata Fermentata (MMF) fermentation. In this study, bacterial and fungal communities were investigated based on the culture-dependent method and polymerase chain reaction-denaturing gradient gel electrophoresis analysis. Meanwhile the dynamic changes of digestive enzyme activities were also examined. Plating results showed that MMF fermentation comprised two stages: pre-fermentation stage (0–4 days) was dominated by bacterial community and post-fermentation stage (5–9 days) was dominated by fungal community. The amount of bacteria reached the highest copy number 1.2 × 10¹⁰ CFU/g at day 2, but the fungi counts reached 6.3 × 10⁵ CFU/g at day 9. A total of 170 isolates were closely related to genera Enterobacter, Klebsiella, Acinetobacter, Pseudomonas, Mucor, Saccharomyces, Rhodotorula, and Amylomyces. DGGE analysis showed a clear reduction of bacterial and fungal diversity during fermentation, and the dominant microbes belonged to genera Enterobacter, Pediococcus, Pseudomonas, Mucor, and Saccharomyces. Digestive enzyme assay showed filter paper activity; the activities of amylase, carboxymethyl cellulase, and lipase reached a peak at day 4; and the protease activity constantly increased until the end of the fermentation. In this study, we carried out a detailed and comprehensive analysis of microbial communities as well as four digestive enzymes' activities during MMF fermentation process. The monitoring of bacterial and fungal biodiversity and dynamics during MMF fermentation has significant potential for controlling the fermentation process.