Identification of bacteria associated with underground parts of Crocus sativus by 16S rRNA gene targeted metagenomic approach.

Saffron (Crocus sativus L), an autumn-flowering perennial sterile plant, reproduces vegetatively by underground corms. Saffron has biannual corm-root cycle that makes it an interesting candidate to study microbial dynamics in its rhizosphere and cormosphere (area under influence of corm). Culture independent 16S rRNA gene metagenomic study of rhizosphere and cormosphere of Saffron during flowering stage revealed presence of 22 genera but none of the genus was common in all the three samples. Bulk soil bacterial community was represented by 13 genera with Acidobacteria being dominant. In rhizosphere, out of eight different genera identified, Pseudomonas was the most dominant genus. Cormosphere bacteria comprised of six different genera, dominated by the genus Pantoea. This study revealed that the bacterial composition of all the three samples is significantly different (P < 0.05) from each other. This is the first report on the identification of bacteria associated with rhizosphere, cormosphere and bulk soil of Saffron, using cultivation independent 16S rRNA gene targeted metagenomic approach.

Extracellular synthesis and characterization of nickel oxide nanoparticles from Microbacterium sp. MRS-1 towards bioremediation of nickel electroplating industrial effluent.

In the present study, a nickel resistant bacterium MRS-1 was isolated from nickel electroplating industrial effluent, capable of converting soluble NiSO4 into insoluble NiO nanoparticles and identified as Microbacterium sp. The formation of NiO nanoparticles in the form of pale green powder was observed on the bottom of the flask upon prolonged incubation of liquid nutrient medium containing high concentration of 2000ppm NiSO4. The properties of the produced NiO nanoparticles were characterized. NiO nanoparticles exhibited a maximum absorbance at 400nm. The NiO nanoparticles were 100-500nm in size with unique flower like structure. The elemental composition of the NiO nanoparticles was 44:39. The cells of MRS-1 were utilized for the treatment of nickel electroplating industrial effluent and showed nickel removal efficiency of 95%. Application of Microbacterium sp. MRS-1 would be a potential bacterium for bioremediation of nickel electroplating industrial waste water and simultaneous synthesis of NiO nanoparticles.

Microbial phylogeny and diversity: small subunit ribosomal RNA sequence analysis and beyond.

Small subunit ribosomal RNA (16S rRNA) gene sequence analysis is used for the identification and classification of prokaryotes. In addition, sequencing of 16S rRNA genes amplified directly from the environment is used to estimate microbial diversity. The presence of mosaicism, intra-genomic heterogeneity and the lack of a universal threshold sequence identity value limit 16S rRNA-based phylogenetic analysis. PCR-amplification bias and cloning bias can also result in an inaccurate representation of the microbial diversity. In this review, recently reported complexities of 16S rRNA gene sequence analyses and the requirement of additional tools for microbial phylogeny and diversity analyses are discussed.

Human microbiomics.

The sequencing of the human genome has driven the study of human biology in a significant way and enabled the genome-wide study to elucidate the molecular basis of complex human diseases. Recently, the role of microbiota on human physiology and health has received much attention. The influence of gut microbiome (the collective genomes of the gut microbiota) in obesity has been demonstrated, which may pave the way for new prophylactic and therapeutic strategies such as bacteriotherapy. The significance and recent understandings in the area of "human microbiomics" are discussed here.

Characterization of multiple promoters and transcript stability in the sacB-sacC gene cluster in Zymomonas mobilis.

In Zymomonas mobilis, the extracellular levansucrase (SacB) and extracellular sucrase (SacC) are involved in sucrose hydrolysis. Genes coding for these two enzymes (sacB and sacC) are arranged in a cluster in the genome and separated by a short intervening sequence. The level of sacC transcript was 12-fold higher than that of sacB transcript. On the other hand, transcript stability analysis in sucrose grown cultures revealed that the half-life of the sacB transcripts (153 s) was more than twofold higher than that of sacC transcript (66 s). The decay curves of sacB and sacC transcripts analyzed by the semi-quantitative RT-PCR correlated well with the decay curves of the respective enzyme activities. In the sacB promoter disruption mutant, Z. moblis BT2, the extracellular sucrase activity decreased from 2.6 to 2.0 U mg(-1) in sucrose medium due to the loss of SacB expression. The expression of sacC in the absence of the sacB promoter suggested that these two genes could be transcribed as different mRNAs. The promoter-lacZ fusion studies in Escherichia coli proved that the short intervening region acts as a strong promoter for the sacC gene.

Strategies for accessing soil metagenome for desired applications.

Most of the microorganisms in nature are inaccessible as they are uncultivable in the laboratory. Metagenomic approaches promise the accessibility of the genetic resources and their potential applications. Genetic resources from terrestrial environments can be accessed by exploring the soil metagenome. Soil metagenomic analyses are usually initiated by the isolation of environmental DNAs. Several methods have been described for the direct isolation of environmental DNAs from soil and sediments. Application of metagenomics largely depends on the construction of genomic DNA libraries and subsequent high-throughput sequencing or library screening. Thus, obtaining large quantities of pure cloneable DNA from the environment is a prerequisite. This review discusses the recent developments related to efficient extraction and purification of soil metagenome highlighting the considerations for various metagenomic applications.

Application of cross-linked enzyme aggregates of Bacillus badius penicillin G acylase for the production of 6-aminopenicillanic acid.

AIMS: Optimization of 6-aminopenicillanic acid (6-APA) production using cross-linked enzyme aggregates (CLEA) of Bacillus badius penicillin G acylase (PAC). METHODS AND RESULTS: CLEA-PAC was prepared using purified/partially purified PAC with phenylacetic acid as active-site blocking agent and glutaraldehyde as cross-linker. Conversion of penicillin G to 6-APA by CLEA-PAC was optimized using response surface methodology (RSM) (central composite rotatable design) consisting of a three-factor-two-level pattern with 20 experimental runs. CONCLUSION: Nearly, 80% of immobilization yield was obtained when partially purified enzyme was used for the preparation of CLEA-PAC. Quantitative conversion of penicillin G to 6-APA was observed within 60 min and the CLEA-PAC was reusable for 20 repeated cycles with 100% retention of enzyme activity. SIGNIFICANCE AND IMPACT OF THE STUDY: The faster conversion of penicillin G to 6-APA by CLEA-PAC and efficient reusability holds a strong potential for the industrial application.

Optimization of a fermentation medium for the production of Penicillin G acylase from Bacillus sp.

AIMS: Optimization of Penicillin G acylase (PAC) production from a novel isolate of Bacillus sp. METHODS: Fermentation medium for PAC production was optimized using a two-level fractional factorial design with seven components. RESULTS: A maximum production of 9.5 U ml(-1) of PAC was obtained in an optimized medium containing (g l(-1): K2HPO4, 1.0; MgSO4.7H2O, 0.1; CaCl2.2H2O, 0.1; PAA, 2.0; tryptone, 5.0; yeast extract, 3.0; and sucrose, 50.0. SIGNIFICANCE AND IMPACT OF THE STUDY: The two-step medium optimization resulted in a twofold increase in PAC production. Since the strain Bacillus sp. PGS10 produces a high level of PAC, it could be a potential candidate for industrial production of PAC.