Gene Amplification and Sequencing for Bacterial Identification

Optimized production of laccase from Pseudomonas stutzeri and its biodegradation of lignin in biomass

Laccases are multi-copper oxidases that play an important role in the biodegradation of phenolic compounds, lignin, dye, and wastes. Here, we report the screening of potential laccase-producing indigenous bacterial isolates and subsequent optimization of laccase production using crop residues as cheap supplementary energy sources. Among 16 bacterial isolates, seven were selected based on the appearance of reddish-brown bacterial colonies and guaiacol oxidation assay after 10 days of incubation at 37 °C. The maximum laccase activity (2.755 U/mL) was observed for bacterial isolate WR2. Response surface methodology (RSM) was used to maximize laccase production from WR2, identified as Pseudomonas stutzeri. Plackett-Burman design (PBD) was employed to design production runs involving various factors including time, pH, inoculum, wheat straw, cotton stalk, wheat bran, rice straw, copper sulfate, sugarcane bagasse, yeast extract, and peptone. The interactions of different factors were analyzed from the responses (laccase enzyme activity, etc.) in 12 experimental runs. In experimental run 4, the maximum laccase enzymatic activity (1.86 U/mL) was achieved after a 10-day incubation with wheat straw (1%) and cotton stalk (1%) at pH 6.8 and 37 °C, and high-degree lignin degradation was evident from a substantial reduction in the FTIR aromatic stretching peak of the degraded biomass.

Establishment of molecular diagnostics targeting the 23S ribosomal RNA gene for the detection of Mycoplasma suis infection in Thai domestic pigs

Mycoplasma (M.) suis is a pathogenic hemotropic Mycoplasma sp. that causes acute hemolytic anemia or chronic infection in pigs. M. suis infection can be diagnosed using several methods, including molecular diagnosis such as conventional PCR (cPCR) and quantitative PCR (qPCR). In these cases, the common target is the 16S rRNA gene; however, this genetic marker cannot distinguish hemoplasma at the species level owing to high sequence identity. Therefore, the 23S rRNA gene has emerged as another target gene. Other than PCR, the loop-mediated isothermal amplification (LAMP) method can be applied for M. suis. The objective of the present study was to establish cPCR, TaqMan qPCR, and LAMP assays in which the 23S rRNA gene is used to detect M. suis infection in Thai domestic pigs. The analytical sensitivity of cPCR was determined as 7.46 × 10⁴ copies/μl of plasmid DNA, whereas those of qPCR and LAMP were 7.46 × 10² copies/μl. There was no cross reaction with other pathogens in any of the assays. To evaluate the diagnostic performance of the assays, they were tested using 173 samples of genomic DNA. The detection percentage of M. suis infection was 24.86% (43/173; 95% CI: 18.61%-31.89%), 28.32% (49/173; 95% CI: 21.75%-35.66%), and 29.48% (51/173; 95% CI: 22.80%-36.88%) using cPCR, qPCR, and LAMP, respectively. Using qPCR as a reference assay, cPCR showed 81.63% sensitivity, 97.58% specificity, and an almost perfect level of agreement (kappa = 0.823). In comparison, LAMP showed 77.55% sensitivity, 89.52% specificity, and a substantial level of agreement (kappa = 0.662). All assays tested here could be applied in veterinary diagnostic laboratories for monitoring porcine health in the herds. Furthermore, the LAMP assay could be used as a screening test in farm practice without the need for any special equipment.

Molecular detection of Mycoplasma wenyonii and its closely related hemotropic Mycoplasma sp. in blood-sucking flies from a buffalo farm in Chachoengsao province, Thailand

Bovine hemoplasmosis is a disease in buffaloes and cattle caused by hemotropic mycoplasmas or hemoplasmas. Only two bovine hemoplasma species, Mycoplasma wenyonii and Candidatus Mycoplasma haemobos, have been described in several countries. Hemoplasmas induce acute hemolytic anemia or chronic infection, leading to production loss. Bovine hemoplasma DNA was also detected in blood-sucking arthropods, suggesting vector transmission in farms. To date, no studies of the molecular detection of bovine hemoplasmas in Thai buffaloes and arthropod vectors have been reported. This study aimed to study the 1-year diversity of hematophagous flies in a buffalo farm located in Chachoengsao province, Thailand, and to investigate the molecular occurrence of bovine hemoplasmas in those flies using a polymerase chain reaction (PCR) assay and sequence analyses. A total of 1,488 mosquitoes, 867 stable flies, and 312 tabanid flies were collected during this study. The most abundant mosquitoes, stable flies, and tabanid flies were Culex tritaeniorhynchus, Stomoxys calcitrans, and Tabanus megalops, respectively. A total of 249 genomic DNA samples of flies were tested using a PCR assay based on the 16S rRNA gene; 23.69% (59/249) of the insect samples were positive in this assay. Positive samples (n = 8) were subjected to bidirectional sequencing. The BLAST results showed that only three samples from Stomoxys calcitrans and two samples from Tabanus megalops showed 99.90% and 99.17% similarities to the M. wenyonii isolate B003 (MG948626/Water buffalo/Cuba) and the M. wenyonii isolate C124 (MG948625/Cattle/Cuba), respectively. This molecular occurrence of bovine hemoplasmas in blood-sucking flies suggested that those flies are the mechanical vectors for bovine hemoplasmas in Thailand. Based on the phylogenetic analysis of the 16S rRNA gene, the sequences of M. wenyonii were likely classified into two subgroups (A and B), suggesting closely related bovine hemoplasma species. Finally, the genetic analysis of the 23S rRNA gene from these two subgroups revealed that subgroup A could be M. wenynoii and subgroup B may be a subspecies of M. wenyonii or another putative novel species. However, further investigation should be conducted in buffaloes, cattle, and blood-sucking flies to gain more 16S rRNA and 23 rRNA gene sequences of bovine hemoplasmas.

Characteristics changes on Applications of Antibiotics and Current Approaches to Enhance Productivity with Soil Microbiome

The contamination of environmental sully with antibiotics is regarded as a major problem today and predictable to attain more recognition in near future. However, human intervention resulting in antibiotic consumption is being enhancing all around the world. Our review of literature revealed the role of microbiome in sully and how antibiotic resistant genes raised. The structure of antibiotics basically influenced by natural components such as biotic and abiotic push which shifts based on different soils. Therefore, management of microbiome in soil and their expression studies were distinctively revealed. The assessment of antibiotic resistance genes with help of next generation sequencing provided a clear comprehension on genome and transcriptome of the bacterial genes. Thus, interaction of microbiome with soil can also be well understood. The current findings in our study will guide every researcher to follow logical protocol in analyzing microbiota composition is covered as well and also to understand its metagenomic and sequenced with next-generation sequencer which helps to comprehend the diverse micro-flora present in soil and its operation. Finally, later progresses in bioinformatics computer program, flow of work, and applications for analyzing metagenomic information are put in a nutshell.

Isolation, characterization, and molecular identification of soil bacteria showing antibacterial activity against human pathogenic bacteria

BACKGROUND

The present study dealt with the screening of soil bacteria with antibacterial activity from different locations in Bangalore, India. Antibiotics play the role of self-defense mechanism for the bacteria and are produced as secondary metabolites to protect themselves from other competitive microorganisms. The need for new antibiotics arose as the pathogenic bacteria acquire resistance to various antibiotics meant for treating human diseases. Given the importance of antibiotics of bacterial origin, standard techniques have been used to isolate and characterize the soil bacteria which showed antibacterial activity.

RESULTS

The isolated bacteria were tested against human pathogenic bacteria like Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae by primary and secondary screening methods. The isolates PR1, PR2, and PR3 were confirmed to have antibacterial activity against S. aureus, E. coli, P. aeruginosa, and K. pneumoniae by both methods. Studies on the effect of filter sterilization, autoclaving, and proteinase K treatment on culture filtrates showed filter sterilization as the best method. The effect of different carbon and nitrogen sources on the antibacterial activity showed that preference by each isolate differed for carbon and nitrogen requirements. The isolates PR1, PR2, and PR3 were identified as Bacillus aryabhattai strain PR-D07, Arthrobacter humicola strain PR-F07, and Neomicrococcus lactis strain PR-F11 through 16S rRNA sequencing.

CONCLUSION

Findings from this research work are encouraging and could proceed further to applied aspects. Only 3 bacterial isolates out of 263 isolates from soil samples displayed antibacterial activity against human pathogens S. aureus, E. coli, P. aeruginosa, and K. pneumoniae. They were identified as B. aryabhattai, A. humicola, and N. lactis by 16S rRNA studies and all of them are Gram-positive. Each isolate preferred different carbon and nitrogen sources for their enhanced antibacterial activity. Efficacy of the culture filtrates of these isolates was tested by filter sterilization, autoclaving, and proteinase K treatment. Filter-sterilized culture filtrates showed higher antibacterial activity than other treatments. A comparison of the antibacterial activity of culture filtrates and antibiotic streptomycin produced an inhibition zone of 18.5 mm and 15.5 mm respectively. This is the first report on the antibacterial activity of all the 3 bacterial strains (B. aryabhattai strain PR-D07, A. humicola strain PR-F07, and N. lactis strain PR-F11), against all the human pathogens, mentioned earlier. It is also found that the antibiotic factor is proteinaceous as proteinase K considerably reduced the antibacterial activity of the culture filtrates. With the above significant results, these 3 bacteria are considered to be promising candidates for the isolation of new antibacterial agents.

Herbicidal Ionic Liquids: A Promising Future for Old Herbicides? Review on Synthesis, Toxicity, Biodegradation, and Efficacy Studies

The transformation of agrochemicals into herbicidal ionic liquids (HILs) has been suggested as a solution to problems associated with commercial forms of herbicides. The aim of this review was to summarize the latest progress in the field of HILs, including their synthesis as well as physicochemical and biological properties, and to address the areas that require further research in order to ensure their safe commercialization (e.g., data regarding biodegradability, toxicity, and environmental fate). The first part of the review provides an in-depth summary of the current state of knowledge regarding HILs, particularly the anions and cations used for their synthesis. The second part highlights the employed synthesis methods and elucidates their respective advantages and limitations. The third section is focused on the characterization of HILs with emphasis on the methods and factors that are significant in terms of their practical application. Subsequently, the issues associated with the biodegradation and toxic effects of HILs are discussed based on the relevant literature reports. All sections include comprehensively tabulated data in order to enable rapid comparison of utilized approaches. Finally, all the findings are critically analyzed in terms of crucial disadvantages (especially the lack of standardization), which allowed us to establish future recommendations and basic guidelines that are presented in the last section.

Antibacterial activity of soil bacteria isolated from Kochi, India and their molecular identification

The present study, deal about the antibiosis activity of soil bacteria, isolated from 10 different locations of rhizosphere and diverse cultivation at Kochi, Kerala, India. The bacteria were isolated by standard serial dilution plate techniques. Morphological characterization of the isolate was done by Gram’s staining and found that all of them gram positive. Isolated bacteria were tested against 6 human pathogens viz., Escherichia coli, Enterococcus sp., Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus and Acinetobacter sp. Primary screening was carried out by perpendicular streaking and seed overlay method. Based on the result of primary screening most potential isolates of S1A1 and S7A3 were selected for secondary screening. Both the isolates showed positive results against Enterococcus sp. and S.aureus. The maximum antagonistic activity of 20.98 and 27.08 mm zone of inhibition was recorded at S1A1 against Enterococcus sp. and S. aureus respectively, at 180 µl concentration. Molecular identification was carried out by 16S rRNA sequence. The 16S rRNA was amplified from the DNA samples by using PCR. The amplified 16S rRNA PCR products were purified and sequenced. The sequences were subjected to NCBI BLAST. The isolates S1A1 and S7A3 BLAST results showed 99% and 95% respectively, similarity with the available database sequence of Bacillus amyloliquefaciens. The sequences were deposited in GenBank and the accession numbers KY864390 (S1A1) and KY880975 (S7A3) were obtained.