Diversity of culturable bacteria endowed with antifungal metabolites biosynthetic characteristics associated with tea rhizosphere soil of Assam, India

Background Rhizosphere soil is a crucial niche for the diverse beneficial microbial communities in plant-microbe interactions. This study explores the antagonistic potential and diversity of the rhizosphere soil bacteria from commercial tea estates of Assam, India which comes under the Indo-Burma mega-biodiversity hotspot. Rhizosphere soil samples were collected from six different tea estates to isolate the bacteria. The bacterial isolates were subjected to evaluate for the antagonistic activity against fungal pathogens. The potential isolates were investigated for chitinase production and the presence of chitinase gene. The bacterial genetic diversity was studied by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and BOX-PCR fingerprinting. Results A total of 217 rhizobacteria were isolated from tea rhizosphere soil, out of which 50 isolates exhibited the potential antagonistic activity against fungal pathogens. Among them, 12 isolates showed extracellular chitinase activity and the presence of chitinase genes. The chitinase genes were sequenced and the analysis of the sequences was performed by using PDB protein databank at the amino acid level. It showed the presence of ChiA and ChiA74 gene in the 6 most potent isolates which are involved in the hydrolysis of chitin. These isolates also exhibited antagonistic activity against all tested fungal pathogens. The diversity of 50 antagonistic bacterial isolates were analyzed through ARDRA and BOX-PCR fingerprinting. Diversity analysis and molecular identification of the rhizosphere isolates revealed that these antagonistic isolates predominantly belonged to the genus Bacillus followed by Enterobacter, Serratia, Lysinibacillus, Pseudomonas, and Burkholderia. Conclusion The present study establishes that rhizobacteria isolated from the poorly explored tea rhizosphere soil could be a rich reservoir for the investigation of potential antagonistic bacterial candidates for sustainable agricultural and industrial applications.

Strain Typing of Trichosporon asahii Clinical Isolates by Random Amplification of Polymorphic DNA (RAPD) Analysis

Objective The aim of this study was to identify and isolate Trichosporon asahii (T. asahii) from clinical samples and to assess the genetic relatedness of the most frequently isolated strains of T. asahii using random amplification of polymorphic DNA (RAPD) primers GAC-1 and M13. Methods All the clinical samples that grew Trichosporon species, identified and confirmed by polymerase chain reaction (PCR) using Trichosporon genus-specific primers, were considered for the study. Confirmation of the species T. asahii was carried out by T. asahii-specific PCR. Fingerprinting of the most frequently isolated T. asahii isolates was carried out by RAPD using random primers GAC-1 and M13. Results Among the 72 clinical isolates of Trichosporon sp. confirmed by Trichosporon-specific PCR, 65 were found to be T. asahii as identified by T. asahii-specific PCR. Fingerprinting of the 65 isolates confirmed as T. asahii using GAC-1 RAPD primer yielded 11 different patterns, whereas that of M13 primer produced only 5 patterns. The pattern I was found to be the most predominant type (29.2%) followed by pattern III (16.9%) by GAC-1 primer. Conclusions This study being the first of its kind in India on strain typing of T. asahii isolates by adopting RAPD analysis throws light on genetic diversity among the T. asahii isolates from clinical samples. Fingerprinting by RAPD primer GAC-1 identified more heterogeneity among the T. asahii isolates than M13.

Prevalence, Genetic Diversity, Antimicrobial Resistance, and Toxigenic Profile of Vibrio vulnificus Isolated from Aquatic Environments in Taiwan

Vibrio vulnificus is a gram-negative, opportunistic human pathogen associated with life-threatening wound infections and is commonly found in warm coastal marine water environments, globally. In this study, two fishing harbors and three tributaries of the river basin were analyzed for the prevalence of V. vulnificus in the water bodies and shellfish that are under the pressure of external pollutions. The average detection rate of V. vulnificus in the river basins and fishing harbors was 8.3% and 4.2%, respectively, in all seasons. A total of nine strains of V. vulnificus were isolated in pure cultures from 160 samples belonging to river basins and fishing harbors to analyze the antibiotic susceptibility, virulence gene profiles, and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) fingerprinting. All isolates were susceptible to 10 tested antibiotics. The genotypic characterization revealed that 11.1% (n = 1/9) strain was nonvirulent, whereas 88.9% (n = 8/9) isolates were virulent strains, which possessed the four most prevalent toxin genes such as vcgC (88.9%), 16S B (88.9%), vvhA (88.9%), and manIIA (88.9%), followed by nanA (77.8%), CPS1 (66.7), and PRXII (44.4%). Additionally, ERIC-PCR fingerprinting grouped these nine isolates into two main clusters, among which the river basin isolates showed genetically diverse profiles, suggesting multiple sources of V. vulnificus. Ultimately, this study highlighted the virulent strains of V. vulnificus in the coastal aquatic environments of Taiwan, harboring a potential risk of infection to human health through water-borne transmission.

Diversity of culturable bacteria endowed with antifungal metabolites biosynthetic characteristics associated with Tea rhizosphere soil of Assam, India

Background Rhizosphere soil is a crucial niche for the diverse beneficial microbial communities for plant-microbe interactions. This study explores the antagonistic potential and diversity of the rhizosphere soil bacteria from commercial tea estates of Assam, India which comes under Indo-Burma mega-biodiversity hotspot. Rhizosphere soil samples were collected from six different tea estates to isolate the bacteria. The bacterial isolates were subjected to evaluate for the antagonistic activity against fungal pathogens. The potential isolates were investigated for chitinase production and presence of chitinase gene. The bacterial genetic diversity was studied by ARDRA and BOX-PCR fingerprinting. Results A total of 217 rhizobacteria were isolated from tea rhizosphere soil and of which 50 isolates exhibited the potential antagonistic activity against fungal pathogens. Among them, 12 isolates showed extracellular chitinase activity and the presence of chitinase genes. The sequencing and analysis of the chitinase gene using PDB protein databank at the amino acid level showed the presence of ChiA and ChiA74 gene in the isolates which involved in the hydrolysis of chitin. The analysis showed that 6 most potential isolates exhibited antagonistic activity against all tested fungal pathogens and presence of chitinase genes within their genome. The diversity of 50 antagonistic bacterial isolates were analysed through ARDRA and BOX-PCR fingerprinting. Diversity analysis and molecular identification of the rhizosphere isolates revealed that these antagonistic isolates predominantly belonged to the genus Bacillus followed by Enterobacter, Serratia, Lysinibacillus, Pseudomonas, and Burkholderia. Conclusion The present study establishes that rhizobacteria isolated from the poorly explored tea rhizosphere soil could be a rich reservoir for the investigation of potential antagonistic bacterial candidates for sustainable agricultural and industrial applications.

Characterization of Clostridium tyrobutyricum Strains Using Three Different Typing Techniques

Clostridium tyrobutyricum is well known as one of the main causative agents of severe cheese spoilage. The metabolism of this anaerobic bacterium during ripening leads to textural and sensory defects in cheese and consequential loss of product value. The potential to induce cheese spoilage, however, may vary among different strains of the same species. Therefore, a better understanding of the intra-species diversity of C. tyrobutyricum may be of practical relevance for the dairy industry. In the present study, we compared the ability of three typing techniques to differentiate 95 C. tyrobutyricum strains on the subspecies level: (1) repetitive element palindromic PCR (rep-PCR) fingerprinting combined with conventional agarose gel electrophoresis, (2) hexaplex-PCR followed by an automated capillary electrophoresis and (3) matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) typing. MALDI-TOF MS fingerprinting provided only moderate reproducibility and low discriminatory power. Both PCR-based methods were highly reproducible and discriminative, with hexaplex-PCR fingerprinting being slightly more discriminative than rep-PCR typing. Overall, a high intra-species diversity was observed among the tested strains, indicating that further investigations on the strain level may be of interest.