Diversity and functional properties of acid-tolerant bacteria isolated from tea plantation soil of Assam

Goswami, Gunajit; Deka, P. C.; Das, Pompi; Bora, Sudipta Sankar; Samanta, R.; Boro, Robin Chandra; Barooah, Madhumita

doi:10.1007/s13205-017-0864-9

Cited by 32 publications

(13 citation statements)

References 60 publications

(41 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The 16S rRNA gene sequence-based phylogenetic analysis has been used widely to study the evolutionary relationships of microbes (Janda and Abbott 2002 , 2007 ; Goswami et al 2017 ). The phylogenetic tree generated using 16S rRNA gene sequences of the two isolates viz .…”

Section: Discussionmentioning

confidence: 99%

Characterization of methicillin-resistant Staphylococcus aureus through genomics approach

2020

Self Cite

View full text Add to dashboard Cite

In the present study, a total of 35 S. aureus isolates collected from two different geographical locations viz., Germany and Hungary were tested for their methicillin-resistant phenotype which revealed a high incidence of methicillin-resistant S. aureus. The quantitative test for biofilm production revealed that 73.3% of isolates were biofilm producers. The isolates were further characterized using a set of biochemical and genotypic methods such as amplification and analysis of S. aureus species-specific sequence and mecA gene. The 33 mecA positive isolates were then characterized by the amplification of SCCmec and pvl toxin genes. Further, based on the biofilm-forming phenotype, 15 isolates were selected and characterized through PCR–RFLP of coa gene, polymorphism of spa gene and amplification of biofilm-associated genes. The dendrogram prepared from the results of both biochemical and genotypic analyses of the 15 isolates showed that except for the isolates SA G5 and SA H29, the rest of the isolates grouped themselves according to their locations. Thus, the two isolates were selected for further characterization through whole-genome sequencing. Comparative genome analysis revealed that SA G5 and SA H29 have 97.20% ANI values with 2344 gene clusters (core-genome) of which 16 genes were related to antibiotic resistance genes and 57 genes encode virulence factors. The highest numbers of singleton genes were found in SA H29 that encodes proteins for virulence, resistance, mobile elements, and lanthionine biosynthesis. The high-resolution phylogenetic trees generated based on shared proteins and SNPs revealed a clear difference between the two strains and can be useful in distinguishing closely related genomes. The present study demonstrated that the whole-genome sequence analysis technique is required to get a better insight into the MRSA strains which would be helpful in improving diagnostic investigations in real-time to improve patient care.

show abstract

Section: Discussionmentioning

confidence: 99%

Characterization of methicillin-resistant Staphylococcus aureus through genomics approach

2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…Although Aeromonas spp. are widely distributed in soil ( 19 ), foodstuffs ( 20 ), and aquatic environments ( 21 ), they usually constitute a small percentage of the human gut flora ( 22 ). As such, the number of Aeromonas spp.…”

Section: Discussionmentioning

confidence: 99%

Alkaline Peptone Water-Based Enrichment Method for mcr-3 From Acute Diarrheic Outpatient Gut Samples

Sun

Zhou

et al. 2018

Front. Med.

View full text Add to dashboard Cite

A third plasmid-mediated colistin resistance gene, mcr-3, is increasingly being reported in Enterobacteriaceae and Aeromonas spp. from animals and humans. To investigate the molecular epidemiology of mcr in the gut flora of Chinese outpatients, 152 stool specimens were randomly collected from outpatients in our hospital from May to June, 2017. Stool specimens enriched in alkaline peptone water or Luria-Bertani (LB) broth were screened for mcr-1, mcr-2, and mcr-3 using polymerase chain reaction (PCR)-based assays. Overall, 19.1% (29/152) and 5.3% (8/152) of the stool samples enriched in alkaline peptone water were PCR-positive for mcr-1 and mcr-3, respectively, while 2.7% (4/152) of samples were positive for both mcr-1 and mcr-3. Strains isolated from the samples that were both mcr-1- and mcr-3-positive were subjected to antimicrobial susceptibility testing by broth microdilution. They were also screened for the presence of other resistance genes by PCR, while multilocus sequence typing and whole-genome sequencing were used to investigate the molecular epidemiology and genetic environment, respectively, of the resistance genes. mcr-3-positive Aeromonas veronii strain 126-14, containing a mcr-3.8-mcr-3-like2 segment, and mcr-1-positive Escherichia coli strain 126-1, belonging to sequence type 1485, were isolated from the sample from a diarrheic butcher with no history of colistin treatment. A. veronii 126-14 had a colistin minimum inhibitory concentration (MIC) of 2 µg/mL and was susceptible to antibiotics in common use, while E. coli 126-1 produced TEM-1, CTX-M-55, and CTX-M-14 β-lactamases and was resistant to colistin, ceftazidime, and cefotaxime. Overall, there was a higher detection rate of mcr-3-carrying strains with low colistin MICs from the samples enriched in alkaline peptone water than from samples grown in LB broth.

show abstract

“…Endophytic bacteria occur at lower population densities than pathogens, and generally do not induce any hypersensitive response in their host, indicating that they are not considered by the host plant as pathogens [7]. Several endophytic and rhizospheric bacteria have been reported for their beneficial effects in crop health [8–11]. The bacterial genera that have been reported as endophytes in different plants include Bacillus , Burkholderia , Cellulomonas , Clavibacter , Curtobacterium , Paenibacillus , Pseudomonas , Rhizobium , Serratia , etc.…”

Section: Introductionmentioning

confidence: 99%

Lipopeptide mediated biocontrol activity of endophytic Bacillus subtilis against fungal phytopathogens

et al. 2019

Self Cite

View full text Add to dashboard Cite

Background The use of chemical fungicides against fungal pathogens adversely affects soil and plant health thereby resulting in overall environmental hazards. Therefore, biological source for obtaining antifungal agents is considered as an environment-friendly alternative for controlling fungal pathogens. Results In this study, seven endophytic bacteria were isolated from sugarcane leaves and screened for its antifungal activity against 10 fungal isolates belonging to the genera Alternaria, Cochliobolus, Curvularia, Fusarium, Neodeightonia, Phomopsis and Saccharicola isolated from diseased leaves of sugarcane. Among the seven bacterial isolates, SCB-1 showed potent antagonistic activity against the tested fungi. Based on the phenotypic data, Fatty Acid Methyl Esters (FAME) and 16S rRNA gene sequence analysis, the isolate SCB-1 was identified as Bacillus subtilis . The bacterial isolate was screened negative for chitinase production; however, chloroform and methanol extracts of the bacterial culture caused significant inhibition in the growth of the fungal isolates on semisolid media. Volatile component assay showed highest inhibitory activity against Saccharicola bicolor (SC1.4). A PCR based study detected the presence of the genes involved in biosynthesis of surfactin, bacillaene, difficidin, macrolactins and fengycin. Mass spectrometric analysis of the bacterial extract detected the presence of antifungal lipopeptide surfactin, but other metabolites were not detected. The biocontrol activity of the bacterial isolate was established when bacterial pretreated mung bean seeds were able to resist Fusarium infection, however, the untreated seeds failed to germinate. Conclusion The antifungal potential of isolate Bacillus subtilis SCB-1 was established against taxonomically diverse fungal pathogens including the genera Saccharicola , Cochliobolus, Alternaria and Fusarium . The potent antifungal compound surfactin as well as volatiles produced by the bacterial isolate could be responsible for its bio-control activity against fungal infections. Electronic supplementary material The online version of this article (10.1186/s12866-019-1440-8) contains supplementary material, which is available to authorized users.

show abstract

Diversity and functional properties of acid-tolerant bacteria isolated from tea plantation soil of Assam

Cited by 32 publications

References 60 publications

Characterization of methicillin-resistant Staphylococcus aureus through genomics approach

Characterization of methicillin-resistant Staphylococcus aureus through genomics approach

Alkaline Peptone Water-Based Enrichment Method for mcr-3 From Acute Diarrheic Outpatient Gut Samples

Lipopeptide mediated biocontrol activity of endophytic Bacillus subtilis against fungal phytopathogens

Contact Info

Product

Resources

About