Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community

Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies

The potential of halophilic and halotolerant bacteria for the production of antineoplastic enzymes: L-asparaginase and L-glutaminase

L-asparaginase and L-glutaminase can be effectively used for the treatment of patients who suffer from accute lymphoblastic leukemia and tumor cells. Microbial sources are the best source for the bulk production of these enzymes. However, their long-term administration may cause immunological responses, so screening for new enzymes with novel properties is required. Halophilic and halotolerant bacteria with novel enzymatic characteristics can be considered as a potential source for production of enzymes with different immunological properties. In this study, L-asparaginase and L-glutaminase production by halophilic bacteria isolated from Urmia salt lake was studied. Out of the 85 isolated halophilic and halotolerant bacterial strains, 16 (19 %) showed L-asparaginase activity and 3 strains (3.5 %) showed L-glutaminase activity. Strains with the highest activities were selected for further studies. Based on 16S rDNA sequence analysis, it was shown that the selected isolates for L-asparaginase and L-glutaminase production belong to the genus Bacillus and Salicola, respectively. Both enzymes were produced extracellularly. The strain with the most L-asparaginase production did not show L-glutaminase production which is medically important. The effects of key parameters including temperature, initial pH of the solution, and concentrations of glucose, asparagine or glutamine, and sodium chloride were evaluated by means of response surface methodology (RSM) to optimize enzymes production. Under the obtained optimal conditions, L-asparaginase and L-glutaminase production was increased up to 1.5 (61.7 unit/mL) and 2.6 fold (46.4 unit/mL), respectively

Metagenomic discovery and functional validation of L-asparaginases with anti-leukemic effect from the Caspian Sea

By screening 27,000 publicly available prokaryotic genomes, we recovered ca. 6300 type I and ca. 5200 type II putative L-asparaginase highlighting the vast potential of prokaryotes. Caspian water with similar salt composition to the human serum was targeted for in silico L-asparaginase screening. We screened ca. three million predicted genes of its assembled metagenomes that resulted in annotation of 87 putative L-asparaginase genes. The L-asparagine hydrolysis was experimentally confirmed by synthesizing and cloning three selected genes in E. coli. Catalytic parameters of the purified enzymes were determined to be among the most desirable reported values. Two recombinant enzymes represented remarkable anti-proliferative activity (IC50 <1IU/ml) against leukemia cell line Jurkat while no cytotoxic effect on human erythrocytes or human umbilical vein endothelial cells was detected. Similar salinity and ionic concentration of the Caspian water to the human serum highlights the potential of secretory L-asparaginases recovered from these metagenomes as potential treatment agents

Evaluation of biodecolorization of the textile azo dye by halophilic archaea

Introduction: Azo dyes are the biggest group of colors. One of the special characteristic of this group of dye is the presence of double bonds of Nitrogen (N=N). Several studies reported biodecolorization using microorganisms, so far. However, it is for the first time to our knowledge that decolorization by halophilic archaea have been reported. Materials and methods: Among the 15 strains of archaea isolated from Qeshm saline cave and 7 type strains from Iranian biological resource center, 2 strains showed high ability in decolorization of azo dye. Effects of different factors including pH (5-9), temperature (30-50 °C), various salt concentrations (12.5-30%), different concentrations of dye (400-5000 mg/L), different carbon sources and several nitrogen sources and agitation have been measured after 4 days of incubation in static condition. Moreover, the toxicity tolerance of halo archaeal strains to dye, growth and decolorization rates were studied. Statistical significance was assessed by ANOVA Tukey’s multiple comparison test. Results: Strain A with 99.1 % similarity to Halogeometricum borinquense and strain B with 99.4 % similarity to Haloferax mediterranei were the best decolorizing strains. Both strains had their highest decolorization rate in the presence of NaCl (15-17.5 %), pH 7, microaerophilic condition and yeast extract as nitrogen source. Halogeometricum borinquense showed higher decolorization rate in the presence of saccharose and glucose as carbon sources at 45 oC temperature and for Haloferax mediterranei temperature of 40 oC and propionic acid as carbon source were best decolorizing conditions. These strains were able to decolorize dyes at 1000 mg/L concentration and tolerate dye concentrations to the highest level of 5000 mg/L. Discussion and conclusion: In conclusion, our results indicate that halophilic archaea have very high potential to decolorize azo dyes. Regarding high amounts of salts in textile wastewaters, using such microorganisms which can tolerate the harsh environment in order to decolorize azo dyes, could be a new approach in this field