Alkaliphilic Soil Actinomycetes

Distribution and Characterization of Actinomycetes in Mangrove Habitats (Red Sea, Egypt) with Special Emphasis on Streptomyces mutabilis M3MT483919

Ten sediment samples were gathered from several geographical locations around mangrove habitat, Red Sea coast, Egypt, during summer 2019. Actinobacteria are widespread in most mangrove soil samples. The average actinomycetes counts in sediment samples were ranged from 4 to 15 CFUg-1, also physico-chemical characters for soil samples were determined. Statistical analysis was applied to assess if the geographical location and physico-chemical characters influenced the communities of actinomycetes. A total of 10 actinomycetes were isolated and characterized physiologically and biochemically. The antimicrobial activities of different actinomycetes isolates were assessed. Isolate M3 was chosen as the most promising isolate with broad antagonistic activity against Bacillus subtilis ATCC 6633, Escherichia coli ATCC 19404, Staphylococcus aureus ATCC6538, Pseudomonas aeruginosa ATCC 9027, and Candida albicans ATCC 10231 with inhibition zones ranged from 12.0 ± 0.9 to 20.0 ± 1.9 mm. Genotypic characterization of isolate M3 was made using 16S rDNA sequence analysis and identified as Streptomyces mutabilis M3 with accession number MT483919. This strain exhibited anticancer activity against breast cancer cell line (Mcf7), liver cancer cell line (HepG2) and colon cancer cell line (HCT116) and the IC50 values were 324.77, 333.71 and 354.46, respectively. Streptomyces mutabilis M3 MT483919 had high bio-flocculating activity for seawater treatment, and the recovery of the samples ranged between 71.97 and 76.05%. The crude extract of Streptomyces mutabilis MT483919 M3 was analyzed by Fourier transform infrared spectrum (FT-IR) and Gas chromatography-mass spectrometry (GC-MS).

Antagonistic Properties of Some Halophilic Thermoactinomycetes Isolated from Superficial Sediment of a Solar Saltern and Production of Cyclic Antimicrobial Peptides by the Novel Isolate Paludifilum halophilum

This study has focused on the isolation of twenty-three halophilic actinomycetes from two ponds of different salinity and the evaluation of their ability to exert an antimicrobial activity against both their competitors and several other pathogens. From the 23 isolates, 18 strains showed antagonistic activity, while 19 showed activities against one or more of the seven pathogen strains tested. Six strains exhibited consistent antibacterial activity against Gram-negative and Gram-positive pathogens characterized at the physiological and molecular levels. These strains shared only 94-95% 16S rRNA sequence identity with the closely related species of the Thermoactinomycetaceae family. Among them, the potent strain SMBg3 was further characterized and assigned to a new genus in the family for which the name Paludifilum halophilum (DSM 102817T) is proposed. Sequential extraction of the antimicrobial compounds with ethyl acetate revealed that the crude extract from SMBg3 strain had inhibitory effect on the growth of the plant pathogen Agrobacterium tumefaciens and the human pathogens Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa. Based on the HRESI-MS spectral data, the cyclic lipopeptide Gramicidin S and four cyclic dipeptides (CDPs) named cyclo(L-4-OH-Pro-L-Leu), cyclo(L-Tyr-L-Pro), cyclo(L-Phe-L-Pro), and cyclo(L-Leu-L-Pro) were detected in the fermentation broth of Paludifilum halophilum. To our knowledge, this is the first report on the isolation of these compounds from members of the Thermoactinomycetaceae family.

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.