Bacterial diversity in the soil from Kumutag Desert and screening of actinomycetes with quorum sensing inhibitory activity

Abstract:

[Background] Quorum sensing inhibitor (QSI), promising alternatives to antibiotics, can reduce the infectivity and virulence of pathogenic bacteria by interrupting quorum sensing pathways. Desert soils contain rich actinomycetes, which are an important source for the mining of QSI. [Objective] To investigate the bacterial diversity in the soil from Kumutag Desert and screen out the actinomycetes with the quorum sensing inhibitory activity. [Methods] Illumina NovaSeq high-throughput sequencing was employed to reveal the composition of bacterial community in the soil of Kumtag Desert, and the culture method to isolate the actinomycetes. The Chromobacterium violaceum 026 model was used for the screening of the actinomycetes with quorum sensing inhibitory activity. The functions of the strains screened out were initially evaluated. [Results] The soil samples harbored 150 genera of bacteria belonging to 96 orders of 23 phyla. The dominant phyla were Proteobacteria (61%) and Actinobacteria (28%). As for Actinobacteria, the genus with the highest relative abundance was Mycobacterium (87.3%), followed by Rhodococcus (6.8%) and Cutibacterium (0.9%). A total of 108 isolates were obtained and identified as actinomycetes belonging to 10 genera of nine families, in which the dominant genus was Streptomyces (65.76%). Thirteen strains with quorum sensing inhibitory activity were screened out, including 10 strains of Streptomyces and each one strain of Nocardiopsis, Bailinhaonella, and Kibdelosporangium. Strain Streptomyces sp. D67 exhibited broad-spectrum antimicrobial activities. [Conclusion] The bacteria in the soil of Kumutag Desert have high diversity and contain multiple strains of actinomycetes with quorum sensing inhibitory activity. Several strains with quorum sensing inhibitory activity demonstrate strong antimicrobial activity, which provide strain resources for the subsequent development of natural QSI and antimicrobial agents and lay a theoretical foundation for the development of biopharmaceuticals and biocontrol.