Diversity Of Actinomycetes Of The Micromonosporaceae Family

Actinomycetes are the main antibiotics producing microorganisms and have contributed greatly to human health in the past more than half a century.In recent years,because of the crazy spread of various new infectious diseases and the continuous emergence of drug-resistant bacteria,people's demand for antibiotics with novel structure and remarkable efficacy is increasing,forcing us to explore excellent microbial drug-producing bacteria resources.The family of Micromonosporaceae,encompassing rich diversity of species,is a group of dominant rare actinomycetes widely distributed in the natural environments.Some of the secondary metabolites produced by the Micromonosporaceae have been successfully applied in clinical medicine and agriculture.The aim of this study is to explore the actinomycetes with the potential abilities to produce novel active substances based on the investigation of the diversity of Micromonosporaceae resouces.Firstly,high-throughput sequencing technology was used to analyze the diversity of Micromonosporaceae in three different types of ecosystem.Subsequently,the co-occurrence network diagram was constructed to investigate the interaction between the members of Micromonosporaceae and other actinobacterial communities in their ecosystems.Then,guided by the above culture-independent sequencing results,culture-dependent scheme was optimized to isolate the Micromonosporaceae strains.Finally,based on the genomic annotation analysis and the polyphasic taxonomy study,the application potential of some Micromonosporaceae isolates were evaluated.The V3-V4 region of the 16S rRNA gene of the environmental microorganisms was sequenced by high-throughput sequencing method.A total of 69,923,59,963 and 56,741 qualified sequences were obtained from 10 groups of rhizosphere soil samples collected from Xinjiang medicinal plants,6 groups of surface water samples from Erhai Lake in Dali,Yunnan,and 11 groups of rhizosphere soil samples of Yunnan mulberry parasitic medicinal plants,respectively.And 4133 OTUs,1975 OTUs and 2344 OTUs were classified.These OTUs represented 678 genera of 269 families in 151 orders of 55 classes within 26 phyla in the bacterial domain,among which actinomycetes accounted for 38.49%of the total number of bacteria,and 13 genera of Micromonosporaceae accounted for 5.21%of the members of actinomycetes in Xinjiang medicinal plants rhizosphere soil samples.In the surface water samples of Erhai Lake,the OTUs belonged to 580 genera of 248 families in 140 orders of 534 classes within 24 phyla in the bacterial domain,including 10 genera of Micromonosporaceae.Actinomycetes accounted for 8.23%of the total bacteria,and strains of Micromonosporaceae accounted for 0.86%of the total bacteria.The OTUs detected from rhizosphere soil samples of Yunnan Morus parasiticus belonged to 508 genera of 296 families in 165 orders of 60 classes within 27 phyla in the bacterial domain,in which actinomycetes accounted for 21.23%of the total number of bacteria in the community,and strains of Micromonosporaceae accounted for 2.08%of the members of actinomycetes,covering 8 genera of Micromonosporaceae.The co-occurrence network analysis of microbial communities based on high-throughput analysis showed that there was a positive interaction between strains of Micromonosporaceae and other actinomycetes in the rhizosphere soil of medicinal plants in Xinjiang and the surface water of Erhai Lake,and they were the core communities of actinomycetes in these two habitats.There was no significant interaction between strains of Micromonosporaceae and other actinomycetes in the rhizosphere environment of Yunnan mulberry parasitic plants.As a result,502 isolates were recovered from the rhizosphere environment of medicinal plants in Xinjiang by culture-dependent method,including 287 members of Micromonosporaceae belonging to 6 genera,and 52 strains were isolated from the surface water samples of the Erhai Lake,including 9 strains of Micromonosporaceae,which were affiliated to Micromonospora and Phytomonospora.As well,101 strains were obtained from the rhizosphere of mulberry parasitic medicinal plants,including 43 strains of Micromonosporaceae,which belonged to Micromonospora and Asanoa.The genomes of 8 newly isolates of Micromonosporaceae obtained from the above three different habitats were sequenced and analyzed.Generally,the genes corresponding to environmental stress were retrieved from all of these genomes,which might partially demonstrate the diversity of the ecological distribution of Micromonosporaceae.The ubiquitous presence of a variety of antibiotics,siderophores and other related biosynthetic gene clusters,and phytohormone-related coding genes in these genomes suggested that these strains of Micromonosporaceae possess the potential to synthesize rich secondary metabolites,assist plants to resist the pathogens and promote the plants growth.Polyphasic taxonomy study including morphological and physiological characteristics,chemotaxonomic properties and molecular analysis was carried out on the strain CPCC 205371T.The phenotypic and genotypic data of the tested strain supported to establish a novel species in the genus Micromonospora.The strain CPCC 205371T isolated from the rhizosphere of a medicinal plant,for which the name Micromonospora herbihabitans sp.nov.was proposed with CPCC 205371T as the type strain.