Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

Abstract

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns

“…Within the strain library used in this study was the high BGC containing, newly described A. vastitatis isolated from Cerro Chajnantor soil at 4000 m [89]. Similar conclusions can be drawn from phylogenomic studies on representatives of the genus Micromonospora [90]. Amongst actinobacteria, micromonosporae are second only to streptomycetes in their ability to synthesize natural products, notably antibiotics, including ones that are not only in clinical use [32] but considered essential to global health [91].…”

Extreme environments: microbiology leading to specialized metabolites

“…In recent times innumerable filamentous actinobacteria have been isolated from desert soils and assigned not only to the ubiquitous genus Streptomyces but also to rare and poorly studied taxa, such as the genera Actinomadura, Amycolatopsis, Nocardiopsis, Nonomuraea, Saccharopolyspora and Saccharothrix (Okoro et al ; Goodfellow et al ). The application of cutting edge taxonomic and screening methods, especially those based on whole‐genome sequence data; show that such filamentous actinobacteria are a significant source of novel specialized metabolites (Bull et al ; Carro et al ; Carro et al ). In this context, especially gifted isolates from Atacama Desert habitats have been classified as novel species of Streptomyces , such as Streptomyces asenjonii (Goodfellow et al ), Streptomyces deserti (Santhanam et al ), Streptomyces atacamaensis (Santhanam et al ), Streptomyces bullii (Santhanam et al ) and Streptomyces leeuwenhoekii (Busarakam et al ).…”

“…In this context, especially gifted isolates from Atacama Desert habitats have been classified as novel species of Streptomyces , such as Streptomyces asenjonii (Goodfellow et al ), Streptomyces deserti (Santhanam et al ), Streptomyces atacamaensis (Santhanam et al ), Streptomyces bullii (Santhanam et al ) and Streptomyces leeuwenhoekii (Busarakam et al ). Recently, presumptively gifted isolates from a high‐altitude Cerro Chajnantor gravel soil in northern Chile have been validly named as Micromonospora acroterricola (Carro et al ), Micromonospora arida and Micromonospora inaquosa (Carro et al ). Similarly, novel dereplicated isolates belonging to less well‐known genera have been validly named, as exemplified by Amycolatopsis vastitatis (Idris et al ), Lentzea chajnantorensis (Idris et al ) and Pseudonocardia nigra (Trujillo et al ).…”

“…In light of these developments, it clearly makes good sense to focus bioprospecting campaigns on micro‐organisms with moderate to large genomes. Another important development is the realization that in some actinobacterial taxa, such as the genera Amycolatopsis , Frankia and Micromonospora , there is a link between the distribution of NP‐BGCs and phylogeny (Adamek et al ; Carro et al ; Nouioui et al ). In addition, information drawn from whole‐genome sequences is providing fascinating insights into how micro‐organisms adapt to extreme habitats, as witnessed by the ability of members of the actinobacterial family Geodermatophilaceae to withstand extreme environmental conditions that prevail in hyperarid desert habitats (Castro et al , b).…”

Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus

“…Whole genome sequence based analysis could lead to the development of phylogenomic trees with significantly high average bootstrap support [5]. Whole genome and core genome based reclassification have addressed the problems of conventional classification in several genera within the phylum Actinobacteria including Rhodococcus and Micromonospora [6,7]. Both whole genome and phylogenomic based classification have emerged as important tools in species reclassification in the genus Streptomyces [8][9][10].…”