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

Lorena Carro,Hans-Peter Klenk,Tanja Woyke,Markus Göker,Maria Del Carmen Montero-Calasanz,Nikos C Kyrpides,Vartul Sangal,Shweta Deshpande,Kristi E Kim,Imen Nouioui,Jan P Meier-Kolthoff,Nicole Shapiro,Paul Peluso,Michael Goodfellow,Nevzat Sahin,Martha E Trujillo,Darren Lee Smith

doi:10.1038/s41598-017-17392-0

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.

Highlights

Prokaryotic systematics is a core scientific discipline that encompasses classification, nomenclature, identification, and evolutionary processes[1]
The analysis of whole genome sequences of type strains under the auspices of the Genetic Encyclopaedia of Bacteria and Archaea (GEBA) project is greatly improving our understanding of phylogenetic relationships within and between these taxa, as well as generating an invaluable framework, technology and organisation for large scale genome sequencing of prokaryotes that will lead to an unprecedented coverage of prokaryotic diversity on the planet[35,36,37,38,39]
High quality draft genomes were obtained for 40 Micromonospora type strains, 17 of which were completely closed

Summary

Introduction

Prokaryotic systematics is a core scientific discipline that encompasses classification, nomenclature, identification, and evolutionary processes[1]. It is essential that taxonomies based on whole genome sequence data follow sound taxonomic practice, notably by following the nomenclatural type concept and the requirement to deposit type strains in two public culture collections in different countries[33,34] In this context, the analysis of whole genome sequences of type strains under the auspices of the Genetic Encyclopaedia of Bacteria and Archaea (GEBA) project is greatly improving our understanding of phylogenetic relationships within and between these taxa, as well as generating an invaluable framework, technology and organisation for large scale genome sequencing of prokaryotes that will lead to an unprecedented coverage of prokaryotic diversity on the planet[35,36,37,38,39]. On a broader front Micromonospora strains have been considered to be a potential source of biocontrol agents, biofuels, plant growth products and plant probiotics[82,83,84,85]

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Discussion

Conclusion