Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen-Isolated Amycolatopsis Strains

Abstract

Actinomycetes have been extensively exploited as one of the most prolific secondary metabolite-producer sources and continue to be in the focus of interest in the constant search of novel bioactive compounds. The availability of less expensive next generation genome sequencing techniques has not only confirmed the extraordinary richness and broad distribution of silent natural product biosynthetic gene clusters among these bacterial genomes, but also has allowed the incorporation of genomics in bacterial taxonomy and systematics. As part of our efforts to isolate novel strains from unique environments, we explored lichen-associated microbial communities as unique assemblages to be studied as potential sources of novel bioactive natural products with application in biotechnology and drug discovery. In this work, we have studied the whole genome sequences of two new Amycolatopsis strains (CA-126428 and CA-128772) isolated from tropical lichens, and performed a comparative genomic analysis with 41 publicly available Amycolatopsis genomes. This work has not only permitted to infer and discuss their taxonomic position on the basis of the different phylogenetic approaches used, but has also allowed to assess the richness and uniqueness of the biosynthetic pathways associated to primary and secondary metabolism, and to provide a first insight on the potential role of these bacteria in the lichen-associated microbial community.

Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach

“…A ML tree generated from concatenated core proteins resolved Amycolatopsis strains, representing 34 species (including 29 type strains), into four major groups and several singletons ( Figure 1 ). These groupings are consistent with both the MLSA based phylogenies albeit with minor exceptions ( Adamek et al, 2018 ; Sanchez-Hidalgo et al, 2018 ). We have applied the same group designations as used by Adamek et al (2018) .…”

“…Amycolatopsis taiwanensis DSM 45107 T , Amycolatopsis sacchari DSM 44468 T , Amycolatopsis nigrescens CSC17Ta 90 T and Amycolatopsis xylanica CPCC202699 T are present as singletons within the Amycolatopsis clade ( Figure 1 ). These strains were also recovered as singletons in the MLSA analysis of Sanchez-Hidalgo et al (2018) , except for A. xylanica which was located at the periphery of the strains in our cluster A. Of the other singletons, A. sacchari DSM 44468 T is consistently associated with A. dongchuanensis in 16S rRNA gene trees [e.g.…”

“…A recent multilocus sequence analysis (MLSA) based on seven housekeeping genes ( atpD , clpB , gapA , gyrB , nuoD , pyrH and rpoB ) revealed the presence of four major groups of species within the genus, with some singletons ( Adamek et al, 2018 ), whilst Sanchez-Hidalgo et al (2018) described 11 subgroups in a 16 S rRNA analysis, and four major groupings based on an MLSA with four housekeeping genes ( atpD, dnaK, recA and rpoB ). The type strains of Amycolatopsis halophila and Amycolatopsis marina were found to be quite distinct from other Amycolatopsis strains.…”

The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid

“…S. viridis DSM 4301(T) was used as an outgroup. Amycolatopsis species are grouped into three major subclades: the mesophilic or moderately thermophilic A. orientalis subclade (AOS); the thermophilic A. methanolica subclade (AMS); and the mesophilic A. taiwanensis subclade (ATS) [41,42]. The AOS subclade is formed by nine groups designated A-E and G-J, while the ATS and AMS subclades are formed by groups F1 and F2, respectively [41,43].…”

Microbial communities of the Mediterranean rocky coast: ecology and biotechnological potential

“…Although there are previous studies regarding microbial communities that inhabit the supralittoral zone and some authors have worked on the improvement of enriched media to increase the cultivability of these microorganisms [5][6][7][8][9][10][11], there is not and in-depth characterization of both their ecology and biotechnological potential at the same time. The extreme conditions those communities have to deal with as a result of living in the interphase between the aquatic and terrestrial worlds make them a good target for the search of biotechnologically-relevant microorganisms.…”