Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity

Lichens are specific symbiotic organisms harboring various microorganisms in addition to the two classic partners (algae or cyanobacterium and fungus). Although lichens produce many antibiotic compounds such as (+)-usnic acid, their associated microorganisms possess the ability to colonize an environment where antibiosis exists. Here, we have studied the behavior of several lichen-associated bacterial strains in the presence of (+)-usnic acid, a known antibiotic lichen compound. The effect of this compound was firstly evaluated on the growth and metabolism of three bacteria, thus showing its ability to inhibit Gram-positive bacteria. This inhibition was not thwarted with the usnic acid producer strain Streptomyces cyaneofuscatus. The biotransformation of this lichen metabolite was also studied. An ethanolamine derivative of (+)-usnic acid with low antibiotic activity was highlighted with chemical profiling, using HPLC-UV combined with low resolution mass spectrometry. These findings highlight the way in which some strains develop resistance mechanisms. A methylated derivative of (+)-usnic acid was annotated using the molecular networking method, thus showing the interest of this computer-based approach in biotransformation studies.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Mabikibacter ruber Choi et al. 2017 is a later heterotypic synonym of Notoacmeibacter marinus Huang et al. 2017

The present study aimed to examine the taxonomic relationship between two alphaproteobacterial species, Mabikibacter ruber Choi et al. 2017 and Notoacmeibacter marinus Huang et al. 2017. Comparison of the 16S rRNA gene sequences revealed that they shared 99.9 % sequence similarity. Digital DNA-DNA hybridization (dDDH) estimate (79.8 %) and average nucleotide identity (ANI) value (97.8 %) compared between M. ruber YP382-1-A and N. marinus XMTR2A4^T, were both greater than the threshold for bacterial species delineation, strongly supporting the hypothesis that they represented a single species. Moreover, M. ruber YP382-1-A and N. marinus XMTR2A4^T shared similar physiological and biochemical properties and fatty acid profiles though they displayed distinct colony colours and other minor different properties, including genome size and ability to degrade cellulose, which were presumably due to the presence of a megaplasmid in the genome of M. ruber YP382-1-A. On the basis of the results of genomic analysis, phenotypic and physiological properties, and fatty acid composition, Mabikibacter ruber Choi et al. 2017 is a later heterotypic synonym of Notoacmeibacter marinus Huang et al. 2017 according to the priority of names determined by the date of original publication.