Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

Abstract

SUMMARY The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades ( viz ., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia ) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria . The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria -specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria .

Taxonomy, Physiology, and Natural Products of Actinobacteria

“…The order Actinomycetales is now restricted to the members of the family Actinomycetaceae, and the other suborders that were previously part of this order are now designated distinct orders (19). Consequently, 43 of the 53 families within the phylum Actinobacteria are assigned to a single class, Actinobacteria, whereas the other five classes together contain only 10 families (21).…”

“…That update eliminated the taxonomic ranks of subclasses and suborders, elevating the former subclasses and suborders to the ranks of classes and orders, respectively (19). The phylum is thus divided into six classes: Actinobacteria, Acidimicrobiia, Coriobacteriia, Nitriliruptoria, Rubrobacteria, and Thermoleophilia.…”

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

“…Such a coherence appears all the more surprising in that the most responsive bacterial phyla, Actinobacteria and Acidobacteria, form broad, diverse groups that likely cover a wide metabolic range (Quaiser et al, 2003;Gao and Gupta, 2012). Our findings suggest that deep taxonomic nodes may constitute meaningful ecological units for the response to drying and rewetting.…”

Visualization of Imbalances in Sulfur Assimilation and Synthesis of Sulfur-Containing Amino Acids at the Single-Cell Level

“…The synthesis of both sulfurcontaining amino acids has been explored in C. glutamicum (6)(7)(8), and L-cysteine can be produced with Escherichia coli (9,10). C. glutamicum is not a pathogen but belongs with its close pathogenic relatives C. diphtheriae, C. ulcerans, and C. urealyticum to the large clade Corynebacteriales, which also includes the Mycobacterium species (11). Because of its ease of handling, C. glutamicum serves as a model organism for M. tuberculosis studies.…”