Abstract
Recent metagenomic surveys of microbial community suggested that species associated with the class Acidimicrobiia are abundant in diverse aquatic environments such as acidic mine water, waste water sludge, freshwater, or marine habitats, but very few species have been cultivated and characterized. The current taxonomic framework of Acidimicrobiia is solely based on 16S rRNA sequence analysis of few cultivable representatives, and no molecular, biochemical, or physiological characteristics are known that can distinguish species of this class from the other bacteria. This study reports the phylogenomic analysis for 20 sequenced members of this class and reveals another three major lineages in addition to the two recognized families. Comparative analysis of the sequenced Acidimicrobiia species identified 15 conserved signature indels (CSIs) in widely distributed proteins and 26 conserved signature proteins (CSPs) that are either specific to this class as a whole or to its major lineages. This study represents the most comprehensive phylogenetic analysis of the class Acidimicrobiia and the identified CSIs and CSPs provide useful molecular markers for the identification and delineation of species belonging to this class or its subgroups.
Highlights
The class Acidimicrobiia is a deep-rooting lineage within the phylum Actinobacteria
Phylogenetic Analysis of the Class Acidimicrobiia Based on Combined Protein Dataset and 16S rRNA Trees
Our analysis identified two conserved signature indels (CSIs) that are shared by members of Acidimicrobiaceae, namely A. ferrooxidans, F. acidiphilum, F. thermotolerans, and Acidithrix ferrooxidans
Summary
The class Acidimicrobiia is a deep-rooting lineage within the phylum Actinobacteria. This class is comprised of few cultivable representatives that were mostly isolated from extremely acidic environments (Zhi et al, 2009; Gao and Gupta, 2012b; Ludwig et al, 2012). Four type species of this class namely, Acidimicrobium ferrooxidans, Acidithrix ferrooxidans, Ferrimicrobium acidiphilum, and Ferrithrix thermotolerans are extremely acidophilic, with optimal growth pH at around 2.0, and are able to oxidize ferrous iron at relatively fast rates (Cleaver et al, 2007; Ludwig et al, 2012; Norris, 2012). These species were mainly isolated from acidic mine waters or geothermal sites, and were responsible for the regeneration of ferric iron within the acidic ecosystem (Clark and Norris, 1996; Johnson et al, 2009; Jones and Johnson, 2015). Neutrophilic Iamia majanohamensis was isolated from the abdominal epidermis of a sea cucumber, filamentous “Candidatus Microthrix parvicella” ( called M. parvicella) from wastewater sludge, while members of the genus Ilumatobacter from estuary sediment or seashore sand (Kurahashi et al, 2009; Matsumoto et al, 2009; Mcllroy et al, 2013)
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