Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils

Abstract

SummaryDespite the apparent severity of the environmental conditions in the McMurdo Dry Valleys, Eastern Antarctica, recent phylogenetic studies conducted on mineral soil samples have revealed the presence of a wide diversity of microorganisms, with actinobacteria representing one of the largest phylotypic groups. Previous metagenomic studies have shown that the majority of Antarctic actinobacterial populations are classified as 'uncultured'. In this study, we assessed the diversity of actinobacteria in Antarctic cold desert soils by complementing traditional culture-based techniques with a metagenomic study. Phylogenetic analysis of clones generated with actinobacteriumand streptomycete-specific PCR primers revealed that the majority of the phylotypes were most closely related to uncultured Pseudonocardia and Nocardioides species. Phylotypes most closely related to a number of rarer actinobacteria genera, including Geodermatophilus, Modestobacter and Sporichthya, were also identified. While complementary culturedependent studies isolated a number of Nocardia and Pseudonocardia species, the majority of the cultured isolates (> 80%) were Streptomyces speciesalthough phylotypes affiliated to the genus Streptomyces were detected at a low frequency in the metagenomic study. This study confirms that Antarctic Dry Valley desert soil harbours highly diverse actinobacterial communities and suggests that many of the phylotypes identified may represent novel, uncultured species.

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau

“…Some of the bacterial autotroph lineages observed in the current study were similar to those detected in agricultural soils, e.g., Rhizobiales and Burkholderiales, while Actinomycetales abundantly observed in the alpine grassland soils did not occur in agricultural soils (Xiao et al 2014a;Wu et al 2014a). Numerous species of Actinomycetales were reported to be cold adapted and could grow at or below 0°C and were observed in Antarctic soils (Babalola et al 2009). Rhizobiales consisted of Bradyrhizobium, Starkeya, Rhizobium, and Mesorhizobium which were reported to degrade diverse organic matters and are typical symbiotic rhizobia that establish an N 2 -fixing symbiosis with its legume host soybean (Borodina et al 2005;Gourion et al 2011;Singh and Tabita 2010).…”

Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats

“…The variability in the environmental factors, together with the less than ideal levels of nutrients required for biological activity, severely restrict microbial communities in polar environments. In the absence of other photoautotrophic clades, it is accepted that cyanobacteria are largely responsible for providing the most important ecosystem services, and that cyanobacterial autotrophy supports substantial and diverse populations of heterotrophic microorganisms (such as Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes) together with smaller numbers of organisms in higher trophic levels (Aislabie et al 2006;Babalola et al 2009;Chan et al 2012;Stomeo et al 2012;Makhalanyane et al 2013a;de los Rios et al 2014;Yung et al 2014).…”

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

“…However, microscopic observations and mathematical modeling estimates that 99 % of bacteria are non-culturable under standard laboratory conditions [8]. Different studies have been focused on the diversity of uncultured microorganisms in this inhospitable habitat [1,9,10].…”