Novel Culturing Techniques Select for Heterotrophs and Hydrocarbon Degraders in a Subantarctic Soil

Abstract

The soil substrate membrane system (SSMS) is a novel micro-culturing technique targeted at terrestrial soil systems. We applied the SSMS to pristine and diesel fuel spiked polar soils, along with traditional solid media culturing and culture independent 454 tag pyrosequencing to elucidate the effects of diesel fuel on the soil community. The SSMS enriched for up to 76% of the total soil diversity within high diesel fuel concentration soils, in contrast to only 26% of the total diversity for the control soils. The majority of organisms originally recovered with the SSMS were lost in the transfer to solid media, with all 300 isolates belonging to Proteobacteria, Firmicutes, Actinobacteria or Bacteroidetes, the four phyla most frequently associated with soil culturing efforts. The soils spiked with high diesel fuel concentrations exhibited reduced species richness, diversity and a selection towards heterotrophs and hydrocarbon degraders in comparison to the control soils. Based on these observations and the unusually high level of overlap in microbial taxa observed between methods, we suggest the SSMS holds potential to exploit hydrocarbon degraders and other targets within simplified bacterial systems, yet is inadequate for soil ecology and ecotoxicology studies where identifying rare oligotrophic species is paramount.

Insight into heavy metal resistome of soil psychrotolerant bacteria originating from King George Island (Antarctica)

“…The diversity of cultivable bacteria identified in this study was biased toward Gram-negative strains, mostly belonging to the Proteobacteria phylum. This is in good agreement with several previous studies concerning identification of cultivable bacteria from Antarctica (Zdanowski et al 2004(Zdanowski et al , 2013van Dorst et al 2016). Notably, almost 25% of bacterial strains isolated in this study belonged to Actinobacteria phylum, and bacteria representing this group are commonly isolated from Antarctic soils (Smith et al 2006;Zdanowski et al 2013;Cowan et al 2014;Pudasaini et al 2017).…”

Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods

“…It is well established that very low percentages of bacteria have been recovered into pure culture (Handelsman, 2004; Ferrari et al, 2008), and here 1.7% of the total bacteria diversity was recovered into artificial media. This recovery increased to 34% within the SSMS enrichments, highlighting the potential of this approach to recover novel species (van Dorst et al, 2016). This is comparable to the recovery of 50% of total bacterial diversity using the ichip method (a similar culturing technique) described by Nichols et al (2010).…”

“…The absence of consistency between techniques, or a “culture clash” has been consistently observed between clone libraries and cultivation attempts (Maturrano et al, 2006). Previously, higher community diversity (2.4% of bacterial and 8.2% of fungal communities) has been shared between artificial media and tag pyrosequencing from hydrocarbon contaminated soils(Stefani et al, 2015; van Dorst et al, 2016). The rapid growth of microfungi, particularly yeasts on the SSMS may have occurred following the addition of water to the soils (Vishniac, 1996) with freely available water potentially aiding the germination of spores.…”

“…The excessive supply of nutrients in the artificial media often selects for fast-growing fungi and bacteria and to address this problem in soil, a simulated environment that mimics the natural soil environment called the soil slurry membrane system (SSMS) was developed (Ferrari et al, 2005). The diffusion chamber approach relies on the use of soil as the substrate for growth and has been found to enrich for members from a diversity of cultured and uncultured bacterial phyla, including the Saccharibacteria, better known as Candidate division TM7 (van Dorst et al, 2016). While the approach has been adopted to enrich for bacteria, the suitability of the method to select for fungi is not yet known.…”

Isolation and Characterization of Phenanthrene Degrading Bacteria from Diesel Fuel-Contaminated Antarctic Soils

“…These physical and chemical changes promote rearrangements in the soil bacterial communities as well, with Proteobacteria from Burkholderia, Sphingomonas and specially Pseudomonas species heavily dominating over bacteria from Bacteroidetes, Cyanobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Verrucomicrobia, and other phyla which compose the normal inhabitants non-polluted Antarctic soils. Altogether, this results in a significant decrease in species richness and evenness, and a large decline in soil biodiversity of contaminated soils (Saul et al, 2005 ; van Dorst et al, 2014 , 2016 ).…”