Novel Psychrophiles and Exopolymers from Permafrost Thaw Lake Sediments

Abstract

Thermokarst lakes are one of the most abundant types of microbial ecosystems in the circumpolar North. These shallow basins are formed by the thawing and collapse of ice-rich permafrost, with subsequent filling by snow and ice melt. Until now, permafrost thaw lakes have received little attention for isolation of microorganisms by culture-based analysis. The discovery of novel psychrophiles and their biomolecules makes these extreme environments suitable sources for the isolation of new strains, including for potential biotechnological applications. In this study, samples of bottom sediments were collected from three permafrost thaw lakes in subarctic Québec, Canada. Their diverse microbial communities were characterized by 16S rRNA gene amplicon analysis, and subsamples were cultured for the isolation of bacterial strains. Phenotypic and genetic characterization of the isolates revealed affinities to the genera Pseudomonas, Paenibacillus, Acinetobacter,Staphylococcus and Sphingomonas. The isolates were then evaluated for their production of extracellular enzymes and exopolymers. Enzymes of potential biotechnological interest included α and β-glucosidase, α and β-maltosidase, β-xylosidase and cellobiohydrolase. One isolate, Pseudomonas extremaustralis strain 2ASCA, also showed the capability to produce, in the loosely bound cell fraction, a levan-type polysaccharide with a yield of 613 mg/L of culture, suggesting its suitability as a candidate for eco-sustainable alternatives to commercial polymers.

Keywords: Pseudomonas; bacterial diversity; exopolysaccharides; lake sediments; microbial ecology; permafrost thaw lake; psychrophiles; subarctic.

Figure 1

Bacterial community composition determined by Illumina MiSeq 16S rRNA gene sequencing. Only operational taxonomy units (OTUs) with a relative proportion of >1% are shown.

Figure 2

Neighbor-joining tree showing the phylogenetic position of bacterial strains isolated in the present study and the closest relatives based on partial 16S rRNA gene sequences, reconstructed using the Kimura 2-parameter method with 1000 bootstrap replications. The scale represents a genetic distance of 0.02 nucleotide substitutions per site.

Figure 3

1D-NMR analysis of the Lev_2ASCA polymer: ¹H (upper) and ¹³C (lower) traces were recorded with a 600 MHz Bruker spectrometer. The x-axis for each spectrum were in chemical shifts reported as parts per million (ppm) with reference to D₂O and to CD₃OD for ¹H and ¹³C spectrum, respectively.

Figure 4

2D-NMR analysis of the Lev_2ASCA polymer: The HSQC spectrum was recorded with a 600 MHz Bruker spectrometer.