Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic.

Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples.

The total community genomic DNA (gDNA) from permafrost was extracted using four commercial DNA extraction kits. The gDNAs were compared using quantitative real-time PCR (qPCR) targeting 16S rRNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16S rRNA (V3 region) amplified in single or nested PCR. The FastDNA(®) SPIN (FDS) Kit provided the highest gDNA yields and 16S rRNA gene concentrations, followed by MoBio PowerSoil(®) (PS) and MoBio PowerLyzer™ (PL) kits. The lowest gDNA yields and 16S rRNA gene concentrations were from the Meta-G-Nome™ (MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted UniFrac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed ß- and γ-Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that gDNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using gDNAs from the three bead-beating lysis extraction kits.

Magnetic gamma-Fe(2)O(3) nanoparticles coated with poly-l-cysteine for chelation of As(III), Cu(II), Cd(II), Ni(II), Pb(II) and Zn(II).

Poly-l-cysteine (PLCys(n)) (n=20) was immobilized onto the surface of commercially available magnetic gamma-Fe(2)O(3) nanoparticles, and its use as a selective heavy metal chelator was demonstrated. Magnetic nanoparticles are an ideal support because they have a large surface area and can easily be retrieved from an aqueous solution. PLCys(n) functionalization was confirmed using FTIR and the quantitative Ellman's test. Metal binding capacities for As(III), Cd(II), Cu(II), Ni(II), Pb(II) and Zn(II) were determined at pH 7.0 and compared to adsorption capacities for unfunctionalized gamma-Fe(2)O(3) nanoparticles. The effect of pH on the PLCys(n) functionalized nanoparticles was also investigated. For all of the metals examined, binding capacities (mumol metal/g support) were more than an order of magnitude higher than those obtained for PLCys(n) on traditional supports. For As(III), Cu(II), Ni(II) and Zn(II), the binding capacities were also higher than the metal adsorption capacities of the unfunctionalized particles. Metal uptake was determined to be rapid (< 2.5 min) and metal recoveries of >50% were obtained for all of the metals except As(III). PLCys(n), which has a general metal selectivity towards soft metals acids, was chosen to demonstrate the proof of concept. Greater metal selectivity may be achievable through the use of combinatorial peptide library screening or by using peptide fragments based on known metal binding proteins.