Brines, glacial ice and permafrost might contain DNA and RNA molecules that remain trapped inside for long geological eras, thus representing a key to reconstruct past ecosystems1. This work was aimed at analysing both the total bacterial community (TC) composition and its metabolically active fraction (AC) in Antarctic liquid brines. Samples were collected from two adjacent ice-covered lakes in Boulder Clay (BC-1 and BC2 from Lake-1, 2.5 and 0.95m depth, respectively; BC-3 from Lake-2, 2.0 m depth). DNA and RNA were extracted from each sample (150 to 600ml) and DNA/RNA libraries for Ion Torrent sequencing were prepared in triplicates by PCR using the engineered primers 27f and 338r. The sequencing process was provided with the Ion 314 chip. Raw data were analyzed using bioinformatics tools to determine the quality criteria of the reads. Bacterial functionality was characterized using a functional inference-based (predicting functional profiles from metagenomic 16S rRNA, Tax4Fun software) approach. Taxonomic differences among samples were explored via linear discriminant analysis effect size (LEfSe). The analysis of DNA sequences generally showed the predominance of Bacteroidetes (range 19.8-33.9%), followed by Proteobacteria (19.8-36.1%) and Actinobacteria (1.43-12.36%). Firmicutes and Cyanobacteria (0.36-0.96 and 0.3-6.5%, respectively) were less represented. The highest percentage of active bacteria (by the analysis of RNA sequences) was observed in BC3 (80.2%), whereas in BC1 and BC2 they accounted only for 6.0 and 1.7%, respectively. The AC was mainly represented by Bacteroidetes (range 8.8-57.7%), followed by Proteobacteria (16.4-22.7%), Actinobacteria (5.0-9.2%) and Firmicutes (0.5-10.1%). Despite AC in both BC1 and BC2 was at low percentages, such samples were characterized by a higher diversity than BC3. nMDS analysis highlighted that the AC in BC3 was dissimilar from those in BC1 and BC2, but it was similar to TC in BC2 and BC3. Finally, TC in BC1 clusterized separately from the other samples.
Study of bacterial communities in Antarctic brines (Boulder Clay, Northern Victoria Land) by a combination of 16S rRNA and 16S rDNA sequencing
Papale M;Azzaro M;La Ferla R;Lo Giudice A
2017
Abstract
Brines, glacial ice and permafrost might contain DNA and RNA molecules that remain trapped inside for long geological eras, thus representing a key to reconstruct past ecosystems1. This work was aimed at analysing both the total bacterial community (TC) composition and its metabolically active fraction (AC) in Antarctic liquid brines. Samples were collected from two adjacent ice-covered lakes in Boulder Clay (BC-1 and BC2 from Lake-1, 2.5 and 0.95m depth, respectively; BC-3 from Lake-2, 2.0 m depth). DNA and RNA were extracted from each sample (150 to 600ml) and DNA/RNA libraries for Ion Torrent sequencing were prepared in triplicates by PCR using the engineered primers 27f and 338r. The sequencing process was provided with the Ion 314 chip. Raw data were analyzed using bioinformatics tools to determine the quality criteria of the reads. Bacterial functionality was characterized using a functional inference-based (predicting functional profiles from metagenomic 16S rRNA, Tax4Fun software) approach. Taxonomic differences among samples were explored via linear discriminant analysis effect size (LEfSe). The analysis of DNA sequences generally showed the predominance of Bacteroidetes (range 19.8-33.9%), followed by Proteobacteria (19.8-36.1%) and Actinobacteria (1.43-12.36%). Firmicutes and Cyanobacteria (0.36-0.96 and 0.3-6.5%, respectively) were less represented. The highest percentage of active bacteria (by the analysis of RNA sequences) was observed in BC3 (80.2%), whereas in BC1 and BC2 they accounted only for 6.0 and 1.7%, respectively. The AC was mainly represented by Bacteroidetes (range 8.8-57.7%), followed by Proteobacteria (16.4-22.7%), Actinobacteria (5.0-9.2%) and Firmicutes (0.5-10.1%). Despite AC in both BC1 and BC2 was at low percentages, such samples were characterized by a higher diversity than BC3. nMDS analysis highlighted that the AC in BC3 was dissimilar from those in BC1 and BC2, but it was similar to TC in BC2 and BC3. Finally, TC in BC1 clusterized separately from the other samples.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
