Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost. Issue 10 (1st September 2021)

• Record Type: Journal Article
• Authors: Varliero, Gilda; Rafiq, Muhammad; Singh, Swati; Summerfield, Annabel; Sgouridis, Fotis; Cowan, Don A; Barker, Gary
• Is Part Of: FEMS microbiology ecology. Volume 97:Issue 10(2021)
• Publication Date: 2021-09-01
• Subjects: cold-adapted proteins -- soil metagenomics -- soil metatranscriptomics -- permafrost -- Greenland Ice Sheet (GrIS) -- bioengineering; Microbial ecology -- Periodicals; Microbiology -- Periodicals; 579.17
• DOI: 10.1093/femsec/fiab127
• Languages: English
• ISSNs: 0168-6496

Abstract

ABSTRACT: Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering. Abstract : Permafrost active layer shows similar microbial communities along a proglacial transect in southwest Greenland, and was used to create the Cold-Adapted Predicted Protein (CAPP) database.