Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth

Abstract

Ancient microbial communities of permafrost soils and frozen animal remains represent an archive that has barely been explored. This yet unexplored microbial world is a vast resource that can provide us with new evolutionary insights, metabolic pathways and novel chemistry. Here, we reveal that Actinobacteria isolated from a faecal sample from the intestinal tract of a 28,000-year-old Siberian mammoth are phylogenetically and metabolically distinct from currently known modern siblings. Ancient Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of the ancestors show a large phylogenetic distance to strains isolated today and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides a snapshot into Actinobacteria of the past, yielding unexplored genomic information that is not yet present in current databases.

Permafrost microbial communities follow shifts in vegetation, soils, and megafauna extinctions in Late Pleistocene NW North America

“…Rather our Bison , Mammuthus , and Discrotonyx sedaDNA has strong positive correlations here with Clavibacter , Amycolatopsis , Streptomyces , Micromonospora , Pseudonocardia , Methanobrevibacter , and Microlunatus . These species have been found previously to be associated with either cold/permafrost sediments (Deng et al., 2015; Gilichinsky et al., 2008; Wang, Wang, et al., 2021; Zaitseva et al., 2022) or Pleistocene megafauna (Jorns et al., 2020; van Bergeijk et al., 2022).…”

The impact of late Pleistocene mammal extinctions on pathogen richness in extant hosts

“…While there is limited empirical evidence of microbe diversification as a direct result of megafauna extinction, support for this mechanism comes from the theory of island biogeography (Heaney, 2000). Bergeijk et al (2022) recently showed the high degree of phylogenetic and metabolic dissimilarity between Actinobacteria from the gut of a 28,000year-old mammoth and modern members of this bacterial phylum. The authors highlight that these differences may be due to a low number of reference genomes available in certain Actinobacteria taxa.…”