A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands

Abstract

The Kerguelen Islands, located in the southern part of the Indian Ocean, are very isolated geographically. The microbial diversity and communities present on the island, especially associated to geothermal springs, have never been analyzed with high-throughput sequencing methods. In this article, we performed the first metagenomics analysis of microorganisms present in Kerguelen hot springs. From four hot springs, we assembled metagenomes and recovered 42 metagenome-assembled genomes, mostly associated with new putative taxa based on phylogenomic analyses and overall genome relatedness indices. The 42 MAGs were studied in detail and showed putative affiliations to 13 new genomic species and 6 new genera of Bacteria or Archaea according to GTDB. Functional potential of MAGs suggests the presence of thermophiles and hyperthermophiles, as well as heterotrophs and primary producers possibly involved in the sulfur cycle, notably in the oxidation of sulfur compounds. This paper focused on only four of the dozens of hot springs in the Kerguelen Islands and should be considered as a preliminary study of the microorganisms inhabiting the hot springs of these isolated islands. These results show that more efforts should be made towards characterization of Kerguelen Islands ecosystems, as they represent a reservoir of unknown microbial lineages.

Figure 1

Sampling locations at the plateau des Fumerolles in the Rallier du Baty Peninsula (Kerguelen Islands, French Southern and Antarctic Lands), and photographs of the four hot springs studied here with their associated temperature and pH conditions. The world map and details of the Kerguelen seashore were generated using the ‘cowplot’, ‘ggplot2’, ‘lwgeom’, ‘rnaturalearth’, ‘rnaturalearthdata’, ‘rworldmap’, ‘sf’ and ‘tidyverse’ libraries implemented on the RStudio software (v1.2.5001). A 2018 map of the Kerguelen islands was retrieved from the French national portal of maritime limits (http://limitesmaritimes.gouv.fr/) according to the 2017 Etalab open license (v2.0—https://www.etalab.gouv.fr/). Pictures depicting sampling sites were taken by Marc Le Romancer. Layout was carried out using the free open source vector image editor Inkscape (v1.0).

Figure 2

Venn diagrams showing the shared phyla, families and genera according to GTDB classification in the reconstructed MAGs from the hot springs RB10, RB13, RB32 and RB108.

Figure 3

Metabolic pathway diagram of the 42 MAGs based on KEGG Decoder annotations, showing MAG classification according to GTDB-Tk and estimated genome completion.