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MAG binning and general featuresFrom the four hot springs, we assembled four associated metagenomes and then binned a total of 42 MAGs. We recovered 12 MAGs from RB10 hot spring, 13 from RB13, 14 from RB32 and 3 from RB108. Out of these 42 MAGs, 7 were of high-quality, 25 of nearly-high quality, 9 of medium quality and 1 of low quality (Table 1) based on metagenomic standards26. The GC% was quite variable, ranging from 25.76 to 70.35% among all MAGs and between 32.15 and 69.21% only among the high- and near high-quality MAGs. With the exception of RB108 from which we only recovered bacterial MAGs, we retrieved both bacterial and archaeal MAGs in the other hot springs. Two thirds of the MAGs (26/42) were assigned to the domain Bacteria and the rest to the domain Archaea (16/42) (Table 2).Table 1 General characteristics of the 42 MAGs obtained from RB10, RB13, RB32 and RB108 samples.Full size tableTable 2 Classification of the MAGs based on the taxonomic classification of GTDB-Tk software (v2.1.0) and the Genome Taxonomy Database (07-RS207 release).Full size tableTaxonomic and phylogenomic analyses of MAGsThe taxonomic affiliation of the MAGs was investigated in detail through the workflow classify of GTDB-Tk (v 2.1.0; GTDB reference tree 07-RS207) (Table 2) and through de novo phylogenomic analyses (Fig. S1a–i). We also tried to classify MAGs on the basis of overall genome relatedness indices (OGRI), which is detailed in supplementary material (Text S1, Table S2, Fig. S2).De novo phylogenomic analyses globally confirmed the positioning of MAGs provided by GTDB-Tk, with high branching support. For Bacteria, GTDB-Tk analyses allowed us to place the MAGs in the following clades: six in the phylum Aquificota from the four different springs, comprising four MAGs belonging to the genus Hydrogenivirga (family Aquificaceae) (RB10-MAG07, RB13-MAG10, RB32-MAG07, RB108-MAG02), and two belonging to the family ‘Hydrogenobaculaceae’ (RB10-MAG12, RB32-MAG11) (Table 2, Fig. S1a). Their closest cultured relatives originated either from hot springs or from deep-sea hydrothermal vents27. Three MAGs from three geothermal springs belonged to the phylum Armatimonadota (RB10-MAG03, RB13-MAG04, RB32-MAG03) and had no close cultured relatives. Seven MAGs have been classified into the phylum Chloroflexota: three MAGs belonging to the genus Thermoflexus from three different springs (RB10-MAG04, RB13-MAG05, RB32-MAG02), one affiliating with the genus Thermomicrobium (RB32-MAG08), one falling into the family Ktedonobacteraceae (RB108-MAG03), one belonging to the class Dehalococcoidia (RB32-MAG04) and another one whose phylogenetic position is more difficult to assert because it is a MAG of medium quality (RB32-MAG14). Six MAGs from four various hot springs belonged to the phylum Deinococcota, and to the genera Thermus (RB10-MAG08, RB10-MAG11, RB13-MAG09, RB32-MAG10, RB108-MAG01) and Meiothermus (RB13-MAG13). One MAG belonged to the family ‘Sulfurifustaceae’ (RB13-MAG01), in the phylum Proteobacteria (Gamma-class). The MAG referenced as RB32-MAG13 was classified into the phylum ‘Patescibacteria’, in the class ‘Paceibacteria’, and was distantly related to MAGs originating from groundwater and from hot springs. Finally, two MAGs from two different springs belonged to the phylum WOR-3, in the Candidatus genus ‘Caldipriscus’ (RB32-MAG12, RB10-MAG09).For Archaea, almost all the MAGs reconstructed in this study, e.g. 15 of the 16 archaeal MAGs, belonged to the phylum Thermoproteota. Among them, four belonged to the genus Ignisphaera (RB10-MAG05, RB13-MAG08, RB13-MAG11, RB32-MAG05), three to the genus Infirmifilum (RB10-MAG06, RB13-MAG03, RB32-MAG09), two to the genus Zestosphaera (RB10-MAG02, RB13-MAG06), three to the family Acidilobaceae (RB10-MAG01, RB13-MAG02, RB32-MAG01) and two to the order Geoarchaeales (RB10-MAG10, RB32-MAG06). Additionally, one belonged to the family Thermocladiaceae (RB13-MAG07). Lastly, the MAG belonging to another phylum (RB13-MAG12) was affiliated with the ‘Aenigmatarchaeota’, class ‘Aenigmatarchaeia’, and was distantly related to MAGs from hot springs and from deep-sea hydrothermal vent sediments28,29.Out of these 42 MAGs, at least 19 MAGs corresponded to different taxa at the taxonomic rank of species or higher according to GTDB (Table 2). Eighteen of them belonged to lineages with several cultivated representatives including the species Thermus thermophilus. 13 new genomic species within the GTDB genera Hydrogenivirga, HRBIN17, Thermoflexus, SpSt-223, CADDYT01, Zestosphaera, Ignisphaera, Infirmifilum, Thermus, Thermus_A, Meiothermus_B, JAHLMO01 and Caldipriscus, and 6 putative new genomic genera belonging to the GTDB families Hydrogenobaculaceae, Acidilobaceae, WAQG01, Thermocladiaceae, Sulfurifustaceae and HR35 could be identified (Table 2). In addition, 9 MAGs belonged to lineages that are predominantly or exclusively known through environmental DNA sequences. Thus, these 42 MAGs comprised a broad phylogenetic range of Bacteria and Archaea at different levels of taxonomic organization, of which a large majority were not reported before.The approaches implemented here were not intended to describe the microbial diversity present in these sources in an exhaustive way or to compare them in a fine way, and cannot allow it because of a 2-year storage at 4 °C. This long storage has probably led to changes in the microbial communities and to the selective loss or enrichment of some taxa. As a result, no analysis of abundance or absence of taxa can be conducted from these metagenomes and the results are discussed taking this bias into account. However, they do provide an overview of the microbial diversity effectively present. If we compare the phylogenetic diversity of the MAGs found in the four hot springs, we can observe that 3 shared phyla (Deinococcota, Aquificota and Chloroflexota: phyla names according to GTDB), 2 shared families (Thermaceae and Aquificaceae), and one shared genus (Hydrogenivirga) were found among the four sources (Fig. 2). In addition, hot springs RB10, RB13 and RB32, that are geographically close ( More