Search

Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.

Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.

Figure S1. Geographical distribution of the six locations studied here and their inter-location distances (given in the table). The distances given in each location refer to Mallorca. The hypersaline here are: Mallorca (Es Trenc and S’Avall and separated by 3.5 km) and Santa Pola in Spain, Fără Fund in Romania, Great Salt Lake (USA), Pampa (Laguna Colorada Chica and Laguna Colorada Grande, separated by 23 Km), and Lake Grassmere (New Zealand). Table S1. Statistics of Salinibacter MAGs recovered using different bioinformatic tools. MAGs selected for further analysis and taxonomic classification are marked in red. Text S1: In addition to the taxonomic study, here we assessed the different tools SPADES and MegaHIT assemblers, and MetaBAT binning tools selecting contigs with length > 2,000 pbs or > 5,000 pbs to retrieve the best quality MAG (Sup. Table S1). We observed that different tools and combinations rendered different qualities of the MAGs. The selection of contigs with length > 5,000 pbs binning rendered MAGs with a lower genome size, lower completeness and similar contamination. From the FF metagenome (Romania), the highest quality MAG was retrieved using the assembler SPADES and MetaBAT binning tool using a minimum contig length of 2,000 pbs. From CCH and CG metagenomes (Argentina), the highest quality MAGs were retrieved using the assembler MegaHIT and MetaBAT binning tool using a minimum contig length of 2,000 pbs (Sup. Table S1). Figure S2. Genomic clustering based on Average Amino-acid Identity (AAI) of genomes included in the study. Figure S3. Pangenome hierarchical clustering based on the presence (grey) or absence (black) of orthologous genes. Table S2. Pangenome statistics between genomes belonging to the same species. Table S3: CRISPR-Cas systems found in the Salinibacter pepae and Salinibacter grassmerensis genomes. Table S4. Cell morphologies of the new isolates. All cells have been cultivated onto MA agar. for 10 days at 12ºC. The morphology was ob