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. 2023 Jan 20:14:1109549.
doi: 10.3389/fmicb.2023.1109549. eCollection 2023.

Genomic-based phylogenetic and metabolic analyses of the genus Natronomonas, and description of Natronomonas aquatica sp. nov

Alicia García-Roldán  1 , Ana Durán-Viseras  1 , Rafael R de la Haba  1 , Paulina Corral  2 , Cristina Sánchez-Porro  1 , Antonio Ventosa  1
Affiliations

Genomic-based phylogenetic and metabolic analyses of the genus Natronomonas, and description of Natronomonas aquatica sp. nov

Alicia García-Roldán et al. Front Microbiol. .

Abstract

The genus Natronomonas is classified on the family Haloarculaceae, within the class Halobacteria and currently includes six species isolated from salterns, saline or soda lakes, and salt mines. All are extremely halophilic (optimal growth at 20-25% [w/v] NaCl) and neutrophilic, except Natronomonas pharaonis, the type species of the genus, that is haloalkaliphilic (showing optimal growth at pH 9.0) and possesses distinct phenotypic features, such as a different polar lipid profile than the rest of species of the genus. We have carried out a genome-based study in order to determine the phylogenetic structure of the genus Natronomonas and elucidate its current taxonomic status. Overall genomic relatedness indexes, i.e., OrthoANI (Average Nucleotide Identity), dDDH (digital DNA-DNA hybridization), and AAI (Average Amino acid Identity), were determined with respect to the species of Natronomonas and other representative taxa of the class Halobacteria. Our data show that the six species of Natronomonas constitute a coherent cluster at the genus level. Besides, we have characterized a new haloarchaeon, strain F2-12T, isolated from the brine of a pond of a saltern in Isla Cristina, Huelva, Spain, and we determined that it constitutes a new species of Natronomonas, for which we propose the name Natronomonas aquatica sp. nov. Besides, the metabolic analysis revealed a heterotrophic lifestyle and a versatile nitrogen metabolism for members of this genus. Finally, metagenomic fragment recruitments from a subset of hypersaline habitats, indicated that the species of Natronomonas are widely distributed in saline lakes and salterns as well as on saline soils. Species of this haloarchaeal genus can be considered as ubiquitous in intermediate to high salinity habitats.

Keywords: Natronomonas; extremophiles; haloarchaea; hypersaline environments; metabolism; phylogenomics; polar lipids; salterns.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be constructed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Approximately maximum-likelihood phylogenomic tree reconstruction based on the translated core orthologous genes of members of the genus Natronomonas, including strain F2-12T and related species. This tree was obtained after the alignment and concatenation of the translated sequences of 870 shared orthologous single-copy genes of these genomes. Bootstrap values higher than 70% are indicated at branch points. Bar, 0.1 substitutions per nucleotide position.
Figure 2
Figure 2
Average Amino acid Identity (AAI) percentages among the species of the genus Natronomonas, including strain F2-12T, and other related haloarchaeal genera. Strains: 1, Natronomonas aquatica F2-12T (GCA_024449025.1); 2, Natronomonas pharaonis DSM 2160T (GCA_000026045.1); 3, Natronomonas gomsonensis JCM 17867T (GCA_013391635.1); 4, Natronomonas halophila C90T (GCA_013391085.1); 5, Natronomonas moolapensis 8.8.11T (GCA_000591055.1); 6, Natronomonas salina YPL13T (GCA_013391105.1); 7; Natronomonas salsuginis F20-122T (GCA_005239135.1); 8, Halapricum salinum CBA1105T (GCA_004799665.1); 9, Haloarcula vallismortis ATCC 29715T (GCA_000337775.1); 10, Halomicroarcula pellucida JCM 17820T (GCA_014647235.1); 11, Halomicrobium mukohataei DSM 12286T (GCA_000023965.1); 12, Halorhabdus utahensis DSM 12940T (GCA_000023945.1); 13, Halorientalis regularis IBRC-M 10760T (GCA_9001023 05.1); 14, Halosimplex carlsbadense 2-9-1T (GCA_000337455.1).
Figure 3
Figure 3
Maximum-parsimony phylogenetic tree based on the comparison of the 16S rRNA gene sequences showing the relationship between strain F2-12T, the species of the genus Natronomonas and other related haloarchaeal genera. The sequence accession numbers are shown in parentheses. Bootstrap values equal or higher than 70% are indicated above the nodes. Black circles indicate that the corresponding nodes were also obtained in the trees generated with the maximum-likelihood and neighbor-joining algorithms. Haloferax mediterranei ATCC 33500T was used as outgroup. Bar, 0.01 substitutions per nucleotide position.
Figure 4
Figure 4
Maximum-parsimony phylogenetic tree based on the comparison of rpoB’ gene sequences showing the phylogenetic relationship between strain F2-12T, the species of the genus Natronomonas and other related haloarchaeal genera. The sequences accession numbers are shown in parentheses. Bootstrap values equal or higher than 70% are indicated above the nodes. Black circles indicate that the corresponding nodes were also obtained in the trees generated with the maximum-likelihood and neighbor-joining algorithms. Haloferax mediterranei ATCC 33500T was used as outgroup. Bar, 0.01 substitutions per nucleotide position.
Figure 5
Figure 5
Average Nucleotide Identities (orthoANI) and digital DNA–DNA hybridization (dDDH) calculated by the Genome-to-Genome Distance Calculator (GGDC) percentages of strain F2-12T, the species of the genus Natronomonas and other related genera. Strains: 1, Natronomonas aquatica F2-12T (GCA_024449025.1); 2, Natronomonas pharaonis DSM 2160T (GCA_000026045.1); 3, Natronomonas gomsonensis JCM 17867T (GCA_013391635.1); 4, Natronomonas halophila C90T (GCA_013391085.1); 5, Natronomonas moolapensis 8.8.11T (GCA_000591055.1); 6, Natronomonas salina YPL13T (GCA_013391105.1); 7; Natronomonas salsuginis F20-122T (GCA_005239135.1); 8, Halapricum salinum CBA1105T (GCA_004799665.1); 9, Haloarcula vallismortis ATCC 29715T (GCA_000337775.1); 10, Halomicroarcula pellucida JCM 17820T (GCA_014647235.1); 11, Halomicrobium mukohataei DSM 12286T (GCA_000023965.1); 12, Halorhabdus utahensis DSM 12940T (GCA_000023945.1); 13, Halorientalis regularis IBRC-M 10760T (GCA_9001023 05.1); 14, Halosimplex carlsbadense 2-9-1T (GCA_000337455.1).
Figure 6
Figure 6
Recruitment plots of Natronomonas aquatica F2-12T against different metagenomic datasets: (A) SS13, (B) SS19, (C) SS33, (D) SS37, (E) LM18, (F) LM30, (G) IC21, (H) SMO1, and (I) SMO2. In each panel the Y axis represents the identity percentage and X axis represents the genome length. The black dashed line shows the threshold for the presence of same species (95% identity). Abbreviations: SS13: metagenome from Santa Pola saltern (Spain) with 13% salinity (SRX328504; Fernández et al., 2014a), SS19: metagenome from Santa Pola saltern (Spain) with 19% salinity (SRX090228; Ghai et al., 2011), SS33: metagenome from Santa Pola saltern (Spain) with 33% salinity (SRX347883; Fernández et al., 2013), SS37: metagenome from Santa Pola saltern (Spain) with 37% salinity (SRX090229; Ghai et al., 2011), LM18: metagenome from Lake Meyghan (Iran) with 18% salinity (ERS1455390; Naghoni et al., 2017), LM30: metagenome from Lake Meyghan (Iran) with 30% salinity (ERS1455391; Naghoni et al., 2017), IC21: metagenome from Isla Cristina saltern (Spain) with 21% salinity (Fernández et al., 2014b,c), SMO1: metagenome from Odiel saltmarshes hypersaline soil, 24 mS/cm conductivity (SRR5753725; Vera-Gargallo and Ventosa, 2018), SMO2: metagenome from Odiel saltmarshes hypersaline soil, 54 mS/cm conductivity (SRR5753724; Vera-Gargallo and Ventosa, 2018).
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