Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species

Citation: Straková, D.; Sánchez-Porro, C.; de la Haba, R.R.; Ventosa, A. Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species. Microorganisms 2024, 12, 334. https://doi.org/10.3390/ microorganisms12020334 Academic Editor: Hermann J. Heipieper Received: 29 December 2023 Revised: 24 January 2024 Accepted: 28 January 2024 Published: 5 February 2024 Copyright: © 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). microorganisms Article Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species Dáša Straková, Cristina Sánchez-Porro , Rafael R. de la Haba and Antonio Ventosa * Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain; [email protected] (D.S.); [email protected] (C.S.-P.); [email protected] (R.R.d.l.H.) *Correspondence: [email protected] Abstract: The genus Halomicroarcula, classified within the family Haloarculaceae, presently comprises eight haloarchaeal species isolated from diverse saline habitats, such as solar salterns, hypersaline soils, marine salt, and marine algae. Here, a detailed taxogenomic study and comparative genomic analysis of the genus Halomicroarcula was carried out. In addition, two strains, designated S1CR25-12 T and S3CR25-11 T , that were isolated from hypersaline soils located in the Odiel Saltmarshes in Huelva (Spain) were included in this study. The 16S rRNA and rpoB’ gene sequence analyses affiliated the two strains to the genus Halomicroarcula. Typically, the species of the genus Halomicroarcula possess multiple heterogeneous copies of the 16S rRNA gene, which can lead to misclassification of the taxa and overestimation of the prokaryotic diversity. In contrast, the application of overall genome relatedness indexes (OGRIs) augments the capacity for the precise taxonomic classification and categorization of prokaryotic organisms. The relatedness indexes of the two new isolates, particularly digital DNA–DNA hybridization (dDDH), orthologous average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that strains S1CR25-12 T (= CECT 30620 T = CCM 9252 T ) and S3CR25-11 T (= CECT 30621 T = CCM 9254 T ) constitute two novel species of the genus Halomicroarcula. The names Halomicroarcula saliterrae sp. nov. and Halomicroarcula onubensis sp. nov. are proposed for S1CR25-12 T and S3CR25-11 T , respectively. Metagenomic fragment recruitment analysis, conducted using seven shotgun metagenomic datasets, revealed that the species belonging to the genus Halomicroarcula were predominantly recruited from hypersaline soils found in the Odiel Saltmarshes and the ponds of salterns with high salt concentrations. This reinforces the understanding of the extreme halophilic characteristics associated with the genus Halomicroarcula. Finally, comparing pan-genomes across the twenty Halomicroarcula and Haloarcula species allowed for the identification of commonalities and differences between the species of these two related genera. Keywords: haloarchaea; hypersaline soil; taxogenomic analysis; comparative genomic analysis; pan-genome 1. Introduction Hypersaline soils are terrestrial ecosystems characterized by their high salt content, showing an electrical conductivity higher than 4 mS/cm [ 1 ]. However, their microbiota can be influenced by various factors beyond salt concentration, including temperature, pH, and the presence of high levels of toxic substances [ 2 , 3 ]. The Odiel Saltmarshes, a protected natural area located in southwestern Spain, harbor extensive areas of hypersaline soils, influenced by the confluence of the Odiel and Tinto rivers and the presence of tidal waters. This area contains elevated concentrations of metals (arsenic, cadmium, copper, lead, zinc) due to natural geological processes, such as accumulation through evaporation, and due to the historical metallurgical operations in this region [4,5]. The genus Halomicroarcula belongs to the family Haloarculaceae, order Halobacteriales and class Halobacteria, within the phylum Methanobacteriota (formerly “Euryarchaeota”), and Microorganisms 2024,12, 334. https://doi.org/10.3390/microorganisms12020334 https://www.mdpi.com/journal/microorganisms Microorganisms 2024,12, 334 2 of 20 it was first described in 2013 by Echigo et al. [ 6 ]. It currently contains eight halophilic species: Halomicroarcula pellucida (type species), Halomicroarcula amylolytica,Halomicroarcula laminariae,Halomicroarcula limicola,Halomicroarcula marina,Halomicroarcula nitratireducens, Halomicroarcula rubra, and Halomicroarcula salinisoli [ 7 ]. Besides, the species Halomicroarcula salina has been recently transferred to the genus Haloarcula, as Haloarcula salina [ 8 ]. Halomicroarcula species have been isolated from diverse habitats, such as solar salterns, saline soils, solar salt, marine seaweed, and salt mines [ 6 , 8 – 12 ]. They are extremely halophilic, showing optimal growth at 20–25% (w/v) NaCl. The cells of the species are motile, Gram-stain- negative, and pleomorphic. They are aerobic or facultatively anaerobic microorganisms [ 6 ]. Halomicroarcula species exhibit pink, red, or orange pigmentation or can be transparent [ 12 ]. The major polar lipids are phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and phosphatidylglycerol sulfate (PGS). Some species additionally possess a glycolipid chromatographically identical to sulfated diglycosil diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1) [6,9]. In this study, a comparative genomic analysis, insights into the ecological distribution across various hypersaline habitats, and a detailed taxogenomic study of the species of the genus Halomicroarcula as well as two new strains isolated from hypersaline soils of the Odiel Saltmarshes Natural Area located in Huelva (Southwest Spain) are presented. The new strains, designated as S1CR25-12 T and S3CR25-11 T , are described as two new haloarchaeal species, based on the phylogenetic, phenotypic, and chemotaxonomic characterization and the whole genome analysis. 2. Materials and Methods 2.1. Soil Sample Analysis and Isolation/Cultivation Conditions of Haloarchaeal Strains Strains S1CR25-12 T and S3CR25-11 T were isolated from a hypersaline soil located in the Odiel Saltmarshes, southwestern Spain, in July 2020 (Supplementary Figure S1). The physicochemical characteristics of the soil samples were examined, including pH and electrical conductivity, which were measured using a pH meter (CRISON BASIC 20) and a conductometer (CRISON 35+), respectively, after a 1:5 dilution. Additionally, soil samples, designated as 1C (37 ◦ 12 ′ 26.6 ′′ N 6 ◦ 57 ′ 52.5 ′′ W) and 3C (37 ◦ 13 ′ 18.0 ′′ N 6 ◦ 57 ′ 44.8 ′′ W), corresponding to the isolation places of the studied strains, were analyzed by Innoagral Laboratories, in Brenes (Sevilla, Spain) to assess their salinity-related ion contents and heavy metal concentrations determined by atomic absorption spectroscopy. Serial dilutions and plating techniques were carried out under sterile conditions, followed by incubation of the Petri dishes at 37 ◦ C for up to 3 months to isolate strains. After successive subculturing, they were obtained in a pure culture. To isolate and cultivate the strains, Reasoner’s 2A (R2A) medium (Difco, Beirut, Lebanon) was used, with the following composition per liter: yeast extract (0.5 g), proteose peptone no. 3 (0.5 g), casamino acids (0.5 g), dextrose (0.5 g), soluble starch (0.5 g), sodium pyruvate (0.3 g), dipotassium phosphate (0.3 g), and magnesium sulfate (0.05 g) containing 25% (w/v) total salts (designated as 25% R2A medium). This was prepared by diluting a 30% (w/v) stock salt solution [ 13 ], and it had the following composition per liter: NaCl (195 g), MgCl 2· 6H 2 O (32.5 g), MgSO 4· 7H 2 O (50.8 g), CaCl 2 (0.83 g), KCl (5.0 g), NaHCO 3 (0.17 g), and NaBr (0.58 g). The pH of the medium was adjusted to 7.5 with 1 M KOH, and when necessary, solid media were prepared by adding purified agar to a final concentration of 2% (w/v). Cultures were preserved at −80 ◦C in 25% R2A liquid medium containing 40% (v/v) glycerol for long-term storage. 2.2. DNA Extraction, Amplification, and Sequencing The Marmur methodology [ 14 ], modified for small volumes, was employed to extract the genomic DNA of strains S1CR25-12 T and S3CR25-11 T . The Bio-Rad T100 Thermal Cycler was used for PCR reactions to amplify the 16S rRNA and rpoB’ genes. For amplification of these genes, the universal archaeal primers ArchF and ArchR (5 ′ -TTC CGG TTG ATC CTG CCG GA-3 ′ , 5 ′ -GGT TAC CTT GTT ACG ACT T-3 ′ ) [ 15 , 16 ], as well as the rpoBF and rpoBR (5 ′ -TGT AAA ACG ACG GCC AGT TCG AAG AGC CGG ACG ACA TGG-3 ′ , 5 ′ -CAG GAA Microorganisms 2024,12, 334 3 of 20 ACA GCT ATG ACC GGT CAG CAC CTG BAC CGG NCC-3 ′ ) primers were selected [ 17 , 18 ]. The integrity of the genomic DNA and PCR amplicons was verified by 1% (w/v) agarose gel electrophoresis. To purify the genomic DNA and PCR products, the MEGAquick-spin TM Plus Fragment DNA Purification Kit (iNtRON Biotechnology, Seongnam, Republic of Korea) was used following the manufacturer’s instructions. The PCR reaction for amplifying the 16S rRNA gene involved denaturation of the prokaryotic DNAs at 95 ◦ C for 5 min, followed by 25 cycles of denaturation at 94 ◦ C for 1 min, primer hybridization at 50 ◦ C for 1 min, and extension at 72 ◦ C for 2 min. The reaction concluded with a final elongation step at 72 ◦ C for 10 min. The DNA concentration was measured using the Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), and the quality of the extracted DNA was assessed spectrophotometrically using the NanoDrop One spectrophotometer (Thermo Fisher Scientific). The PCR amplicons were sequenced using the Sanger chain-termination method by Stab Vida (Caparica, Portugal). Furthermore, Novogene Europe (Cambridge, UK) performed whole genome sequencing of strains S1CR25-12 T and S3CR25-11 T using the Illumina (San Diego, CA, USA) NovaSeq 6000 platform. 2.3. Phylogenetic and Phylogenomic Analyses The ChromasPro software (Technelysium Pty Ltd., Brisbane, Australia), version 1.5, was used to assemble the 16S rRNA and rpoB’ gene sequences of the isolated strains. These sequences were then compared with those available in the EzBioCloud database [ 19 ] and the NCBI GenBank database using the BLASTN search tool [ 20 ] to establish their taxonomic affiliation with phylogenetic neighbors. The alignment of the rpoB’ gene sequences was performed using the BioEdit program v.3.3.19.0 [ 21 ]. The ARB software v.7.0 [ 22 ] was employed for phylogenetic tree construction based on the sequence data of the 16S rRNA and rpoB’ genes. Maximum-likelihood [ 23 ], neighbor-joining [ 24 ], and maximum-parsimony algorithms [ 25 ] were used for phylogenetic tree reconstructions. The “gitana” script [ 26 ] was used for formatting and visualization of the phylogenetic trees. To estimate branch support in the phylogenetic treeing, a bootstrap analysis with 1000 replications was performed [ 27 ]. The 16S rRNA and rpoB’ gene sequences of strains S1CR25-12 T and S3CR25-11 T were deposited in GenBank/EMBL/DDBJ under the accession numbers ON653025 and ON653386 (rrnA), ON653026 and ON653385 (rrnB), and ON668041 and ON668045 (rpoB’), respectively. To conduct the taxogenomic analysis, genomic sequences of closely related species from the GenBank database were obtained, following the established guidelines for taxonomic use of genome data [ 28 ]. The genomic reads of strains S1CR25-12 T and S3CR25-11 T were subjected to k-mer assembly employing Spades v.3.13.0 [ 29 ], followed by verification of assembly integrity using CheckM v.1.0.5 [ 30 ] to ensure the absence of contamination. Subsequently, the standard genome annotation was performed using Prokka v.1.12 [ 31 ]. The whole-genome sequences of strains S1CR25-12 T and S3CR25-11 T were deposited in the GenBank/EMBL/DDBJ databases, and they were assigned the accession numbers JAMQON000000000 and JAMQOS000000000, respectively. The amplified 16S rRNA and rpoB’ gene sequences obtained via PCR correlated with the sequences derived from genomic sequencing. The Enveomics toolbox [ 32 ] was used to identify clusters of orthologous proteins shared by all strains subjected to analysis. The approximately maximum-likelihood phylogenomic tree, based on 157 core-orthologous protein sequences, was reconstructed using FastTreeMP v.2.1.8, as described by Price et al. [33]. 2.4. Comparative Genomic Analysis The overall genome relatedness indexes (OGRIs) were computed to assess the genomic relatedness between strains S1CR25-12 T and S3CR25-11 T , and the type strains of other species within the family Haloarculaceae. The orthologous average nucleotide identity (OrthoANI) values were determined using the OrthoANIu tool v.1.2 [ 34 ]. The digital DNA–DNA hybridization (dDDH) values were obtained using the genome-to-genome distance calculator (GGDC v.3.0) provided by the Leibniz Institute DSMZ (Braunschweig, Microorganisms 2024,12, 334 4 of 20 Germany) [ 35 ]. Average amino acid identity (AAI) values were calculated using the ‘aai.rb’ script from the Enveomics collection [32]. In addition, the Enveomics tool was employed to conduct a pan-genome analysis [ 32 ]. The pan-genome encompasses three sets of genes: core, variable (shared by some but not all of the strains), and singleton (strain-specific) gene clusters [ 36 ]. The visualization of the pan-genome was carried out using the Anvi’o tool [ 37 ]. To display the core, variable (shell), and strain-specific genes, a flower plot was generated using the ‘plotrix’ package in R v.3.8.2. Characteristic curves illustrating the evolution of the pan-genome and core-genome of the genus Halomicroarcula were represented using the pan-genome profile analysis tool (PanGP) [ 38 ]. A heatmap based on the presence and absence of the genes within the shell genome was produced using the “gplot” R package v.3.1.3. To compare the orthologous clusters (OCs) between strains S1CR25-12 T and S3CR25-11 T and its phylogenomically closest related species, namely, Halomicroarcula salinisoli F24A T and Halomicroarcula laminariae LYG-108 T , the OrthoVenn3 online tool was used [ 39 ]. Additionally, the isoelectric points of predicted proteins were computed using the ‘iep’ program from the EMBOSS package v.6.5.7.0 [40]. 2.5. Phenotypic and Chemotaxonomic Characterization A complete phenotypic characterization was conducted in accordance with the minimal standards for the description of new taxa within the order class Halobacteria [ 41 ]. Cell morphology and motility were examined by cultivating the strains on 25% R2A liquid medium in a shaking incubator at 200 rpm at 37 ◦ C, and the cells were observed using a light phase-contrast microscope (Zeiss Axioscope 5). Gram staining was performed following the method described by Dussault [ 42 ]. To determine the optimal salt requirements, strains S1CR25-12 T and S3CR25-11 T were cultured in R2A medium with different salt concentrations (0.5%, 5%, 7.5%, 10%, 12%, 15%, 17%, 20%, 22%, 25%, and 30% [w/v]). Similarly, the pH (5.0, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, and 9.5) and temperature (from 20 ◦ C to 55 ◦ C, at 5 ◦ C intervals, in addition to 37 ◦ C) ranges and optimal values supporting growth were determined in 25% R2A buffered medium. Colonial morphology, pigmentation, and size were examined on 25% R2A solid medium after 10 days of incubation at 37 ◦ C. Anaerobic growth capability was assessed by incubating 25% R2A medium plates supplemented with alternative electron acceptors (L-arginine, DMSO, and KNO 3 ) for 14 days at 37 ◦ C in a GasPak system using AnaeroGen (Oxoid, Horsham, UK). The catalase test involved the addition of a few drops of 3% H 2 O 2 (v/v) to a young culture of the microorganisms [ 43 ]. Oxidase activity was determined using 1% (v/v) tetramethyl-p-phenylenediamine [ 44 ]. Tween 80 hydrolysis was examined as described by Gutiérrez and González [ 45 ]. The hydrolyses of starch, gelatin, and casein were detected according to Mata et al. [ 46 ]. Aesculin hydrolysis was examined as described by Barrow et al. [ 47 ]. H 2 S production was detected using a lead-acetate-impregnated strip [ 48 ]. The urease test [ 49 ] was carried out to evaluate the ability of the strains to hydrolyze urea. Methyl red and Voges–Proskauer tests were determined according to Oren et al. [ 41 ]. The determination of nitrate and nitrite reduction was performed by following the methodology of Gerhardt et al. [ 50 ]. The indole test was conducted as described by Kovács [ 51 ]. Acid production from carbohydrates and the utilization of carbohydrates, alcohols, organic acids, and amino acids as sole carbon or/and nitrogen sources of energy were determined following the methodology described by Ventosa et al. [ 52 ]. Recently, Durán-Viseras [ 12 ] conducted a phenotypic characterization in the same laboratory of the following strains: Halomicroarcula pellucida CECT 7537 T , Halomicroarcula limicola JCM 18640 T ,Halomicroarcula nitratireducens F27 T ,Halomicroarcula rubra F13 T , and Halomicroarcula salinisoli F24A T , employing the same methodology as that used in our study. Therefore, we used those species as reference strains for comparative phenotypic characterization in our investigation. The characterization and differentiation of haloarchaea at the genus level have benefited from the analysis of polar lipids, which serve as useful taxonomic markers [ 41 , 53 ]. In this study, the polar lipids were extracted from the cell biomass of the investigated strains, Microorganisms 2024,12, 334 5 of 20 S1CR25-12 T and S3CR25-11 T , as well as from the reference strains Halobacterium salinarum DSM 3754 T ,Halorubrum saccharovorum DSM 1137 T ,Halomicroarcula pellucida CECT 7537 T , Halomicroarcula nitratireducens F27 T ,Halomicroarcula rubra F13 T , and Halomicroarcula salinisoli F24A T , using a chloroform/methanol extraction system. The identification of polar lipid profiles was accomplished through high-performance thin-layer chromatography (HPTLC) on silica gel glass plates (Merck, Rahway, NJ, USA), employing a chloroform-methanol-90% (v/v) acetic acid (39.4/2.42/18.18 mL) solvent system [ 54 , 55 ]. The visualization of polar lipids was achieved by applying 5% (v/v) sulfuric acid followed by heating at 160 ◦ C, while phospholipids were detected using the molybdenum blue spray reagent. 2.6. Metagenomic Fragment Recruitment Analyses Fragment recruitments with seven environmental metagenomic datasets available from databases were carried out to identify and quantify the presence of the eight Halomicroarcula species, as well as of strains S1CR25-12 T and S3CR25-11 T in various saline habitats (Supplementary Table S1). Genomes of Haloquadratum walsbyi C23 T (GCF_000237865.1), and Spiribacter salinus M19-40 T (GCF_000319575.2) were included as references for comparison. To minimize analysis bias, contigs from each genome were concatenated, and subsequently, rRNA gene sequences were masked. A Blastn search was executed with specific parameters (alignment length ≥ 50 nt, similarity > 95%, E-value ≤ 10 −5 ) to map quality-filtered metagenomic reads against each genome. Recruitment plot representations were generated in R v.4.2.1 using the library “Hmisc” [56]. 3. Results and Discussion 3.1. Physicochemical Features of the Sampling Sites Two soil samples, designated as 1C and 3C, collected from the hypersaline soils of the Odiel Saltmarshes in Huelva (Spain) were analyzed. The physicochemical properties of sample 1C, from which strain S1CR25-12 T was isolated, exhibited a pH of 8.4 and electrical conductivity of 35.7 mS/cm. Sample 3C, corresponding to the isolation place of strain S3CR25-11 T , displayed a pH value of 7.3 and electrical conductivity of 112.6 mS/cm. The high electrical conductivity indicated that the soils under study can be classified as hypersaline. However, these samples were subjected to analytical testing for the presence of heavy metals (Table 1) because of previous metallurgical and industrial activities in the area. The concentrations of certain prevalent heavy metals (cadmium, copper, and lead) in both soil samples were high, but they were found to conform to the established standards for non-contaminated soils as stipulated by the Environment Department of the regional Government of Andalusia [ 57 ]. However, the concentrations of arsenic and zinc in the tested soil samples exceeded the reference intervals, indicating a potential heavy metal tolerance and/or resistance of the two isolated strains, as it is known that some Halomicroarcula species possess metal resistance genes against the mentioned heavy metals [ 12 ]. Haloarchaeal strains have previously demonstrated significant capabilities in resisting toxic heavy metals [ 58 – 62 ] and further investigations should be pursued, as they exhibit considerable potential for effective implementation in bioremediation strategies. Table 1. Concentrations of the most abundant heavy metals present in the two soil samples (1C and 3C) and reference ranges for non-contaminated soils. Heavy Metal 1C (mg/kg) 3C (mg/kg) * Range for Non-Contaminated Soils (mg/kg) Arsenic 11.1 9.8 2–5 Cadmium 0.5 0.6 0.4–0.8 Copper 85.7 88.0 17–100 Lead 28.8 22.5 10–50 Zinc 84.4 82.5 10–70 * The reference ranges stand for non-contaminated soils in Andalucia (Spain) [ 57 ], where the Odiel Saltmarshes National Area is located. Values higher than the reference ranges for non-contaminated soils are highlighted in red. Microorganisms 2024,12, 334 6 of 20 3.2. Unveiling Two Novel Species of the Genus Halomicroarcula through Phylogenetic and Phylogenomic Analyses Strains S1CR25-12 T and S3CR25-11 T were isolated as part of an investigation focused on the characterization of prokaryotes from hypersaline soils located in the Odiel Saltmarshes Natural Area in Huelva, Spain. The analysis of the 16S rRNA gene sequences allowed us to determine the initial phylogenetic position of the isolates, which were related to the genus Halomicroarcula. Species within the genus Halomicroarcula typically possess multiple copies of the 16S rRNA gene with sequence heterogeneity [ 6 , 8 – 12 ]. In the case of the studied strains, we determined and compared the following 16S rRNA gene sequences with type strains of the Halomicroarcula species: rrnA 1464 bp, and rrnB 1323 bp of strain S1CR25-12 T , and rrnA 1464 bp, and rrnB 1463 bp of strain S3CR25- 11 T . Strains S1CR25-12 T and S3CR25-11 T displayed the highest sequence identity with Halomicroarcula salinisoli F24A T (97.9% and 99.1%, respectively) and Halomicroarcula laminariae LYG-108 T (98.1% and 98.0%, respectively). The presence of multiple copies with sequence variations can pose challenges in classification and may lead to an overestimation of prokaryotic diversity [ 63 , 64 ]. It has been demonstrated that the 16S rRNA gene has limitations as a taxonomic marker in the class Halobacteria [ 65 ], while the rpoB’ gene serves as a useful complementary tool to determine the phylogenetic position of new strains within this class [ 66 ]. Analysis of the rpoB’ gene sequences revealed that isolates S1CR25-12 T and S3CR25-11 were again most closely related to Halomicroarcula laminariae LYG-108 T and Halomicroarcula salinisoli F24A T , showing sequence identities of 94.0–92.7, and 93.5–92.7%, respectively. Phylogenetic reconstructions based on the 16S rRNA gene (Figure 1) and rpoB’ gene (Figure 2) sequences confirmed the affiliation of isolates S1CR25- 12Tand S3CR25-11Twithin the genus Halomicroarcula. The relevant genomic characteristics of strains S1CR25-12 T , S3CR25-11 T , and the type strains of the eight species of the genus Halomicroarcula are shown in Supplementary Table S2. The maximum-likelihood phylogenomic tree reconstruction, based on the comparison of 157 core-orthologous proteins, revealed that the two new strains formed a cluster with Halomicroarcula salinisoli F24ATand Halomicroarcula laminariae LYG-108T. However, their phylogenomic divergence suggests that strains S1CR25-12 T and S3CR25- 11 T might constitute two new species within the genus Halomicroarcula (Figure 3). To confirm that hypothesis, orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) were calculated among the studied strains and the type strains of the species of the family Haloarculaceae. The comparative analysis of genomic identity revealed that the new isolates exhibited percentages ranging from 86.0 to 78.9% (OrthoANI), 30.9 to 22.7% (dDDH), and 84.2 to 72.6% (AAI) when compared to Halomicroarcula species. Specifically, the OrthoANI and dDDH values between strains S1CR25-12 T and S3CR25-11 T were 84.4% and 28.1%, respectively, unequivocally confirming that these two strains represent distinct species based on established thresholds for prokaryotic species classification [ 67 – 70 ]. Additionally, the AAI value between the two studied strains was 82.2%, providing further evidence that strains S1CR25-12 T and S3CR25-11 T are two different species and they should be classified within the genus Halomicroarcula (Figures 4and 5). Microorganisms 2024,12, 334 7 of 20 Microorganisms 2024, 12, x FOR PEER REVIEW 7 of 20 S3CR25-11T are two different species and they should be classified within the genus Halomicroarcula (Figures 4 and 5). Figure 1. Neighbor-joining phylogenetic tree based on the 16S rRNA gene sequence comparison of strains S1CR25-12T and S3CR25-11T, and other related species within the family Haloarculaceae. The species Haloferax volcanii NCIMB 2012T was used as outgroup. Sequence accession numbers are shown in parentheses. Bootstrap values higher than 70% are shown at branch points. Filled circles indicate branches that were recovered for the trees obtained using the neighbor-joining, maximumlikelihood, and maximum-parsimony algorithms. Bar, 0.01 expected substitutions per nucleotide position. Figure 1. Neighbor-joining phylogenetic tree based on the 16S rRNA gene sequence comparison of strains S1CR25-12 T and S3CR25-11 T , and other related species within the family Haloarculaceae. The species Haloferax volcanii NCIMB 2012 T was used as outgroup. Sequence accession numbers are shown in parentheses. Bootstrap values higher than 70% are shown at branch points. Filled circles indicate branches that were recovered for the trees obtained using the neighbor-joining, maximum-likelihood, and maximum-parsimony algorithms. Bar, 0.01 expected substitutions per nucleotide position. Microorganisms 2024,12, 334 8 of 20 Microorganisms 2024, 12, x FOR PEER REVIEW 8 of 20 Figure 2. Neighbor-joining phylogenetic reconstruction based on rpoB’ gene sequences of strains S1CR25-12T and S3CR25-11T, and related species of the family Haloarculaceae. The species Haloferax volcanii JCM 8879T was used as outgroup. Sequence accession numbers are shown in parentheses. Bootstrap values (%) higher than 70% are indicated at branch points. Filled circles indicate that the corresponding nodes were obtained in the trees generated with the neighbor-joining and maximumlikelihood algorithms. Bar, 0.01 expected substitutions per nucleotide position. Figure 3. Maximum-likelihood phylogenomic tree based on the comparison of 157 core-orthologous proteins showing the relationships between strains S1CR25-12T, S3CR25-11T, members of the genus Halomicroarcula, and other related species within the family Haloarculaceae. Sequence accession T Halococcoides cellulosivorans HArcel1 (CP028858) T Salinirussus salinus YGH44 (WOWO00000000) T Haloglomus irregulare (QMDX00000000)F16-60 T Halosegnis rubeus F17-44 (QJOW00000000) T Halomicroarcula marina DT1 ( )CP100404 T Halomicroarcula laminariae LYG-108 (JAMZFY000000000) T Haloarcula terrestris S1AR25-5A ( )JAMQOM000000000 0.05 T Haloarcula argentinensis DSM 12282 (AOLX00000000) T Haloarcula sebkhae JCM 19018 (BMPD00000000) T Haloarcula japonica DSM 6131 (AOLY00000000) T Haloarcula marismortui ATCC 43049 (CP039138) T Haloarcula hispanica ATCC 33960 (CP002921) T Haloarcula amylolytica JCM 13557 (AOLW00000000) T Haloarcula vallismortis ATCC 29715 (AOLQ00000000) T Haloarcula mannanilytica MD130-1 (BIXZ00000000) T Haloarcula salina JCM 18369 (JAHQXE000000000) T Halomicroarcula salinisoli F24A (RKLQ00000000) T Halomicroarcula sp. S3CR25-11 (JAMQOS000000000) T Halomicroarcula sp. S1CR25-12 (JAMQON000000000) T Halomicroarcula pellucida CECT 7537 (RKLW00000000) T Halomicroarcula rubra F13 (RKLR00000000) T Halomicroarcula limicola JCM 18640 (JAHQXF000000000) T Halomicroarcula nitratireducens F27 (RKLT00000000) T Halomicroarcula amylolytica LR21 (SRIF00000000) T Halomicrobium urmianum IBRC-M 10911 (CP084090) T Halomicrobium salinisoli LT50 (CP084463) T Halomicrobium mukohataei DSM 12286 (CP001688) T Halomicrobium zhouii CGMCC 1.10457 (FOZK00000000) T Halosimplex carlsbadense 2-9-1 (AOIU00000000) T Halorhabdus utahensis DSM 12940 (CP001687) T Natronomonas pharaonis DSM 2160 (CR936257) T Halapricum salinum CBA1105 (CP031310) Halorientalis regularis TNN28 (JALJCL000000000) T 100100 8686 97 99 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100100 100 98 100 100 100 100 100 Figure 2. Neighbor-joining phylogenetic reconstruction based on rpoB’ gene sequences of strains S1CR25-12 T and S3CR25-11 T , and related species of the family Haloarculaceae. The species Haloferax volcanii JCM 8879 T was used as outgroup. Sequence accession numbers are shown in parentheses. Bootstrap values (%) higher than 70% are indicated at branch points. Filled circles indicate that the corresponding nodes were obtained in the trees generated with the neighbor-joining and maximumlikelihood algorithms. Bar, 0.01 expected substitutions per nucleotide position. Microorganisms 2024, 12, x FOR PEER REVIEW 8 of 20 Figure 2. Neighbor-joining phylogenetic reconstruction based on rpoB’ gene sequences of strains S1CR25-12T and S3CR25-11T, and related species of the family Haloarculaceae. The species Haloferax volcanii JCM 8879T was used as outgroup. Sequence accession numbers are shown in parentheses. Bootstrap values (%) higher than 70% are indicated at branch points. Filled circles indicate that the corresponding nodes were obtained in the trees generated with the neighbor-joining and maximumlikelihood algorithms. Bar, 0.01 expected substitutions per nucleotide position. Figure 3. Maximum-likelihood phylogenomic tree based on the comparison of 157 core-orthologous proteins showing the relationships between strains S1CR25-12T, S3CR25-11T, members of the genus Halomicroarcula, and other related species within the family Haloarculaceae. Sequence accession T Halococcoides cellulosivorans HArcel1 (CP028858) T Salinirussus salinus YGH44 (WOWO00000000) T Haloglomus irregulare (QMDX00000000)F16-60 T Halosegnis rubeus F17-44 (QJOW00000000) T Halomicroarcula marina DT1 ( )CP100404 T Halomicroarcula laminariae LYG-108 (JAMZFY000000000) T Haloarcula terrestris S1AR25-5A ( )JAMQOM000000000 0.05 T Haloarcula argentinensis DSM 12282 (AOLX00000000) T Haloarcula sebkhae JCM 19018 (BMPD00000000) T Haloarcula japonica DSM 6131 (AOLY00000000) T Haloarcula marismortui ATCC 43049 (CP039138) T Haloarcula hispanica ATCC 33960 (CP002921) T Haloarcula amylolytica JCM 13557 (AOLW00000000) T Haloarcula vallismortis ATCC 29715 (AOLQ00000000) T Haloarcula mannanilytica MD130-1 (BIXZ00000000) T Haloarcula salina JCM 18369 (JAHQXE000000000) T Halomicroarcula salinisoli F24A (RKLQ00000000) T Halomicroarcula sp. S3CR25-11 (JAMQOS000000000) T Halomicroarcula sp. S1CR25-12 (JAMQON000000000) T Halomicroarcula pellucida CECT 7537 (RKLW00000000) T Halomicroarcula rubra F13 (RKLR00000000) T Halomicroarcula limicola JCM 18640 (JAHQXF000000000) T Halomicroarcula nitratireducens F27 (RKLT00000000) T Halomicroarcula amylolytica LR21 (SRIF00000000) T Halomicrobium urmianum IBRC-M 10911 (CP084090) T Halomicrobium salinisoli LT50 (CP084463) T Halomicrobium mukohataei DSM 12286 (CP001688) T Halomicrobium zhouii CGMCC 1.10457 (FOZK00000000) T Halosimplex carlsbadense 2-9-1 (AOIU00000000) T Halorhabdus utahensis DSM 12940 (CP001687) T Natronomonas pharaonis DSM 2160 (CR936257) T Halapricum salinum CBA1105 (CP031310) Halorientalis regularis TNN28 (JALJCL000000000) T 100100 8686 97 99 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100100 100 98 100 100 100 100 100 Figure 3. Approximately maximum-likelihood phylogenomic tree based on the comparison of 157 core-orthologous proteins showing the relationships between strains S1CR25-12 T , S3CR25-11 T , members of the genus Halomicroarcula, and other related species within the family Haloarculaceae. Sequence accession numbers are shown in parentheses. Branch support values (%) are computed with the Shimodaira–Hasegawa test and are shown at branch points. Bar, 0.05 substitutions per amino acid position. Microorganisms 2024,12, 334 9 of 20 Microorganisms 2024, 12, x FOR PEER REVIEW 9 of 20 numbers are shown in parentheses. Branch support values (%) are computed with the Shimodaira– Hasegawa test and are shown at branch points. Bar, 0.05 substitutions per Amino acid position. Figure 4. Heatmap displaying orthologous average nucleotide identity (OrthoANI) (upper right) and digital DNA–DNA hybridization (dDDH) (lower left) percentages among strains S1CR25-12 T and S3CR25-11 T , members of the genus Halomicroarcula, and other related species of the family Haloarculaceae. Figure 4. Heatmap displaying orthologous average nucleotide identity (OrthoANI) (upper right) and digital DNA–DNA hybridization (dDDH) (lower left) percentages among strains S1CR25- 12 T and S3CR25-11 T , members of the genus Halomicroarcula, and other related species of the family Haloarculaceae. 3.3. Comparative Genomic Analysis Provides Insights into the Genome Structure and the Evolutionary Relationships The pan-genome is characterized as the ensemble of genes that includes genes shared by all members (core genome), as well as genes that are unique to specific individuals or subsets of the group [ 71 ]. The 43,781 protein CDSs detected in the 10 analyzed genomes of Halomicroarcula were grouped into 5997 orthologous gene clusters (1931 core genes and 4066 variable genes) and 6387 singletons (cloud), with a pan-genome constituted of a total of 12,384 gene clusters (Figures 6and 7). Pan-genome and core-genome size evolution (Figure 8) describe the changes in the total gene repertoire (pan-genome) and the set of shared genes (core genome) within the genus Halomicroarcula over the number of genomes included into the analyzed group. The pan-genome of the genus Halomicroarcula is considered open as the addition of new genomes consistently introduces new genes, while the core genome is represented as closed as its size is relatively stable over group size and the set of essential genes remains conserved. A visual representation of a binary matrix that indicates the occurrence (presence or absence) of 9657 variable gene clusters Microorganisms 2024,12, 334 16 of 20 Description of Halomicroarcula onubensis sp. nov. Halomicroarcula onubensis (o.nu.ben’sis. L. fem. adj. onubensis, of or belonging to Onuba, the ancient Latin name of Huelva, a city in Spain, where the type strain was isolated). Cells are motile, Gram-stain-negative, 0.5 × 2–5 µ m, pleomorphic rods. Colonies are small, circular, entire, 0.2–0.3 mm in diameter, and have an orange–red pigmentation after 10 days of incubation at 37 ◦ C. They are extremely halophilic, being capable of growth within salt concentrations ranging from 12 and 30% (w/v), with optimal growth at 25% (w/v). They display a pH tolerance range of 6.0–9.0, with an optimum pH of 7.0–8.0, and a temperature range of 25–55 ◦ C, with an optimum temperature of 37 ◦ C. No growth is observed under anaerobic conditions with L-arginine, potassium nitrate, or DMSO. They are catalase positive and oxidase negative. Aesculin is slightly hydrolyzed, but casein, gelatin, starch, and Tween 80 are not. Nitrate is reduced but nitrite is not. H 2 S and indole are not produced. The methyl red test is positive and urease, Voges– Proskauer, and Simmons’ citrate tests are negative. Acid is produced from D-arabinose, D-fructose, D-glucose, D-xylose, glycerol, mannitol, and sucrose and is not produced from D-galactose, D-trehalose, lactose, and maltose. The following compounds are used as sole carbon and energy sources: D-glucose, D-xylose, fumarate, hippurate, sucrose, and xylitol, whereas citrate, D-arabinose, D-galactose, D-cellobiose, D-fructose, D-ribose, D- sorbitol, glycerol, lactose, maltose, propionate, salicin, and valerate are not. L-cysteine and L-serine are used as sole carbon, nitrogen, and energy sources, whereas L-alanine, L-arginine, L-methionine, L-glycine, L-glutamine, L-isoleucine, and valine are not. The major polar lipids are phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), and a glycolipid chromatographically identical to sulfated diglycosyl diether (S-DGD-1). The DNA G+C content is 65.7 mol%. The type strain is S3CR25-11 T (= CECT 30621 T = CCM 9254 T ), isolated from hypersaline soil located in the Odiel Saltmarshes Natural Area, Huelva, Spain. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and rpoB’ gene sequences of strain S3CR25-11 T are ON653386 (rrnA), ON653385 (rrnB), and ON668045, respectively. The GenBank/EMBL/DDBJ accession number of the whole genome sequence of strain S3CR25-11Tis JAMQOS000000000. Supplementary Materials: The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/microorganisms12020334/s1. Table S1: Data related to the metagenomic datasets used for the fragment recruitment analyses. Table S2: Main genomic features of strains S1CR25-12 T , S3CR25-11 T , and the type strains of species of the genus Halomicroarcula. Table S3: Differential characteristics between strains S1CR25-12 T and S3CR25-11 T , and related species of the genus Halomicroarcula. Figure S1: Isolation places designated as 1C and 3C (A) and hypersaline soil located in Odiel Saltmarshes (Huelva, Spain) where studied strains S1CR25-12 T and S3CR25- 11 T were isolated (B). Figure S2: Venn diagrams showing the distribution of the orthologous gene clusters (OCs) determined for strains S1CR25-12 T , S3CR25-11 T , and their phylogenomically closest related species, Halomicroarcula salinisoli F24A T and Halomicroarcula laminariae LYG-108 T (A), and the distribution of the orthologous gene clusters (OCs) between the two studied strains S1CR25-12 T and S3CR25-11 T , respectively (B). Figure S3: Isoelectric point comparison of predicted proteins from the type strains of species of the genus Halomicroarcula, including the new isolates S1CR25-12 T and S3CR25-11 T , and other reference strains. Figure S4: High-performance thin-layer chromatography (HPTLC) showing the comparison of the polar lipid (A) and phospholipid (B) profiles between strains S1CR25-12 T , S3CR25-11 T , and other Halomicroarcula species, as well as Halorubrum saccharovorum and Halobacterium salinarum. Figure S5: Recruitment plots of the two novel strains S1CR25-12 T (A) and S3CR25-11T(B) against seven different hypersaline metagenomic datasets. Author Contributions: Conceptualization, A.V., R.R.d.l.H. and C.S.-P.; methodology, D.S., C.S.-P. and R.R.d.l.H.; formal analysis, investigation, and data curation, D.S., C.S.-P., R.R.d.l.H. and A.V.; writing—original draft preparation, D.S.; writing—review and editing, A.V., R.R.d.l.H. and C.S.-P.; supervision, A.V. and R.R.d.l.H.; project administration, A.V. and C.S.-P.; funding acquisition, A.V. and C.S.-P. All authors have read and agreed to the published version of the manuscript. Microorganisms 2024,12, 334 17 of 20 Funding: This study was supported by grant PID2020-118136GB-I00, funded by MCIN/AEI/ 10.13039/501100011033 (to A.V. and C.S.-P.). A.V. thanks the support from the Junta de Andalucia (P20_01066 and BIO-213), both with FEDER funds. Data Availability Statement: All relevant data can be found within the article and Supplementary Materials. Datasets presented in this study can be found in online repositories. 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