Aliifodinibius salicampi sp. nov., a moderately halophilic bacterium isolated from a grey saltern

Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes

Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota's diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán's water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.

Biotin pathway in novel Fodinibius salsisoli sp. nov., isolated from hypersaline soils and reclassification of the genus Aliifodinibius as Fodinibius

Hypersaline soils are extreme environments that have received little attention until the last few years. Their halophilic prokaryotic population seems to be more diverse than those of well-known aquatic systems. Among those inhabitants, representatives of the family Balneolaceae (phylum Balneolota) have been described to be abundant, but very few members have been isolated and characterized to date. This family comprises the genera Aliifodinibius and Fodinibius along with four others. A novel strain, designated 1BSP15-2V2^T, has been isolated from hypersaline soils located in the Odiel Saltmarshes Natural Area (Southwest Spain), which appears to represent a new species related to the genus Aliifodinibius. However, comparative genomic analyses of members of the family Balneolaceae have revealed that the genera Aliifodinibius and Fodinibius belong to a single genus, hence we propose the reclassification of the species of the genus Aliifodinibius into the genus Fodinibius, which was first described. The novel strain is thus described as Fodinibius salsisoli sp. nov., with 1BSP15-2V2^T (=CCM 9117^T = CECT 30246^T) as the designated type strain. This species and other closely related ones show abundant genomic recruitment within 80-90% identity range when searched against several hypersaline soil metagenomic databases investigated. This might suggest that there are still uncultured, yet abundant closely related representatives to this family present in these environments. In-depth in-silico analysis of the metabolism of Fodinibius showed that the biotin biosynthesis pathway was present in the genomes of strain 1BSP15-2V2^T and other species of the family Balneolaceae, which could entail major implications in their community role providing this vitamin to other organisms that depend on an exogenous source of this nutrient.

Rhodohalobacter sulfatireducens sp. nov., isolated from a marine solar saltern

A novel Gram-stain-negative, oxidase-positive, catalase-positive, non-motile, facultatively anaerobic, rod-shaped bacterium, designated WB101^T, was isolated from a marine solar saltern located in Wendeng, PR China. Strain WB101^T shared a high level of 16S rRNA gene sequence similarity with Rhodohalobacter barkolensis 15182^T (93.5%), R. halophilus JZ3C29^T (93.2%), and 'R. mucosus' 8A47^T (92.1%). Strain WB101^T formed a species-level branch within the genus Rhodohalobacter in both phylogenetic and phylogenomic topologies. The DNA G + C content was 42.0%. Strain WB101^T was found to have menaquinone-7 as the only respiratory quinone. The dominant cellular fatty acid (≥ 10%) was iso-C_15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylcholine. Characterisation based on phylogenetic, physiological, and biochemical properties indicated that strain WB101^T represents a novel species of the genus Rhodohalobacter, and the name Rhodohalobacter sulfatireducens sp. nov. is proposed. The type strain is WB101^T (= KCTC 92204^T = MCCC 1H00518^T).

Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel

The irregular damp dark staining on the stonework of a salt-contaminated twelfth century granite-built chapel is thought to be related to a non-homogeneous distribution of salts and microbial communities. To enhance understanding of the role of microorganisms in the presence of salt and damp stains, we determined the salt content and identified the microbial ecosystem in several paving slabs and inner wall slabs (untreated and previously bio-desalinated) and in the exterior surrounding soil. Soluble salt analysis and culture-dependent approaches combined with archaeal and bacterial 16S rRNA and fungal ITS fragment as well as with the functional genes nirK, dsr, and soxB long-amplicon MinION-based sequencing were performed. State-of-the-art technology was used for microbial identification, providing information about the microbial diversity and phylogenetic groups present and enabling us to gain some insight into the biological cycles occurring in the community key genes involved in the different geomicrobiological cycles. A well-defined relationship between microbial data and soluble salts was identified, suggesting that poorly soluble salts (CaSO4) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO3)2 and Mg(NO3)2) in the thin layer of water formed on the stonework. By contrast, no direct relationship between the damp staining and the salt content or related microbiota was established. Further analysis regarding organic matter and recalcitrant elements in the stonework should be carried out. KEY POINTS : • Poorly (CaSO4) and highly (Ca(NO3)2, Mg(NO3)2) soluble salts were detected • Halophilic and mineral weathering microorganisms reveal ecological impacts of salts • Microbial communities involved in nitrate and sulfate cycles were detected.

Halalkalibacterium roseum gen. nov., sp. nov., a new member of the family Balneolaceae isolated from soil

A Gram-stain-negative, non-motile, moderately halophilic and facultatively anaerobic bacterium, designated YR4-1T, was isolated from a saline-alkali and sorghum-planting soil sample collected in Dongying, Shandong Province, PR China. Growth occurred at 28–45 °C with the presence of 4.0–20.0 % (w/v) NaCl and pH 6.0–9.0. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that YR4-1T shared the highest similarity of 92.1–92.4 % with the valid published species of Aliifodinibius . The isolate formed a separate clade at the genus level in recently described family Balneolaceae . The draft genome of strain YR4-1T is 3.83 Mbp long with 44.0 mol% G+C content. The strain possesses several genes involved in the osmotic stress response mechanism and diverse metabolic pathways, probably for the living in saline environment. This may lead to a better understanding of the underrepresented Balneolaceae lineage. The major menaquinone was MK-7. The main polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipids, aminophosphoglycolipid, one glycolipid, and four unidentified lipids. The predominant cellular fatty acids were iso-C15 : 0 (35.7 %) and anteiso-C15 : 0 (33.5 %). On the basis of its phenotypic, chemotaxonomic and phylogenetic features, strain YR4-1T represents a novel species of a new genus, for which the name Halalkalibacterium roseum gen. nov., sp. nov. is proposed. The type strain is YR4-1T (=CGMCC 1.17777T=KCTC 72795T).

Aliifodinibius salipaludis sp. nov., Isolated from Saline-Alkaline Soil

A Gram-staining-negative, oblong or rod-shaped, non-flagellated and facultatively anaerobic bacterium, designated WN023^T, was isolated from natural saline-alkali wetland soil of Binhai new district, Tianjin, China. The colonies of strain WN023^T on marine agar 2216 (MA) have a brown, circular, wet pigmentation, and its cells are approximately 1-1.5 μm × 2.0-2.5 μm in size. Growth occurred at 15-45 °C, but optimally at 33-37 °C, in the presence of 5.0-25.0% (w/v) NaCl, but optimally at 10.0-15.0% (w/v) NaCl, and at a pH 6.5-11.0, but optimally at 7.5-8.0. Phylogenetic analysis of the 16S rRNA gene indicates that strain WN023^T is a member of the genus Aliifodinibius within the family Balneolaceae, and the 16S rRNA gene sequence similarity of strain WN023^T with its close relative Aliifodinibius halophilus KCTC 42497^T, Aliifodinibius salicampi KACC 19060^T, Aliifodinibius roseus KCTC 23442^T, Aliifodinibius sediminis ACCC 10714^T, and Fodinibius salinus ACCC 10716^T was 97.3%, 94.5%, 93.9%, 93.71%, and 92.7%, respectively. Strain WN023^T contained menaquinone-7 (MK-7) as the predominant menaquinone, and iso C_15:0, Sum in feature 3 (C_16:1ω6c and/or C_16:1ω7c), and iso C_17:1ω9c as the major fatty acids. The major polar lipids were glycolipid (GL), aminolipid (AL), phospholipid (PL), phosphatidylcholine (PC), phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and lipid (L). The size of the draft genome as presented here was 3,583,276 bp in size, and the G+C content is 42.2 mol%. These combined physiological, biochemical, phylogenetic, and genotypic data supported placement of strain WN023^T in the genus Aliifodinibius and indicated that it was distinct from all other members in the genus Aliifodinibius. This was also confirmed by the low DNA-DNA hybridization values (38.4%) between strain WN023^T and the most closely related recognized Aliifodinibius species-A. halophilus KCTC 42497^T. Therefore, we propose a novel species in the genus Aliifodinibius to accommodate the novel isolate: Aliifodinibius salipaludis sp. nov. (type strain WN023^T = KCTC 52855^T = ACCC 19978^T).

Aliifodinibius saliphilus sp. nov., a moderately halophilic bacterium isolated from sediment of a crystallizing pond of a saltern

Two Gram-stain-negative, moderately halophilic bacteria, designated strains ECH52^T and KHM46, were isolated from the sediment of a grey saltern located in Sinui island at Shinan, Korea. The isolates were aerobic, non-motile, short rods and grew at 15-45 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 8.0) and with 3-25 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains ECH52^T and KHM46 belonged to the genus Aliifodinibius in the family Balneolaceae with sequence similarities of 94.3-98.6 % and showed the highest sequence similarity to Aliifodinibius halophilus 2W32^T (98.6 %), A. sediminis YIM J21^T (94.7%), A. salicampi KHM44^T (94.6 %) and A. roseus YIM D15^T (94.3 %). The DNA G+C content of the genomic DNA of strain ECH52^T was 40.8 mol%. The predominant isoprenoid quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were iso-C_17 : 1ω9c, iso-C_15 : 0, and C_16 : 1ω7c and/or iso-C_15 : 0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and four unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic data, strains ECH52^T and KHM46 are considered to represent a novel species of the genus Aliifodinibius , for which the name Aliifodinibius saliphilus sp. nov. is proposed. The type strain is ECH52^T (=KACC 19126^T=NBRC 112664^T).