A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils

Abstract

Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.

The Hypersaline Soils of the Odiel Saltmarshes Natural Area as a Source for Uncovering a New Taxon: Pseudidiomarina terrestris sp. nov

“…In addition, copper was close to the upper limit but did not exceed it. Similarly high values of these heavy metals were also observed in previous studies in this area [ 23 , 24 , 66 ]. The pH of the soil was 8.2, and the electrical conductivity (EC) was 12.80 mS cm −1 at 25 °C, trespassing the criteria to delineate saline soils (4 mS cm −1 at 25 °C) [ 67 ].…”

“…In order to assess the abundance of the new species in hypersaline environments, we analyzed 13 metagenomic datasets previously reported from terrestrial and aquatic hypersaline habitats (Table S1). The distribution of each of the six isolates was very similar and also comparable to that of the reference species Terrihalobacillus insolitus, which has been previously identified as a member of the "rare biosphere" due to its low abundance [24]. Figure 10 shows that the type strain 1APP75-27a T is rarely found in environments with extremely high salinity, such as a Chilean solar saltern (Cáhauil) [100], Spanish solar salterns located in Isla Cristina (IC21) [101] and Santa Pola (SS33 and SS37) [102,103], hypersaline lakes from Australia (Tyrrell 0.1 and Tyrrell 0.8) [104] and Iran (Urmia) [105], as well as the salt crust from the Qi Jiao Jing Lake in China (Xinjiang) [106].…”

“…As stated before, the sampled soils feature extreme heavy metal concentrations, particularly of arsenic and zinc. Previous studies have revealed the existence of heavy metal tolerance strategies in the genomes of bacterial strains isolated from the Odiel Saltmarshes Natural Area [23,24], a characteristic also confirmed by wet lab experiments [89,90].…”

“…The Odiel Saltmarshes Natural Area is settled between the Odiel and Tinto rivers in the province of Huelva (southwest Spain). Its hypersaline soils have been a source for exploring unknown prokaryotic species such as the haloarchaea Halonotius terrestris [ 21 ] and Natronomonas aquatica [ 22 ], and the bacteria Fodinibius salsisoli [ 23 ] and Aquibacillus salsiterrae , as well as the novel genus Terrihalobacillus [ 24 ]. Some of these species have been shown to encode relevant pathways for the biosynthesis of cobalamin and biotin vitamins in their genome [ 21 , 23 ].…”

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

“…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 ].…”