Hypersaline environments are mainly represented by aquatic systems, such as solar salt ponds or natural salt lakes, as well as by the sediments of these hypersaline aquatic ecosystems and soils with ...high salt content ....
Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum
, which includes the genus
, 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
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
, whereas the other cluster constitutes a novel genus of the family
. We propose the designations
sp. nov. and
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
and
, 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
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,
and
, belong to the rare biosphere of representative hypersaline environments.
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
(phylum
) have been described to be abundant, but very few members have been isolated and characterized to date. This family comprises the genera
and
along with four others. A novel strain, designated 1BSP15-2V2
, 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
. However, comparative genomic analyses of members of the family
have revealed that the genera
and
belong to a single genus, hence we propose the reclassification of the species of the genus
into the genus
which was first described. The novel strain is thus described as
sp. nov., with 1BSP15-2V2
(=CCM 9117
= CECT 30246
) 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
analysis of the metabolism of
showed that the biotin biosynthesis pathway was present in the genomes of strain 1BSP15-2V2
and other species of the family
, which could entail major implications in their community role providing this vitamin to other organisms that depend on an exogenous source of this nutrient.
Members of the genus
are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations.
M19-40 is the type species of this genus ...and its first cultivated representative. In the habitats of
M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the
mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes.
M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical
operon. Instead, they are scrambled (
;
) and are physically separated from each other on the
M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the
genes.
M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations.
genome mining revealed that
M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that
M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.
A novel moderately halophilic, Gram-stain-negative and facultatively anaerobic bacterium, designated as strain TBZ242
, was isolated from water of Urmia Lake in the Azerbaijan region of Iran. The ...cells were found to be rod-shaped and motile by a single polar flagellum, producing circular and yellowish colonies. The strain could grow in the presence of 0.5-10 % (w/v) NaCl (optimum, 2.5-5 %). The temperature and pH ranges for growth were 15-45 °C (optimum 30 °C) and pH 7.0-11.0 (optimum pH 8.0) on marine agar. The 16S rRNA gene sequence analysis revealed that strain TBZ242
belonged to the genus
, showing the highest similarities to
DG893
(98.8 %),
F01
(98.8 %),
R9SW1
(98.5 %),
PJ-16
(98.4 %),
W62
(98.0 %) and
JB2H27
(98.0 %). The 16S rRNA and core-genome phylogenetic trees showed that strain TBZ242
formed a distinct branch, closely related to a subclade accommodating
,
,
,
,
,
and
, within the genus
. Average nucleotide identity and digital DNA-DNA hybridization values between strain TBZ242
and the type strains of the related species of
were ≤85.0 and 28.6 %, respectively, confirming that strain TBZ242
represents a distinct species. The major cellular fatty acids of strain TBZ242
were C
and C
7
/C
ω6
and the quinone was ubiquinone Q-9. The genomic DNA G+C content of strain TBZ242
is 57.2 mol%. Based on phenotypic, chemotaxonomic and genomic data, strain TBZ242
represents a novel species within the genus
, for which the name
sp. nov. is proposed. The type strain is TBZ242
(= CECT 30649
= IBRC-M 11466
). Genomic fragment recruitment analysis showed that this species prefers aquatic saline environments with intermediate salinities, being detected on metagenomic databases of Lake Meyghan (Iran) with 5 and 18 % salinity, respectively.
An extremely halophilic archaeon, strain F13-25
, was isolated from a marine saltern located in Isla Cristina, Huelva, on the south-west coast of Spain. The novel strain had pink-pigmented, ...non-motile, coccoid cells. Optimal growth was achieved at 25 % (w/v) NaCl, pH 7.5 and 37 °C. Strain F13-25
possessed two heterogeneous 16S rRNA genes (
and
) most closely related to
D108
(97.6-99.2 % sequence similarity) and
TNN28
(95.9-98.8 %). On the basis of the results of
gene sequence analysis, strain F13-25
was also closely related to
IBRC-M 10043
(89.9 %) and
TNN28
(92.3 %). Relatedness values, computed using the Genome-to-Genome Distance Calculator, between strain F13-25
and
IBRC-M 10043
and
IBRC-M 10760
were 34.6 and 36.2 %, respectively. Average nucleotide identity values based on orthoANI, ANIb and ANIm of strain F13-25
and
IBRC-M 10043
and
IBRC-M 10760
were 88.0 and 88.8, 87.1 and 87.6 %, and 89.2 and 89.6 %, respectively. All values were far below the threshold accepted for prokaryotic species delineation. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and one glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content was 65.7 mol% (genome). The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that strain F13-25
represents a novel species of the genus
, for which the name
sp. nov., with type strain F13-25
(=CECT 9384
=IBRC-M 11176
), is proposed.
An extremely halophilic archaeal strain, designated S1CR25-10
, was isolated from hypersaline soil sampled in the Odiel Saltmarshes Natural Area in Southwestern Spain (Huelva) and subjected to a ...polyphasic taxonomic characterization. The cells were Gram-stain-negative, motile and their colonies were pink-pigmented. It was a strictly aerobic haloarchaeon that could grow at 25-55 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 12-30 % (w/v) total salts (optimum, 20-25 %, w/v). The phylogenetic analysis based on the comparison of the 16S rRNA gene sequences revealed that strain S1CR25-10
belongs to the genus
, with 98.9 % similarity to
SLN56
. In addition, the values of orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity were below the threshold limits accepted for prokaryotic species delineation, with
SLN56
showing the highest relatedness values (92.6 % and 48.4 %, respectively). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a glycolipid chromatographically identical to sulfated diglycosyl diether. The DNA G+C content of the isolate was 63.8 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic characterization and the whole genome results, strain S1CR25-10
represents a new species within the genus
, for which the name
sp. nov., with type strain S1CR25-10
(=CECT 30623
=CCM 9251
), is proposed.
Twenty-three isolates of the widely distributed marine bacteria Alteromonas macleodii have been analysed by multilocus sequence analysis combined with phylogenetic and multivariate statistical ...analyses. The strains originated from the Pacific Ocean, Mediterranean Sea, English Channel, Black Sea and Thailand. Using the nucleotide sequences of nine loci for each of the 23 isolates, a robust identification was achieved of different clades within the single species. Strains generally clustered with the depth in the water column from which the isolate originated. Strains also showed more recombination with isolates from the same vicinity, suggesting that genetic exchange plays a role in diversification of planktonic marine prokaryotes. This study thus shows for the first time for a large set of isolates of a species of planktonic marine prokaryotes that multilocus sequence analysis overcomes the problems associated with the analysis of individual marker genes or presence of extensive recombination events. It can thus achieve intraspecific identification to the level of genotypes and, by comparison with relevant environmental data, ecotypes.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
We analyzed the prokaryotic community structure of a saltern pond with 21% total salts located in Isla Cristina, Huelva, Southwest Spain, close to the Atlantic ocean coast. For this purpose, we ...constructed a metagenome (designated as IC21) obtained by pyrosequencing consisting of 486 Mb with an average read length of 397 bp and compared it with other metagenomic datasets obtained from ponds with 19, 33, and 37% total salts acquired from Santa Pola marine saltern, located in Alicante, East Spain, on the Mediterranean coast. Although the salinity in IC21 is closer to the pond with 19% total salts from Santa Pola saltern (designated as SS19), IC21 is more similar at higher taxonomic levels to the pond with 33% total salts from Santa Pola saltern (designated as SS33), since both are predominated by the phylum Euryarchaeota. However, there are significant differences at lower taxonomic levels where most sequences were related to the genus Halorubrum in IC21 and to Haloquadratum in SS33. Within the Bacteroidetes, the genus Psychroflexus is the most abundant in IC21 while Salinibacter dominates in SS33. Sequences related to bacteriorhodopsins and halorhodopsins correlate with the abundance of Haloquadratum in Santa Pola SS19 to SS33 and of Halorubrum in Isla Cristina IC21 dataset, respectively. Differences in composition might be attributed to local ecological conditions since IC21 showed a decrease in the number of sequences related to the synthesis of compatible solutes and in the utilization of phosphonate.
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