Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation

Kheiri, Roohollah; Mehrshad, Maliheh; Pourbabaee, Ahmad Ali; Ventosa, António; Amoozegar, Mohammad Ali

doi:10.1038/s41598-023-27429-2

Cited by 9 publications

(4 citation statements)

References 60 publications

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“…Reads recruitment normalized against the size of the genomes and the database, denoted as RPKG, was low for all the three isolates in the studied metagenomic datasets ( Figure 12A ). Their abundance was especially rare in environments with (almost-)saturated salt concentration, such as the salterns ponds from Chile (Cáhuil) ( Plominsky et al, 2014 ), Isla Cristina (IC21) ( Fernández et al, 2014b ), and Santa Pola (SS33 and SS37) ( Ghai et al, 2011 ; Fernández et al, 2014a ) in Spain, and Puerto Rico (Cabo Rojo) ( Couto-Rodríguez and Montalvo-Rodríguez, 2019 ), the hypersaline lakes from Australia (Tyrrell 0.1 and Tyrrell 0.8) ( Podell et al, 2014 ) and Iran (Urmia) ( Kheiri et al, 2023 ), and the salt crust from the Qi Jiao Jing Lake in China (Xinjiang) ( Xie et al, 2022 ), and slightly higher at intermediate salinities [SS13 and SS19 from Santa Pola salterns ( Ghai et al, 2011 ; Fernández et al, 2014a ), and microbialites from Campo Naranja in Argentina ( Perez et al, 2020 )]. Recruitment plot from SMO1 and SMO2 metagenomes ( Vera-Gargallo et al, 2018 ), corresponding to samples collected a few years ago from the same hypersaline soils (Odiel) than those analyzed in the present study, displayed similar abundance of the new isolates to that found for intermediate salterns ponds (SS13 and SS19).…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2023

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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.

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Section: Resultsmentioning

confidence: 99%

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

et al. 2023

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“…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 ]. However, it seems that its abundance increases with decreasing salinity, as can be observed in the intermediate salinity ponds of Santa Pola (SS19 and SS13) [ 102 , 103 ], the hypersaline soils of the Odiel Saltmarshes Natural Area (SMO1 and SMO2) [ 66 ], and the hypersaline sediments of the Arctic Spring (Arctic Spring) [ 107 ].…”

Section: Resultsmentioning

confidence: 99%

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

Galisteo,

de la Haba,

Ventosa

et al. 2024

Microorganisms

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The hypersaline soils of the Odiel Saltmarshes Natural Area are an extreme environment with high levels of some heavy metals; however, it is a relevant source of prokaryotic diversity that we aim to explore. In this study, six strains related to the halophilic genus Pseudidiomarina were isolated from this habitat. The phylogenetic study based on the 16S rRNA gene sequence and the fingerprinting analysis suggested that they constituted a single new species within the genus Pseudidiomarina. Comparative genomic analysis based on the OGRIs indices and the phylogeny inferred from the core genome were performed considering all the members of the family Idiomarinaceae. Additionally, a completed phenotypic characterization, as well as the fatty acid profile, were also carried out. Due to the characteristics of the habitat, genomic functions related to salinity and high heavy metal concentrations were studied, along with the global metabolism of the six isolates. Last, the ecological distribution of the isolates was studied in different hypersaline environments by genome recruitment. To sum up, the six strains constitute a new species within the genus Pseudidiomarina, for which the name Pseudidiomarina terrestris sp. nov. is proposed. The low abundance in all the studied hypersaline habitats indicates that it belongs to the rare biosphere in these habitats. In silico genome functional analysis suggests the presence of heavy metal transporters and pathways for nitrate reduction and nitrogen assimilation in low availability, among other metabolic traits.

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“…In spite of such progress, knowledge of virus-microbe interactions (e.g., via infection, gene transfer, and metabolism modulation) in CB and SB is very limited, with virtually nothing known about viral activity in CB or viral microdiversity (i.e., intra-species genetic variation) in either SB or CB. Evidence from a temperate hypersaline lake suggests that high ionic concentrations may increase microdiversity [34]. In our subzero brines, acquiring such information in a comparative sense can provide insights into how viral speciation, niche de nition, and gene selection pressures [35] may differ between stably extreme versus uctuating conditions.…”

Section: Introductionmentioning

confidence: 99%

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

Zhong

Vik

Rapp

et al. 2023

Preprint

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Background: Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea-ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea-ice conditions. Results: We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea-ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg-brine viruses were of marine origin yet distinct from either sea-ice-brine or seawater viruses, while 94% of sea-ice-brine viruses also presented in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred ‘active’ vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacterin cryopeg and sea-ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea-ice environment, while many sea-ice-brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. Conclusions: Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on the different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.

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Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation

Cited by 9 publications

References 60 publications

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

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

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

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

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