Insights into the biogeography, survival, and dispersal mechanisms of the extremely halophilic bacterium Salinibacter ruber

[spa] Salinibacter ruber es el primer miembro reconocido del dominio Bacteria con relevancia ecológica en ambientes hipersalinos. Hasta la fecha, S. ruber ha sido aislado en salinas geográficamente muy distantes los cuales, desde un punto de vista taxonómico constituyen un grupo altamente homogéneo. En este sentido, glándulas secretoras de sal,en narinas de aves marinas migratorias, podrían constituir uno de los mecanismos más rápidos y eficientes para la posible especiación alopátrica de arqueas y otros procariotas halófilos extremos. Por otro parte, estudios metabolómicos revelaron que aislados provenientes de cinco lugares geográficamente distantes, pueden ser distinguidos por diferencias de sus componentes de membrana, las cuales se correlacionan con la distancia geográfica de los aislados. De esta forma, modificaciones en las vías relacionadas con la síntesis y metabolismo de compuestos que constituyen la envoltura celular, parecen ser la primera línea de defensa que protege al organismo frente a las condiciones adversas de su medio circundante.[eng] Salinibacter ruber is the first extremely halophilic member of the Bacteria domain with demonstrated ecological relevance in hypersaline environments. To date, members of S. ruber have been isolated from a large number of widely separated salterns, but all of them have shown an enormous degree of taxonomic resemblance. In this sense, the nostril salt-excreting glands from migratory seabirds may constitute one the most rapid and effective mechanisms to blurry allopatric speciation of the members of this archaea and other halophilic species. On the other hand, metabolomics approaches revealed that isolates from five different sites in the world, could be distinguished by differences in the membrane composition, and these differences could be correlated to their geographical isolation site distances. This response could be attributed to modifications in the synthesis and metabolism of cell envelope compounds, which could be the first line of defense guarding the organism from adverse environmental conditions.[cat] Salinibacter ruber és el primer membre reconegut del domini Bacteri amb rellevància ecològica en ambients hipersalins. Fins ara, S. ruber ha estat aïllat en salines geogràficament molt distants però, les quals des d'un punt de vista taxonòmic constitueixen un grup homogeni. En aquest sentit, les glàndules secretores de sal en narius d'aus marines migratòries, va revelar que aquestes podrien constituir un dels mecanismes més ràpids i eficients per a la especiació alopàtrica d'arqueges i altres halòfils extrems. D'altra banda, l'aproximació metabolòmica, va revelar que aïllats provinents de cinc llocs geogràficament diferents, poden ser distingits per diferències en els seus components de membrana, les quals es correlacionen amb la distància geogràfica dels aïllats. D'aquesta manera, la resposta es va poder atribuir a modificacions en les vies relacionades amb la síntesi i metabolisme de compostos que constitueixen l'embolcall cel·lular, els quals podrien ser la primera línia de defensa que protegeix l'organisme enfront de les condicions adverses del medi que l’envolta

Insights into the biogeography, survival, and dispersal mechanisms of the extremely halophilic bacterium Salinibacter ruber

Peer Reviewe

Fine-scale evolution:genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.This work was funded by projects CGL2006-12714-CO2-01 and 02 from de Spanish Ministry of Science (to JA and RRM). J Dopazo thanks the National Institute of Bioinformatics (www.inab.org), that is a platform of Genoma España. This work was financially supported by the Max Plank Society within the projects Marine Genomics and EnviTools.Peer Reviewe

Occurrence of Halococcus spp. in the nostrils salt glands of the seabird Calonectris diomedea

The nostrils of the seabird Calonectris diomedea are endowed with a salt-excreting gland that could produce a suitable environment for the colonization of extreme halophilic prokaryotes. We have studied in this organ the presence of extreme halophiles by means of culturing techniques. We could easily cultivate members of haloarchaea, and all cultures studied were identified as members of one of the two species Halococcus morrhuae and Hcc. dombrowskii. In order to reveal the diversity of these colonizers, we undertook a taxonomic study. Altogether, the results indicated that members of the genus Halococcus may constitute a part of the natural epizootic microbiota of C. diomedea, and that they exhibit such an important degree of taxonomic variability that appeals for a pragmatic species definition. This seabird nests in the west Mediterranean coasts, but its migratory habits, reaching locations as distant from the Mediterranean as the South Atlantic, may help in the dispersal mechanisms of haloarchaea through the Earth's surface. © 2009 Springer.The project has been funded by the projects CLG2006-12714-C02-01 and CLG2006-12714-C02-02 of the Spanish Ministerio de Ciencia e InnovaciónPeer Reviewe

Changes in the culturability and metabolome composition during adverse environmental conditions in the extremely halophilic bacterium Salinibacter ruber

Trabajo presentado en la IX Reunión de la Red de Microorganismos Extremófilos, celebrada el 1 y 2 de octubre de 2009 en Alcúdia (Mallorca)Peer Reviewe

Response to adverse conditions in two strains of the extremely halophilic species Salinibacter ruber

We have studied the response of the two closest relative strains M8 and M31 of Salinibacter ruber to environmental changes as the transition from exponential to stationary phase in a batch growth, and the submission to two different environmental stresses (dilution of the culture medium and temperature decrease). We monitored the changes in cultivability, ribosomal content by fluorescence in situ hybridization (FISH), and metabolic changes with high-field ion cyclotron Fourier transform mass spectrometry. In all cases, we could observe an important decrease in cultivability that was not accompanied by a decrease in FISH counts, pointing to a transition to viable but non-cultivable state rather than cell death. Furthermore, the metabolomic analyses indicated a common response of both strains to the different conditions assayed. Only a small portion of the detected masses could be annotated due to database constraints. Among them, the most remarkable changes could be attributed to modifications in the composition of the cell envelope, and especially in the cell membrane. We could track changes in the length or saturation of the fatty acids and in the composition of phospholipids involved in aminosugar, glycerolipid, and glycerophospholipid metabolic pathways. © 2011 Springer.This work was supported by the projects CLG2009_12651-C02-01 and 02; and CE-CSD2007-0005 of the Spanish Ministry of Science and Innovation, and all three projects were also co-financed with FEDER support from the European Union. J. Brito-Echeverría was financed by the Government of the Balearic Islands, Ministry of Economy and Finance.Peer Reviewe

Metabolic evidence for biogeographic isolation of the extremophilic bacterium Salinibacter ruber

The biogeography of prokaryotes and the effect of geographical barriers as evolutionary constraints are currently subjected to great debate. Some clear-cut evidence for geographic isolation has been obtained by genetic methods but, in many cases, the markers used are too coarse to reveal subtle biogeographical trends. Contrary to eukaryotic microorganisms, phenotypic evidence for allopatric segregation in prokaryotes has never been found. Here we present, for the first time, a metabolomic approach based on ultrahigh resolution mass spectrometry to reveal phenotypic biogeographical discrimination. We demonstrate that strains of the cosmopolitan extremophilic bacterium Salinibacter ruber, isolated from different sites in the world, can be distinguished by means of characteristic metabolites, and that these differences can be correlated to their geographical isolation site distances. The approach allows distinct degrees of discrimination for isolates at different geographical scales. In all cases, the discriminative metabolite patterns were quantitative rather than qualitative, which may be an indication of geographically distinct transcriptional or posttranscriptional regulations. © 2008 International Society for Microbial Ecology All rights reserved.Funding for this study was provided by the Ministerio de Educación y Ciencia through the research projects CLG2006-12714-C02-01 and -02Peer Reviewe

Number of metabolites responsible for the discrimination between old (reference strains) and new isolates for each experimental set.

<p>The number of masses corresponds to those identified as CHONS in where the isotopes had been removed. SN2 refers to the cellular soluble fraction, and PELLET to the cellular insoluble fraction. Annotable masses refer to those whose molecular formula could be assigned to a given metabolite using <i>Salinibacter ruber</i> strains genomic data.</p><p>1- Total number of masses in the corresponding fraction for the analyzed strain; in brackets, the range of metabolites found in the different strains.</p><p>2- In brackets, the percentage of masses of the discriminative metabolome, and the corresponding set of strains set of strains (new) or (old) respectively.</p

Left column: diagrams based on supervised OPLS analyses showing the discrimination of the different isolates old (blue dots) and new (black dots) of the fractions: cellular soluble fraction of Mallorca new isolates SN2-RM (A) and Santa Pola new isolates SN2- SP (B); and cellular insoluble fractions of Mallorca new isolates Pellet-RM (C) and Santa Pola new isolates Pellet- SP (D).

<p>Grey dots represent the core metabolome of all isolates that do not offer any discrimination. The selection of the compounds is done taking in account the different magnitude of correlation and covariance. The highest value for each list is associated the value 100%. This is the reference percentage and all other values are scaled accordingly to it. The value that present both value of percentages above 50% have been assumed to be a candidate that can be investigate in MassTRIX, the percentage has been set up as a cut-off of the data.</p

Diagrams based on unsupervised PCA analysis of all metabolites present in the cellular soluble fraction of the new isolates (black dots) and old isolates (blue dots) showing the relative homogeneity of the old isolates.

<p>(A) PCA of the cellular soluble fraction (SN2– SP) of the experimental set of Santa Pola isolates; (B) PCA of the cellular soluble fraction (SN2– RM) of the experimental set of Mallorca isolates; (C) PCA of the cellular insoluble fraction (Pellet – SP) of the experimental set of Santa Pola isolates (in this case the best distribution was observed with the components 3 and 4; and (D) PCA of the cellular insoluble fraction (SN2– RM) of the experimental set of Mallorca isolates.</p