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The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, current insights on the genomic diversity of this species is limited to the comparison of the genomes of two co-isolated strains. Here, we present a comparative genomic analysis of eight S. ruber strains isolated at two different time points in each of two different Mediterranean solar salterns. Our results show an open pangenome with contrasting evolutionary patterns in the core and accessory genomes. We found that the core genome is shaped by extensive homologous recombination (HR), which results in limited sequence variation within population clusters. In contrast, the accessory genome is modulated by horizontal gene transfer (HGT), with genomic islands and plasmids acting as gateways to the rest of the genome. In addition, both types of genetic exchange are modulated by restriction and modification (RM) or CRISPR-Cas systems. Finally, genes differentially impacted by such processes reveal functional processes potentially relevant for environmental interactions and adaptation to extremophilic conditions. Altogether, our results support scenarios that conciliate "Neutral" and "Constant Diversity" models of bacterial evolution. ; PG-T was an FPI-MINECO fellow. TG group acknowledges support of the Spanish Ministry of Economy and Competitiveness grants, 'Centro de Excelencia Severo Ochoa 2013–2017' SEV-2012-0208, and BFU2015-67107 cofounded by European Regional Development Fund (ERDF); from the CERCA Program/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and grant from the European Union's Horizon 2020 Research and Innovation Program under the grant agreement ERC-2016-724173 the Marie Sklodowska-Curie grant agreement No. H2020-MSCA-ITN-2014-642095. We acknowledge the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership.

10 pages, 5 figures.-- PMID: 18957079 [PubMed].-- PMCID: PMC2596770. ; Since its discovery in 1998, representatives of the extremely halophilic bacterium Salinibacter ruber have been found in many hypersaline environments across the world, including coastal and solar salterns and solar lakes. Here, we review the available information about the distribution, abundance and diversity of this member of the Bacteroidetes. ; Our work on Salinibacter since 2000 has been supported by several grants of the Spanish Ministry of Science and Education (SMCE), and the Valencia local Government. Currently, work on Salinibacter is being funded by SMCE grants CGL2006-12714-C02-01 and 02. ; Peer reviewed

The prokaryotic communities inhabiting hypersaline sediments underlying a crystallizer pond of a Mediterranean solar saltern have been studied in a polyphasic approach including 16S rRNA and dsrAB gene libraries analysis [the last encoding for dissimilatory (bi)sulfite reductase], most probable number of cultivable counts, and metabolic measurements of sulfate reduction. The samples studied here represent one of the most hypersaline anoxic environments sampled worldwide that harbour a highly diverse microbial community different from those previously reported in other hypersaline sediments. Both bacterial and archaeal types are present but, contrarily to the overlying brine system, the former dominates. Molecular analyses indicated that the bacterial fraction is highly diverse and mostly composed by groups related to sulfate-reducing bacteria (SRB). In good agreement with this, sulfate-reducing activity was detected in the sediment, as well as the metabolic diversity within SRB (as indicated by the use of different electron donors in enrichments). On the other hand, the archaeal fraction was phylogenetically homogeneous and, surprisingly, strongly affiliated with the MBSl-1 candidate division, an euryarchaeotal group only reported in deep-sea hypersaline anoxic basins of the Western Mediterranean, for which a methanogenic metabolism was hypothesized. The hypersaline studied samples constitute a valuable source of new prokaryotic types with metabolisms adapted to the prevalent in situ extreme conditions. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd. ; The present work has been supported by the Spanish Government projects CE-CSD2007-0005 and CLG2006-12714-C02-02, the European projects GOCE-CT-2003-505446 and GOCE-CT-505403 and the FBBVA Project BIOCON05/094. ; Peer Reviewed

To obtain insights into archaeal nitrogen signaling and haloadaptation of the nitrogen/carbon/energy-signaling protein PII, we determined crystal structures of recombinantly produced GlnK2 from the extreme halophilic archaeon Haloferax mediterranei, complexed with AMP or with the PII effectors ADP or ATP, at respective resolutions of 1.49 Å, 1.45 Å, and 2.60 Å. A unique trait of these structures was a three-tongued crown protruding from the trimer body convex side, formed by an 11-residue, N-terminal, highly acidic extension that is absent from structurally studied PII proteins. This extension substantially contributed to the very low pI value, which is a haloadaptive trait of H. mediterranei GlnK2, and participated in hexamer-forming contacts in one crystal. Similar acidic N-extensions are shown here to be common among PII proteins from halophilic organisms. Additional haloadaptive traits prominently represented in H. mediterranei GlnK2 are a very high ratio of small residues to large hydrophobic aliphatic residues, and the highest ratio of polar to nonpolar exposed surface for any structurally characterized PII protein. The presence of a dense hydration layer in the region between the three T-loops might also be a haloadaptation. Other unique findings revealed by the GlnK2 structure that might have functional relevance are: the adoption by its T-loop of a three-turn α-helical conformation, perhaps related to the ability of GlnK2 to directly interact with glutamine synthetase; and the firm binding of AMP, confirmed by biochemical binding studies with ATP, ADP, and AMP, raising the possibility that AMP could be an important PII effector, at least in archaea. ; This work was supported by grants from the Spanish government (BFU2011-30407 and BIO2008_00082, to V. Rubio and M. J. Bonete, respectively) and from the Valencian government (Prometeo 2009/51 to V. Rubio). C. Palanca is a JAE-Predoc fellow of the CSIC and, during this work, L. Pedro-Roig was a FPU fellow of the Spanish Ministry of Education. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007–2013) under BioStruct-X (grant agreement No. 283570).

To obtain insights into archaeal nitrogen signaling and haloadaptation of the nitrogen/carbon/energy-signaling protein PII, we determined crystal structures of recombinantly produced GlnK2 from the extreme halophilic archaeon Haloferax mediterranei, complexed with AMP or with the PII effectors ADP or ATP, at respective resolutions of 1.49 Å, 1.45 Å, and 2.60 Å. A unique trait of these structures was a three-tongued crown protruding from the trimer body convex side, formed by an 11-residue, N-terminal, highly acidic extension that is absent from structurally studied PII proteins. This extension substantially contributed to the very low pI value, which is a haloadaptive trait of H. mediterranei GlnK2, and participated in hexamer-forming contacts in one crystal. Similar acidic N-extensions are shown here to be common among PII proteins from halophilic organisms. Additional haloadaptive traits prominently represented in H. mediterranei GlnK2 are a very high ratio of small residues to large hydrophobic aliphatic residues, and the highest ratio of polar to nonpolar exposed surface for any structurally characterized PII protein. The presence of a dense hydration layer in the region between the three T-loops might also be a haloadaptation. Other unique findings revealed by the GlnK2 structure that might have functional relevance are: the adoption by its T-loop of a three-turn α-helical conformation, perhaps related to the ability of GlnK2 to directly interact with glutamine synthetase; and the firm binding of AMP, confirmed by biochemical binding studies with ATP, ADP, and AMP, raising the possibility that AMP could be an important PII effector, at least in archaea. ; This work was supported by grants from the Spanish government (BFU2011- 30407 and BIO2008_00082, to V.R. and M.J.B, respectively) and from the Valencian government (Prometeo 2009/51 to V.R.). C.P. is a JAE-Predoc fellow of the CSIC and during this work, L.P.R was a FPU fellow of the Spanish Ministry of Education. We thank Diamond Light Source for access to beamlines I-03 and I-04 (mx8035) that contributed to the results presented here. We also thank the ESRF beamlines BM30 and ID23-2 and the personnel assisting these lines. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under BioStruct-X (grant agreement N°283570). ; Peer reviewed