The discovery of CRISPR in archaea and bacteria

CRISPR-Cas are self-/nonself-discriminating systems found in prokaryotic cells. They represent a remarkable example of molecular memory that is hereditarily transmitted. Their discovery can be considered as one of the first fruits of the systematic exploration of prokaryotic genomes. Although this genomic feature was serendipitously discovered in molecular biology studies, it was the availability of multiple complete genomes that shed light about their role as a genetic immune system. Here we tell the story of how this discovery originated and was slowly and painstakingly advanced to the point of understating the biological role of what initially was just an odd genomic feature.FJMM is funded by the Spanish Ministerio de Economía y Competitividad (BIO2014-53029P) and the European Commission/Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (291815 Era-Net ANIHWA). FR-V is funded by projects MEDIMAX BFPU2013-48007-P from the Spanish Ministerio de Economía y Competitividad, MaCuMBA Project 311975 of the European Commission FP7 and PROMETEO II/2014/012 project AQUAMET from the Generalitat Valenciana

Light as an energy source in continuous cultures of bacteriorhodopsin-containing halobacteria

The role of light as an energy source for slightly aereated cultures of halobac­ teria was studied, using continuous cultures with low nutrient concentrations and a low oxygen supply. A series of experiments were carried out with non­ illuminated and differently illuminated cultures and with ditferent oxygen transfer rates. Under low oxygen availability, light proved to be a decisively important energy source that allowed the populations to reach higher growth rates and much higher population densities. Oxygen inftuenced the growth over only a minimal level, below which neither the illuminated nor the dark cultures were atfected by the oxygen transfer rate. From these results, it appears that the bacteriorhodop­ sin-mediated energy supply could have a very important role for the ecology of halobacteria in their microaerophilic habitats. In the illuminated cultures, cells that originated purple colonies on plates appeared. These cells, which could be bacteriorhodopsin-constitutive mutants, are now being studied

Taxonomic Study of Non-alkaliphilic Halococci

Ninety-six extremely halophilic, non-alkaliphilic cocci were isolated from several salterns in different geographical areas of Spain. These strains, together with seven reference strains of the genus Halococcus, were characterized by means of 114 phenotypic features, the results being analysed by numerical techniques using the simple matching (SsM) coefficient and the unweighted pair group clustering (UPGMA) algorithm. At the 70% similarity level, four phenons were obtained. Phenon A contained 87 strains, including all the reference strains, and was considered to comprise members of the only named species of the genus Halococcus, H . rnorrhuae. Phenons B and C , which included five and seven strains respectively, showed greater metabolic versatility than phenon A. The four strains belonging to phenon D were significantly different from the other phenons in that they produced acid from glucose and were able to use most of the organic compounds tested. The results indicate that there is phenotypic diversity among the members of the genus Halococcus and that phenon D may constitute a new taxon

Numerical taxonomy of moderately halophilic Gram-negative rods

A study was made of 516 randomly selected isolates of moderately halophilic bacteria from solar salterns showing salinities between 8.8 and 40.0% (w/v) total salts, located in S.E. Spain. After purification, many cytological, physiological, biochemical, nutritional and an ti biot ic sensitivity characters were determined for 106 selected saltern isolates and two reference strains. Data were coded and analysed by numerical techniques using the Jaccard coefficient ( S J ) ,a nd clusters of strains were obtained by average linkage (UPGMA) analysis. Nine major phenons were found at the 72.5 % similarity level. The properties of each phenon are given, their taxonomic affinities are discussed, and typical reference strains are suggested. Almost all the strains were related to genera known to contain marine species. A large number of the strains could be tentatively assigned to the genus Vibrio, suggesting that this may be an abundant taxon of moderately halophilic Gram-negative rods in solar salterns

Micro-Mar: a database for dynamic representation of marine microbial biodiversity

BACKGROUND: The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes. DESCRIPTION: The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses. The database currently includes 11874 sequences corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA) and many other genes including CDS of marine prokaryotes together with available biogeographical and ecological information. CONCLUSION: The database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface. It is available online at

Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution

BACKGROUND: Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host. RESULTS: Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections. CONCLUSIONS: We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine

Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment

A method for analyzing virus assemblages in aquatic environments was developed and used for studying the highest-salinity ponds (from 13.4 to 35% salinity) from a multi-pond solar saltern in Alicante, Spain. The protocol consisted of a series of concentration and purification steps including tangential flow filtration and ultracentrifugation, followed by the preparation of total viral nucleic acids that were subsequently separated by pulsed-field gel electrophoresis. For every sample analyzed, a characteristic DNA pattern was obtained, whose complexity was related to viral diversity. The comparison of our results with a similar analysis carried out with marine virus assemblages shows that, as expected, the viral diversity corresponding to the analyzed hypersaline environment is considerably lower than that of a marine environment

Numerical taxonomy of moderately halophilic Gram-negative bacteria from hypersaline soils

A total of 132 moderately halophilic bacteria were isolated from hypersaline soils with a C1- content between 2-36 and 12.72% (w/v) located near Alicante (S.E. Spain) and examined for 98 phenotypic characteristics including their response to cytological, physiological, biochemical and nutritional tests. They were submitted to a numerical analysis together with six reference strains using both simple matching (SsM)a nd Jaccard (S,) coefficients, and cluster analysis was carried out by the unweighted pair group method of association (UPGMA), single linkage and complete linkage. With the S, coefficient and UPGMA clustering, eight phenons were obtained at the 65% similarity level. From each phenon representative strains were chosen for the determination of DNA base composition and for electron microscopy. Bacteria belonging to phenons D, E, and F were assigned to the genus Alcaligenes. Phenon G included 27 strains assigned to Acinetobacter, but the high G + C composition (58.9 mol%) of a representative strain of this phenon suggests that it may represent a new taxon. Phenons A, B, and C were designated Flavobacterium and phenon H was Pseudomonas. The bacteria found in these environments are not related to those from hypersaline waters or normal soils

A secure link-layer connectivity platform for multi-site NFV services

Network Functions Virtualization (NFV) is a key technology for network automation and has been instrumental to materialize the disruptive view of 5G and beyond mobile networks. In particular, 5G embraces NFV to support the automated and agile provision of telecommunication and vertical services as a composition of versatile virtualized components, referred to as Virtual Network Functions (VNFs). It provides a high degree of flexibility in placing these components on distributed NFV infrastructures (e.g., at the network edge, close to end users). Still, this flexibility creates new challenges in terms of VNF connectivity. To address these challenges, we introduce a novel secure link-layer connectivity platform, L2S. Our solution can automatically be deployed and configured as a regular multi-site NFV service, providing the abstraction of a layer-2 switch that offers link-layer connectivity to VNFs deployed on remote NFV sites. Inter-site communications are effectively protected using existing security solutions and protocols, such as IP security (IPsec). We have developed a functional prototype of L2S using open-source software technologies. Our evaluation results indicate that this prototype can perform IP tunneling and cryptographic operations at Gb/s data rates. Finally, we have validated L2S using a multi-site NFV ecosystem at the Telefonica Open Network Innovation Centre (5TONIC), using our solution to support a multicast-based IP television service.This article has partially been supported by the European H2020 FISHY Project (grant agreement 952644), and the TRUE5G project funded by the Spanish National Research Agency (PID2019-108713RB-C52/AEI/10.13039/501100011033)