The Molecular Microbial Ecology Group of the University of Alicante is part of the Department of Physiology, Genetics and Microbiology. The group was stablished in 1999 by Dr. Josefa Antón and since then it addresses different aspects of the microbial ecology of hypersaline environments and as microbiota of several marine invertebrates, by using different culture dependent and independent approaches.
From left to right: Manuel Martínez-García, Cristina López-Pascual, Pepa Antón, Mónica LLuesma, Esther Rubio-Portillo, Pedro González-Torres, Loles Ramos-Barbero, Judith Villamor and Fernando Santos.
Our main lines of research are:
- The study of viruses in hypersaline environments; hypersaline environments harbour the highest concentration of viruses reported for aquatic systems. This fact, together with the lack of bacterivors and the high concentration of prokaryotes (mainly Archaea but also Bacteria) make these systems ideal for the study of virus-host interactions. For this purpose we use a suit of techniques that go from isolation to metagenomics, metatranscriptomics and single cell genomics. Our model systems are the solar salterns in Santa Pola, Alicante, but we also characterize the prokaryotic and virus assemblages of unexplored salterns and salt lakes around the world.
- The study of the microdiversity of the extremely halophilic bacterium Salinibacter ruber. This organism thrives in hypersaline environments worldwide and presents an outstanding level of microdiversity. We are interested in the mechanisms driving this microdiversity and in understanding its role in nature. For this purpose, we work on several of the following issues using S. ruber as a model: genomic microdiversity, interactions with viruses, intraspecific interactions, interactions with Archaea.
- In close collaboration with the marine biologists Dr. Esther Rubio-Portillo and Prof. Alfonso Ramos, we study the microbiota associate to different marine invertebrates such as ascidians and corals. Recently, we have characterized the microbiome of the invasive species Oculina patagonica, with an emphasis on the pathogens that maybe involved in coral bleaching in the global warming scenario. Currently, we are studyin the microbiomes, including viruses, of other corals, gorgonians and sponges.
- Last year, on the members of the group, Dr. Martínez-García, has stablished his own line of research on Single Virus Genomics. More information at http://martinez-garcia-science.weebly.com/
CURRENT FUNDED PROJECTS
- Since January 2016, we participate in the coordinated project “Diversity measures, population control and molecular adaptation mechanisms along the salinity gradient” (Salploma), funded by the Spanish Ministry of Economics and Competitiveness. The project is integrated by three subprojects: SP1: IMEDEA, IP: Ramon Rosselló-Móra, SP2: UA, IP: Josefa Antón, and SP3: CAB, IP: Eduardo González Pastor. As the major hypothesis of the coordinated project we understand that the communities along the salinity gradient from seawater to saturation encompass discrete metapopulations of prokaryotes concurrent with their viruses that experienced a whole range of adaptations to their environmental conditions, and those can be detected by metagenomic studies. We will apply the most pioneer next generation sequencing (NGS) platforms to address the major objectives of this proposal. The project aims especially at focusing distinct major questions to the same sets of samples and experiments to synergistically obtain relevant information about the microbial assemblages and their capabilities to thrive in different salt concentrations, from seawater to saturation. Although most of the tasks in the project will be shared by the three subprojects, each of them will be responsible of different aspects. The UA team (SP2) will focus on the study of hosts and virus interactions, their diversity parallelisms and the host population control under different natural or controlled conditions. Some of the goals of this subproject focus on some of the basics of diversity (i.e. what is a population? which are the evolutionary paths between hosts and infective particles?), and of molecular biology of hyperhalophilic viruses (as mechanisms of interaction and ORF function elucidation). In this way we plan to widen our previous findings in hypersaline environments to a higher salinity range.
- Since June 2016 we participate in Horizon2020 project METAFLUIDICS (http://cordis.europa.eu/project/rcn/203253_en.html) “Advanced toolbox for rapid and cost-effective functional metagenomic screening -microbiology meets microfluidics” that includes the participation of 5 companies, 4 universities and 4 research organizations from 6 different countries. The project is coordinated by Dr. Aurelio Hidalgo (CBM-UAM) and has been funded by the European Commission with a total amount of over € 8.8 million. During its course, METAFLUIDICS will integrate a range of technologies into a platform designed to beat the odds of identifying hits in metagenomic libraries faster, more efficiently and by a wider user base. Exploration and exploitation of the metagenome will be made faster and more successful by (i) ultrahigh-throughput screening in picoliter droplets that dramatically lowers the cost per assay to well below 0.01 cents and allows throughput of 107 assays per hour; (ii) workflows that streamline and increase the yield of library construction and functional expression and (iii) workflows for efficient bioinformatic analysis of hits based on user-friendly software solutions for metagenome analysis. This platform will be used to identify enzymes for biosynthesis of therapeutic small molecules, for green bioenergy conversion, bioremediation, food chemistry and other industrial applications.
- During the years 2016 and 2017, our group coordinates the Spanish Network of Extremophiles (http://web.ua.es/es/rnme/) that includes mostly all the Spanish groups working on extremophilic microorganisms, as well four companies working on biotechnological applications of these microbes. The Network is funded by the Spanish Ministry of Economics and Competitiveness.
- In collaboration with Dr. Nicolás Cuenca, expert in retina, we are collaborating in a EXPLORA project on optogenetics to use retinal-binding proteins directly from the environment for the treatment of blindness, using a metagenomic approach similar to the one we used to study natural communities.
SELECTED PUBLICATIONS (LAST 5 YEARS)
González-Torres, P., Pryszcz, L. P., Santos, F., Martínez-García, M., Gabaldón, T., and Antón, J. (2015) Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing. Applied and Environmental Microbiology, 81: 8445-56. This is the first report of the analysis, by means of rRNAseq, of the interactions of strains of the same species in co-culture. Our results show that each strain sensed the presence of the other and responded in a specific manner, which points to fine intraspecific transcriptomic modulation.
Gomariz, M., Martínez-García, M., Santos, F., Rodriguez, F., Capella-Gutiérrez, S., Gabaldón, T., Rosselló-Móra, R., Meseguer I., and Antón, J. (2015). From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists. The ISME Journal, 9. 16-31. This is very likely the most detailed description on the dynamics of microbial communities in solar salterns through a 1-year period. It shows that environments traditionally considered as rather static are indeed very dynamic, underlying the importance of temporal samplings. The application of the already “classical” molecular techniques, such as DGGE, unveiled the presence of a ubiquitous member of the Bacteroidetes phylum. Using single cell technologies we were able to “isolate” it and partially characterize its genomes, that harbored retinal binding proteins.
Martínez-García, M., Santos, F., Moreno-Paz, M., Parro, V., and Antón, J. (2014). Unveiling viral-host interactions within the “microbial dark matter”. Nature Communications, Vol 14. DOI 10.1038/ncomms5542. This paper was selected by the F1000prime following the recommendations of Dr. Gilbert (Argonne National Laboratory de EEUU). His comment summarizes the contents and relevance of the paper: “This paper describes a new method for the unambiguous identification of bacterial-viral host-phage pairs. Basically, they isolated viral genomes from a sample and immobilized them on a microarray and then screened single bacterial cells against this array; those that hybridized must have been infected with a given virus. These can then be characterized as having a host-phage relationship. Simple, but exciting. The authors show some nice test results, and highlight the potential to identify rare microbial-phage relationships.”
Rubio-Portillo, E., Yarza, P., Peñalver, C., Ramos-Esplá, A.A., and Antón, J. (2014). New insights into Oculina patagonica coral diseases and their associated Vibrio spp. Communities. The ISME Journal 8: 1794-807. In an attempt to clarify the relationship between Vibrio spp., seawater temperature and coral diseases, as well as to investigate the putative differences between Eastern and Western Mediterranean basins, we analysed the seasonal patterns of the culturable Vibrio spp. assemblages associated with healthy and diseased O. patagonica colonies. Two sampling points located in the Spanish Mediterranean coast were chosen for this study: Alicante Harbour and the Marine Reserve of Tabarca. A complex and dynamic assemblage of Vibrio spp. was present in O. patagonica along the whole year and under different environmental conditions and coral health status. While some Vibrio spp. were detected all year around in corals, the known pathogens V. mediteranei and V. coralliilyticus were only present in diseased specimens. The pathogenic potential of these bacteria was studied by experimental infection under laboratory conditions. Both vibrios caused diseased signs from 24 1C, being higher and faster at 28 1C. Unexpectedly, the co-inoculation of these two Vibrio species seemed to have a synergistic pathogenic effect over O. patagonica, as disease signs were readily observed at temperatures at which bleaching is not normally observed.
Santos, F., Moreno, M., Meseguer, I., López, C., Rosselló-Mora, R., Parro, V., and Antón, J. (2011). Metatranscriptomic analysis of extremely halophilic viral communities. The ISME Journal 5:1621-1633. This is one of the few published papers on metatranscriptomics of viral communities. The combination of cloning the viral genomes in different vectors and their immobilization in microarrays, allowed the identification of viral sequences that were more actively transcribed in the natural samples and after different types of stress (namely, UV light and dilution). In a previous study (Santos et al. (2020) Env. Microbiol. 12:2965-2976), these sequences had been tentatively assigned to different hosts based on GC content and dinucleotide frequency.
Antón, J. Salty worlds underwater. (2015) Environmental Microbiology 17: 255-256. This in an invited “highlight” paper for the special issue of Environmental Microbiology on Low water activity habitats.
Santos, F., Yarza, P., Parro, V., Meseguer, I., Rosselló-Móra, R., and Antón, J. (2012). Viruses from hypersaline environments: a culture-independent approach. Applied and Environmental Microbiology 9: 1711-1723. This is a mini-review on the use of culture independent techniques, such as metagenomics, to study the viral assembles in high salt environments.
We participate in the degrees of Biology, Nursery, Nutrition and Dietetics, the Masters of Biomedicine and Biotechnology and the PhD program in Experimental and Applied Biology (http://www.ua.es/en/index.html).
If you are interested in joining our group, positions for graduate students and postdocts will be shortly available.
We look for highly motivated students/postdocts with a sound knowledge of Microbiology and related disciplines, able of independent thinking, with a reasonable level of wet lab and computer skills, and fluent English. Candidates must be able to work within a group. We consider this as an extremely important point since our research is normally based on collaborative approaches and on the interchange of knowledge and ideas between the different members of the group, who have a high level of interaction.
A y B. Symbionts of the ascidian Cystodytes dellechiajei. C. Fluorescence in situ hybridization (FISH) the extremely halophilic bacterium Salinibacter ruber. D. Halocine effect on an hyperhalophile culture. E. Haloviruses in Santa Pola salterns. F, G y H. Stromatolites and cyanobacteria from Ruidera Pools.
Universidad de Alicante
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Tel: (+34) 96 590 3400Fax: (+34) 96 590 3464