Microbial diversity and Microbiology of Extreme Environments

Description

The group of microbial diversity and microbiology of extreme environments is devoted to investigate the functional role of microbial diversity in a variety of environments, and different microorganisms, their genes and biomolecules with a special, but not exclusive, focus on extremophiles. A wide range of techniques and procedures are generally applied in our research which includes basic and applied initiatives and a high interest in biotechnology. Please, click here for further reading and contact information.

Innovation is our goal. Read on our research and understand why some of the following keywords are related to our investigation: Microbiology, Genomics, Biochemistry, Environmental Microbiology, Microbial Diversity, Microbial Ecology, Physiology, Bioinformatics, Ecophysiology, Biogeochemistry, Bioengineering, Biotechnology, etc.

Research

Background of our research topics

The great majority of life on Earth is microscopic in size, and it is only visible through the microscope. Microbes are everywhere and they inhabit any environment, from very cold (below 0°C) to very hot (above 100°C) places, from very acidic to very alkaline sites, or high saline concentration, high pressure, or any other environment that might not look normal to humans. Microorganisms thriving under extreme conditions are the extremophiles.

This variable selection of systems is reflected by the huge diversity exiting in the microbial world. Currently, the level of microbial diversity on Earth is a topic of debate but it is accepted that generally a gram of soil contains about 10¹⁰ bacteria with around 30,000 different taxa. A ml of mineral drinking water can contain about 10⁶ bacteria with several thousands different bacteria. While many microorganisms can easily be dispersed across the planet, the extreme environments present strong selectivity for the organisms able to thrive in them. Thus, extreme environments can be considered as ideal model systems for studying ecological properties of microorganisms, their physiology, adaptive properties and many other characteristics related to microbial communities and specific microbial cells.

Due to the small size of microbes, their study is not an easy task. Microscopic examination is required to see them. Classical microbiological studies required the ability to growth the microorganisms in the laboratory to be able to study their properties, such as growth conditions, nutrient sources, metabolic products, and so on. Even today, the growth of microorganisms is an essential step to be able to study in depth how they behave and their actual features and capabilities. We now know that most microorganisms in the environment can not be brought into cultivation. So the design of novel strategies to investigate their diversity, function, and potential applications is required. In order to understand our Planet, we are interested in the who, what, when, where, why and how questions about microbial life. The way to do it brings up an exciting experience to discover step by step the diverse microbial world and how it works.

It is too difficult (just to avoid to say impossible) to duplicate an organism’s host environment/ecosystem in a laboratory. However, some microbial processes or properties can be analyzed in the laboratory using isolated microorganisms. This apparent contradiction suggests a need for a variety of methodologies to be applied either in the laboratory or in the field; none of them excludes the others and so results are complementary and required to understand microbial life.

With the advent of molecular techniques, we can understand the microbial environment in much greater detail. It is possible to use the information hold in the nucleic acids of microorganisms to detect those present in an environment. Thus, molecular methods based on DNA and RNA represent very useful techniques to analyze microbial communities in situ, both presence and metabolic activity. Nucleic acids can be used to both detect the presence of a microorganism and to look at its functional genes. Which genes and metabolic pathways are actively expressed, and we can do similar research on microbial communities through metagenomic (whole community genomics) approaches. Of course, the amount of data to be processed increases exponentially with the number of different microorganisms in a sample and complexity increases exponentially. Bioinformatic tools become an essential part of the research process due to the massive amount of sequencing data to be processed. The use of molecular techniques is not only about detecting microorganisms; detection of microorganisms and their functional genes are complemented with an evaluation and analysis of the processes being carried out by those microbial communities in the environment.

Microorganisms are never alone. They work in communities, often composed by a large number of different types of cells. Frequently, they form biofilms mixing cells into complex polysaccharide matrices. The study of microbial communities and their interaction with the environment are key aspects to understand the role and function of microorganisms in nature, and consequently the implications of microbial life at local and global scales in our planet.

Microorganisms thriving under extreme conditions generally present specific adaptations which allow them to develop in unique environments. The properties of their biomolecules are of interest in biotechnology due to their high stability and durability which are a reference to be used in potential applications in industry or processes of commercial interest. The search for unique microorganisms and molecules (i.e., enzymes to be used as biocatalysts) also require the use of a variety of techniques with an important component of molecular methods.

Our group is keen in searching for novel methodologies and the application of a wide variety of strategies to answer specific questions. Methods involving a wide range of molecular techniques, the cultivation of microorganisms, biochemistry, physiology, ecology, biotechnology, genomics, bioinformatics, among others are some of the procedures commonly applied in our research. We pretend to further study microbial life from a multidisciplinary perspective and we will be glad to collaborate with other groups and individuals interested in related topics and their applications. For a list of our publications and projects, please, visit the corresponding page. To contact on potential collaborations, please, contact us.

Currently, we are mostly working on different aspects of the microbial World that could be summarized in these basic points:

Group name: Microbial diversity and Microbiology of extreme environments
– Microbial diversity and function in different environments.
– Genomics, ecophysiology, biogeochemistry and biotechnology of microorganisms, specially extremophiles.
– Analysis of microbial growth under limiting conditions.
– Heterogeneity in microbial communities.

At present, we are developing culturing tools and analyses to investigate the behavior of microorganisms under strict growth-limiting conditions which are most frequently encountered in nature by microorganisms. Only understanding the microorganisms under those limiting conditions scientists would be able to understand microbial functioning and role under a variety of environmental conditions and in a changing World.

In order to understand the behavior of these cells under radically different conditions (optimum growth versus near-zero growth rates, adverse vs. favorable, feast vs. famine conditions, etc.)

We are developing new methods to rapidly and efficiently monitor the growth status of microorganisms under a broad range of conditions and scenarios. Some of these methods are based on the use of fluorescent approaches.

Another line of interest involves the biotechnological applications of microorganisms and their enzymes and the understanding of how they work in order to optimize production processes and efficiency. The interest of extremophiles in biotechnological applications is critical for the development of a sustainable bioeconomy.

In the next years, we will be approaching novel studies on the variability within microbial populations, both intra- and inter-species. This include how different individual bacteria behave, how is the frequency distribution both in microbial communities and within intra-species (and clonal) populations. A number of approaches are being developed, so if interested on this or some of the above research trends, please, contact us for potential collaborations.

Projects

Functional responses of bacteria at very low growth rates. Ministry of Science and Innovation, Feder funding. PID2020-119373GB-I00.

We inhabit a microbial planet. The diversity and activity of microorganisms control most limiting processes in nature. However, there is a large gap of knowledge in our understanding of the growth rate of different microorganisms in nature and their consequences. Our results so far have shown a different behavior of microorganisms in nature and in the laboratory. Different results have shown that microorganisms in the environment thrive through feast and famine cycles with frequent periods of highly limited growth at very low growth rates. A clear example, and a scarcely explored field, is the case of microorganisms inhabitants of subsurface environments which present minimal growth and this is also the case for many microorganisms in most environments. This study proposes the analysis of functional responses of different bacterial species at different growth rates to comparatively evaluate bacterial behavior at very low growth rates (near-zero growth rates). We will study different bacterial groups to obtain a broad perspective of responses and living strategies. The genome sequence of the proposed bacteria is available so that the whole-cell gene expression transcriptomic analyses (RNA-seq) to be performed will be facilitated. Bacteria will be grown in continuous cultures in a chemostat for optimum growth rates and those at near-zero growth rates will be obtained using a retentostat, specifically setup in our laboratory for this goal. A retentostat represents the only available method to obtain bacteria at such low growth rates (e.g., hundreds of years generation time). Using comparative analysis, we propose to decipher whether different bacterial groups follow different or similar strategies, the mechanisms at gene expression level (transcriptomics) involved in near-zero growth and as a value added we will evaluate different molecular indicators to estimate bacterial growth state based on lifetime fluorescence measurements. As a result, this project will decisively contribute to understand the world of bacterial growth at very reduced rates, to determine if these strategies are universal or species specific and to obtain a comparative and functional perspective of the near-zero growth status and persistence of bacteria which represents the most common state in the bacterial world.

Grant PID2020-119373GB-I00 funded by MCIN/AEI/10.13039/501100011033 and by ERDF A way of making Europe”, by the “European Union”.

Behaviour and adaptative consequences of bacteria at low growth rates. Andalusian Government. P20_00774. P20_00774.

We inhabit a microbial planet. Microbial diversity and activity govern numerous limiting processes in nature. Nevertheless, there is a large gap of knowledge about the growth rates of microorganisms in nature and the consequences. Our previous results have confirmed a distinctive behavior of microorganisms in nature and in the laboratory. It is considered that microorganisms live in nature through cycles of feast and famine on their required resources. As well, it is assumed that this lead to the maintenance of the existing large microbial diversity. Thus, microorganisms must experiment periods of growth and maintenance (or near-zero growth) although this is a mostly unknown topic. This study proposes the study of the characteristics of bacterial growth at near-zero rates by comparative analysis to growth under optimum conditions. Different bacterial groups showing distinct metabolisms and living strategies will be studied. The full genome sequence of the proposed bacterial species is available which will facilitate further gene expression analyses. The near-zero growth rates will be achieved by using a retentostat, specifically designed to this goal because it represents the only procedure to obtain bacteria at those extremely low growth rates. We propose to decipher if different bacterial groups follow distinctive or similar strategies, the mechanisms involved in growth at near-zero rates, and the potential adaptive consequences on the generation of intraspecific heterogeneity at the epigenetic and genomic levels. As a result, this project significantly contributes to understand the world of bacterial growth at highly reduced rates, whether these strategies are species-specific or universal, the mechanisms or strategies of bacterial persistence and to understand the first steps leading to the generation of novel microbial diversity.

Rational design of thermostable enzymes for saccharification of plant biomass under consideration of transport and accessibility. Andalusian Government Feder. PY20_RE_021_LOYOLA.

Within the context of modern Biorefineries, this proposal faces processes of valuation of residues from the agricultural industry. Specifically, we will study the optimization of thermoestable enzymes to obtain bioproducts of high added value from residues of rice straw and citric skin. The major difficulty that the processes of enzymatic hydrolysis of plant biomass encounter center around the resistance that it offers to degradation (recalcitrance) by: (I) difficult access of enzymes to glucosidic links and (ii) phenomena of non-productive adsorption and slow kinetics of desorption. We propose modifications in thermophilic enzymes affecting their size and properties of adsorption/desorption to substrates so that the transport and accesibility by enzymes is improved. This study will center of endoglucanases, which decompose the lignocellulosic material to oligosaccharides, products of high added value as prebiotics and promoters of the plant immune system. In summary, the proposal contains the following basic steps: (a) Synthesis of endoglucanases modified to diminish their size and properties of adsoprtion/desorption to the

substrate. (b) Evaluation of the enzymatic activity and transport properties of the modified enzymes on plant residues and commercial substrates by comparison to the native enzymes. (c) Development of kinetic models that will contribute to explain the obtained results and will allow redirect future enzymatic manipulations. (d) Initial assays for the development of optimized processes for the conversion of residues on oligosaccharides of medium/high added value. Thanks to the multidisciplinarity of the research team, the project globally faces a process highly transversal containing biochemical interests, chemical and process engineering and physico-chemical and mathematic aspects.

Collaborators: Mauricio Zurita (Loyola University; Coordinator), Ladero Galan (Universidad Complutense de Madrid), Juan M. González (IRNAS-CSIC)

Spectrometer for fluorescence lifetime measurements and their use in Microbiology. Ministry f Science, Innovation and Universities. Feder. EQC2019-005634-P.

It is proposed the acquisition of un pectrometry to carry out fluorescent lifetime measurements. The equipment will carry out measurements of TCSPC (“time correlated single photon counting). The equipment will perform TCSPC (“time correlated single photon counting”) measurments, a highly sensible technique which is independent on the concentration of biomolecules allowing the deteccion and analysis of comlex samples, for instance, in cells in vivo. The aim of this activity is to provide with new tools to the field of Microbiology, a technieu that, at presemt, is highly underused. TCSPC techniques, for example, allow determinations of specific biomolecules (proteins, probes and indicators, etc.) as well as to determine the interaction among different other biomolecules, under different conditions. This, will provide with in situ measurements, using non-destructive techniques in complex natural samples, allowing the monitorization of the physiology of prokaryotic cells and microbial and biotechnological processes. The proposed equipment covers the complete spectrum from UV to the infrared in liquid and solid samples (including biofiolms), as well as the possibility to carry out measurements in fluorometry cuvettes and to quantify microscopic examinations (i.e., FLIM or Fluorescence Lifetime Imaging Microscopy) to evaluate the physiological status of individual cells (single-cell analysis). By TCSPC. The equipment will incorporate to the service “Detection and function of microorganisms and their molecules” in IRNAS-CSIC to offer the widest diffussion and potential use among all types of users.

Grant EQC2019-005634-P funded by MCIN/AEI/10.13039/501100011033 and by ERDF A way of making Europe” by the “European Union”.

Sterilization system for a new microbiological laboratory of biosecurity level type II. Andalusian Government, cofunded by FEDER. IE19_181.

The objective of this application is the acquisition e installation of a “System of sterilization for a new microbiological laboratory of biosecurity level type II” ay the Institute of Natural Resources and Agrobiology of Sevilla, Spanish National Council for Research. This laboratory has shown a solid scientific history as shown by their publications, continuous funding, international collaborations and supervision activities, evaluation, networks, and divulgation. Besides, it is important to highlight that the applicant team has received in December 2019 the ISO9001 certification and the equipment proposed will integrate in the certified management system, including maintenance and validation plans. The equipment will be available to IRNAS-CSIC, as well as to other users, both internal and external, that could require to use this equipment. The scientific service from CSIC, where this equipment will integrate and the laboratory of biosecurity level type II will manage external applications. Motivations for this applications will consider important factors related to PRL, a required reform of facilities in a new laboratory aa the Biosecurity level II, improved excessively aged equipment, the needs to function with novel adequate equipment to current conditions and the certification of quality, adapting to the prestige of the laboratory, both national and international, for the research team, the quality certifications of a number of activities for the scientifical-technical service.

Procesos de isomerasas termófilas para Biotecnología. European Union. Horizon 2020. ERA-IB2 7th call. Industrial Biotechnology for Europe. An Integrated Approach. ERA-IB-16-049; Ministerio de Economía y Productividad, Acciones de Programación Conjunta Internacional 2016. PCIN-2016-129.

Isomers are molecules with identical atomic composition but with different structural characteristics. Different isomers can show very distinctive function. Isomerases are enzymes catalyzing the conversion between different types of isomers. Thermostable isomerases are desired because they possess high resistance and durability, are able to withstand harsh industrial process conditions, including heating and organic solvents. Elevated temperatures can also enhance substrate accessibility and solubility. The proposed project includes comparative bioinformatic analyses of sequence data to identify different classes of thermostable isomerases of industrial interest which will be cloned, over-expressed, functionally and structurally characterized and optimized towards their biotechnological application. Three types of isomerases will be targeted: sugar isomerases (to produce new desirable sugars for calorie-free sweeteners and as building blocks for drugs), disulfide isomerases (to improve protein folding and stability of industrial enzymes), and chalcone isomerases (involved in the transformation of flavonoids, secondary metabolites of importance as natural colorants, anti-oxidants, anti-microbial and anti-inflammatory agents). Durable isomerases will allow new opportunities for green, competitive and sustainable biotechnological processes that can replace conventional chemical synthesis.

Collaborators: IRNAS-CSIC (Spain), University of Bergen (Norway), Christian-Albrechts-Universitat Kiel (Germany), University of Exeter (United Kingdom), Bioavan SL (Spain)

Microbial life beyond optimal conditions. Ministry of Economy and Productivity. project CGL2014-58762-P.

Microorganisms are the base to support biogeochemical cycles and terrestrial ecosystems. However, the functioning of microorganisms in natural systems is remains to be deciphered, above all, under conditions considered as extreme or far from the optimum for those cells. It is known that a number of extremophilic microorganisms inhabit soils and sediments although their role has been barely studied. These extremophiles are an ideal target to tackle the role of microorganisms under conditions not included within their usual growth conditions. This proposal is built on the idea that microorganisms are able to perform some activities and maintenance growth at sites with, or during periods of, conditions beyond their usual growth range and the microorganisms in nature behave differently than in laboratory cultures. The actual growth and activity of microorganisms under those unique conditions remains unknown and so are the multiple potential consequences such as explaining high microbial diversity, microbial and enzymatic activities under extreme conditions, cell survival and the interest of applying the knowledge derived from understanding these processes to biotechnology. We propose the analysis of the microbial communities, their enzymatic activity, metabolism, and growth in terrestrial environments using extremophiles as target for this analysis. The use of extremophiles will facilitate the analysis by selecting a specific group of microorganisms from the vast microbial diversity existing in natural environments. Different environmental conditions will be analyzed, including those occurring during the extreme climate events along the year, including summer and winter extremest conditions. Methodologies will include new generation sequencing to characterize the structure of microbial communities under a variety of conditions and their genomic potential based on DNA genomic and amplicon analyses, the identification of metabolically active microbial taxa through their RNA, the determination of enzymatic extracellular activity and microbial metabolism by fluorescence assays and respiration measurements, quantification of growth/death rates through live/dead staining and microscopy and flow cytometer quantification, and evaluation of the potential of these processes and results to biotechnological applications. This study will bring up a significant advance on our understanding of the environmental role of microorganisms and their enzymes under marginalized conditions and it is expected that it will replace the current concept that those situations show minimal relevance. Understanding the behavior of microorganisms under unique conditions will establish a base to apply this knowledge to biotechnology and the sustainability, maintenance and efficient utilization of soils, including global climate changes and the C soil-atmosphere balance.

Effects of water content and temperature on microbial diversity and its activity in soils and sediments. Application to the degradation of halogenated pollutants. Andalusian Government, RNM2529.

Microorganisms in soils and sediments are essential for maintaining these systems. Predictions of global climatic changes and the existence of periods of high temperatures and droughts in our region suggest the importance of knowing the variations in diversity and activity induced on microbial communities in order to achieve an efficient use of resources. These phenomena are critical, for instance, to obtain an appropriate use of soils and sediments for agriculture and the recovery of polluted sites. Microorganisms are the only link able to carry out a high number of processes such as closing the biogeochemical cycles of elements, which are related to the fertilization of terrestrial environments, the degradation of recalcitrant pollutants, and global phenomena. This study will analyze the influence of high temperatures (>40°C) and periods of desiccation on microbial communities, their diversity and activity, in relationship to the decomposition of organic matter and recycling of nutrients in terrestrial environments. This includes their use within a sustainable scheme and the degradation of pollutants under those extreme conditions. To this aim different methods will be used; such as molecular techniques including new generation sequencing to detect the huge microbial diversity existing in soils and sediments, including metagenomics of these natural microbial communities. These methods will be combined with enzyme activity assays that will be designed specifically for these conditions. Experiments will include the analysis of a broad range of temperatures and desiccation conditions both in nature as in the laboratory aiming to understand the functioning and dynamics of microbial communities as a response to changes in water content and temperature, as well as applications to the sustainability of soils and sediments and the recovery of these environments. As an added value, this investigation will search for novel enzymes or biocatalysts which will be characterized. This project represents a collaboration between a research center (IRNAS-CSIC) and a technology-based enterprise (Bioavan SL) which shares a common interest to reach the necessary knowledge to maintain our environment and economic development through sustainability.

Contract funded by the Incentivo de contratacion de personal investigador en Formación (Fase 2, PIF 2012), Andalusian Government.

Integrative analysis of extremophiles in search for new biotechnological solutions. NILS Science and Sustainability programme, EEA Grants, 003-ABEL-CM-2013.

A sustainable bioindustrial economy requires replacing chemical processes by green, renewable bio-based alternatives. Microorganisms represent the best potential target for biotechnology. Among them, the extremophiles (microorganisms living, for example, under extreme temperature and pH) include the most resistant cells and enzymes required to support the hardiest industrial processes. This action focuses on searching for new hydrolytic biocatalysts, a first step in biotransforming complex residues into assimilable molecules. The strategy includes the major stages: cells, genomes, enzymes and mathematics as an integral approach to model, design and discover novel biocatalysts such as highly resistant enzymes or novel functionality for existing genes. This project involves four research groups, one Norwegian (University of Bergen) and three Spanish teams (IRNAS-CSIC, Center of Astrobiology-CSIC, University of Sevilla). The aim is to join multidisciplinary views to generate biotechnological solutions and advancement into the hydrolysis of cellular materials and residues.

Comparative Microbial Genomics. MICROGEN. Ministry of Science and Innovation, project CSD2009-00006.

Microorganisms are still the main cause of death in the world, they are the main source of genetic biodiversity and the main players in ecosystem functioning. However, the way bacterial populations are structured, the way they evolve or interact with other biotic components or the way they adapt to the environment and evolve are still poorly known. This is partly due to the need for pure culture in order to perform experiments and to the application of an evolutionary model imported from eukaryotic systems. With the advent of genomics and the new high-throughput sequencing techniques of low cost, a new era has emerged in which bacteria can be studied through their genomes, obviating the need for culturing the microorganisms and allowing a holistic study of ecosystems. In addition, the study of this vast genetic reservoir may provide access to a wealth of new bioactive compounds previously unreachable by standard techniques. Some important changes in our way of understanding microbes are starting to emerge, a crucial one being the existence of a gigantic pool of genes within each bacterial species, in such a way that this gene pool (the “pan-genome”) is much larger than the genome of each individual strain. This is vital to understand bacterial biology and has important consequences from an applied point of view. The present project aims to study microorganisms by a combination of genomics, bioinformatics, molecular biology, metagenomics and next generation sequencing. This will be achieved by the creation of a multidisciplinary team combining all those skills in an ambitious proposal that would not be possible by standard funding. The consortium will use many different bacterial species as models of pathogenicity and symbiosis in human, animal and plant hosts, as well as studying different natural and human-related ecosystems to unravel the population genomics and genome fluidity of bacteria. This will shed light on the species concept, the structure of bacterial populations, its interaction with viruses and the environment, their adaptation and their evolution, as well as opening new avenues for treating infectious diseases. In addition, a web-based server will be created to study, annotate and analyze bacterial genomes, and new scripts and computer programs will be developed that will be of great use for the scientific community. It is anticipated that the group will serve as a nucleating agent that will permit Spanish Microbiology to remain in the mainstream of international Microbiology and to continue being a support to the future of Spanish Biotechnology and Biomedicine.

The presence and role of low abundance microorganisms could explain the huge microbial diversity of natural systems. A case study in the Doñana National Park. Ministry of Science and Innovation, project CGL2009-12328/BOS.

Microbial diversity in natural environments is huge and difficult to determine. These microbial communities can be considered as formed by a low number of highly abundant microorganisms and a very high number of rare, low abundant, microorganisms. We present the hypothesis that the microorganisms representing that minority are important in natural ecosystems. The study of the rare microorganisms is essential for understanding the functional role of microbial communities in an spatial and temporal environment, as well as to comprehend why exist a so large microbial diversity. The selection of microorganisms adapted to thrive under extreme conditions (high temperature, low or high pH) from moderate environments is proposed. The selected environment is the sediment from the natural ponds at Doñana National Park. Environmental variables will be determined and changes in the microbial communities will be monitored during the selecting process. Molecular methods will be used for the detection of microorganisms based on both fingerprinting techniques and sequencing, and in situ detection methods. Cultures of selected microorganisms will be approached. Microorganisms, Bacteria and Archaea, will be identified and their physiological properties evaluated. Also, their spatial distribution will be analyzed and will contribute to decipher the potential function within their ecosystem. The possibility that those extreme conditions could represent natural situations will be studied. The analyzed processes will represent a model of the dynamic of microbial communities as a consecuence of environmental changes and their potential response both in the ecosystem and global biogeochemical cycles.

Microbial diversity and microbiology of extreme environments. Andalusian Government, BIO288.

Microbial diversity is a broad term that can be approached from very different perspectives. This includes not only the phylogenetic diversity but also includes molecular, functional, and mechanistic points of view. To achieve this broad assessment of the whole microbial world we use a wide and radically different methodologies which point towards a common objective, decipher the functioning of the microbial world. The focus on extremophiles allows to center on a specific type of microorganisms and communities which are of great interest for their potential biotechnological applications as well as model systems for the study of natural communities.

Publications

http://www.microextreme.net/publications.html

Jobs

Our group offers research and training opportunities in a multidisciplinary environment having as common denominator the understanding of microbial life in a broad sense and its applications. Job opportunities and fellowships are available at a variety of levels, including undergraduates, graduates and PhD students, postdoctoral and senior positions, as well as to collaborate in different projects and initiatives. Opportunities are often available and we can arrange and/or apply for grants to obtain additional funding for outstanding candidates and joint projects.

If you are interested to carry out high quality research with us, please, let us know. For those searching for a position or fellowship, please, attach your CV in your contact letter. For information and letters of interest, visit our contact us section or send us an e-mail message.

Marie Curie researcher. The Marie Curie – Individual Fellowship program offers opportunities for researchers to participate in the research of a host institute where they can both learn new perspectives and methodologies as well as introduce important knowledge at the hosting center. Information on this call can be found at the Marie Curie – Individual Fellowship call page. Dynamic and innovative researchers are encouraged to apply for a Marie Curie – Individual Fellowship to develop a research project with our group at IRNAS-CSIC. For information and to discuss on a research project, please, contact us.

FPU (predoctoral fellowships). Opportunity for a four-year predoctoral fellowship from the Spanish Ministry of Education. A new call is opened every year. Consider to get involved in our research through this fellowship and work towards your PhD degree with us. Please, contact us.

JAE-INTRO. A program from CSIC to finance a two month research period in a CSIC institute for students involved in a Master course. Please, consider our team to carry out innovative methodologies, state-of-the-art research. For information and application aid, please, contact us.

Postdoctoral positions. Opportunity for a postdoctoral contract through the Juan de la Cierva program or for a five-year position through the Ramon y Cajal program. Calls are generally opened annually. For more information contact us.

Postdoctoral positions. Annual calls. Opportunity for a postdoctoral contract through the Juan de la Cierva program or for a five-year position through the Ramon y Cajal program. Calls are generally opened annually. For more information contact us. Opportunities are offered each year for permanent positions at CSIC. A number of positions are offered every year at CSIC on selected topics. Check the offers annually. For more information contact us.

Future positions and opportunities. Please, contact us if you are interested in possible positions or research opportunities in the future. Send us an email with your interests and qualifications and we will go back to you if we are aware of opportunities fitting your needs.

Downloads

The following software packages are available. Please, refer to the included readme files and the corresponding publications for additional information. Most of these packages have been developed under a Linux environment.

Ccode

This is a program to detect and evaluate the presence of chimeras and cross-over recombination in sequence data. This program and procedure has been described by Gonzalez et al. (2005; Evaluating putative chimeric sequences from PCR amplified products and other cross-over events. Bioinformatics 21: 333-337).

There are versions to be downloaded for the Linux and Windows operating systems. For the Unix/Linux operating systems you should download the file ccode25.tar and for the Windows/DOS operating systems you should download the file ccode025w.exe (windows version). To align the selected sequences you can use ClustalW or some other program. If you use ClustalW, the right version needs to be installed. Below, please, find links to an UNIX/Linux version as well as to Windows/DOS (not XP or above) and Windows XP versions.

Ccode for UNIX/Linux. Tar file containing: ccode025 executable (Linux Red Hat v. 9.0), ccode025.c (source code), Readme.1st (manual; text file) and run_ccode025 (a shell script requiring clustalw).

Ccode for windows/dos. Zip file containing an executable ccode025 version for windows/dos platforms and some brief installation instructions.

ClustalW 1.83 for UNIX/Linux. Compressed (tar) file containing clustalW1.83 for Unix (including Linux).

ClustalW 1.83 for DOS and Windows (excluding XP and above). Compressed (zip) file containing clustalW1.83 for Windows/DOS platforms (excluding Windows XP).

ClustalW 1.83for Windows XP. Compressed (zip) file containing clustalW1.83 only for the Windows XP operating system.

Fingshuf.

This program allows to compare pairs of communities and determines if they show significant differences. It was originally proposed to differentiate microbial communities based on molecular profiles or fingerprints as described by Portillo and Gonzalez (2008; Statistical differences between molecular fingerprints from microbial communities. Antonie van Leeuwenhoek 94: 157-163). Fingshuf was developed under the Linux operating system and can be downloaded here. (fingshuf.zip)

Fires

This program finds repeated sequences or motifs in DNA fragments and genomes. It was written in C under the Linux operating system. It was reproted in Portillo and Gonzalez (2009; CRISPR-elements in the Thermococcales: evidence of associated horizontal gene transfer in Pyrococcus furiosus. Journal of Applied Genetics 50: 421-430). Fires can be downloaded here. . (fires03.zip)

MPN.

This is a program to perform counts using the Most Probable Number (MPN) procedure. It is useful to obtain complete MPN tables for any desired number of dilutions, tubes, and different amounts of samples, as well as to estimate the MPN for a single experiment. The program has been described by Gonzalez (1996; A general purpose program for obtaining Most Probable Number tables. Journal of Microbiological Methods 26: 215-218). This program was written for the DOS operating system although in works under any MS Windows version (at least until Windows 10) using the command line option. It can be downloaded here. (mpn4.zip)

People

Juan M. González Grau

Alba Cuecas Morano

Beatriz Aranda Cano

Marta Lebrón López

José Antonio Delgado Romero

Contact

Juan M. Gonzalez
Institute of Natural Resources and Agrobiology
Spanish National Research Council
Avda. Reina Mercedes 10, 41012-Sevilla, Spain
Tel. +34 95 462 4711 (ext. 440546)
E-mail: jmgrau[AT]irnase.csic.es