Bio Iliberis Research and Development

Granada, Spain

Bio Iliberis Research and Development

Granada, Spain
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Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: OCEAN.2011-2 | Award Amount: 11.51M | Year: 2012

Micro B3 will develop innovative bioinformatic approaches and a legal framework to make large-scale data on marine viral, bacteria; archaeal and protists genomes and metagenomes accessible for marine ecosystems biology and to define new targets for biotechnological applications. Micro B3 will build upon a highly interdisciplinary consortium of 32 academic and industrial partners comprising world-leading experts in bioinformatics, computer science, biology, ecology, oceanography, bioprospecting and biotechnology, as well as legal aspects. Micro B3 is based on a strong user- and data basis from ongoing European sampling campaigns to long-term ecological research sites. For the first time a strong link between oceanographic and molecular microbial research will be established to integrate global marine data with research on microbial biodiversity and functions. The Micro B3 Information System will provide innovative open source software for data-processing, -integration, -visualisation, and -accessibility. Interoperability will be the key for seamless data transfer of sequence and contextual data to public repositories. Micro B3 will allow taking full advantage of current sequencing technologies to efficiently exploit large-scale sequence data in an environmental context. Micro B3 will create integrated knowledge to inform marine ecosystems biology and modelling. Moreover, it will facilitate detecting candidate genes to be explored by targeted laboratory experiments for biotechnology and for assigning potential functions to unknown genes. Micro B3 will develop clear IP agreements for the protection and sustainable use of pre-competitive microbial genetic resources and their exploitation in high potential commercial applications. To underline the translational character of Micro B3, outreach and training activities for diverse stakeholders are planned as well as an Ocean Sampling Day to transparently make project results accessible and gain valuable user feedback.


Molina L.,University of Huelva | Molina L.,CSIC - Experimental Station of El Zaidín | Udaondo Z.,CSIC - Experimental Station of El Zaidín | Duque E.,CSIC - Experimental Station of El Zaidín | And 9 more authors.
PLoS ONE | Year: 2014

Environmental microbes harbor an enormous pool of antibiotic and biocide resistance genes that can impact the resistance profiles of animal and human pathogens via horizontal gene transfer. Pseudomonas putida strains are ubiquitous in soil and water but have been seldom isolated from humans. We have established a collection of P. putida strains isolated from inpatients in different hospitals in France. One of the isolated strains (HB3267) kills insects and is resistant to the majority of the antibiotics used in laboratories and hospitals, including aminoglycosides, β-lactams, cationic peptides, chromoprotein enediyne antibiotics, dihydrofolate reductase inhibitors, fluoroquinolones and quinolones, glycopeptide antibiotics, macrolides, polyketides and sulfonamides. Similar to other P. putida clinical isolates the strain was sensitive to amikacin. To shed light on the broad pattern of antibiotic resistance, which is rarely found in clinical isolates of this species, the genome of this strain was sequenced and analysed. The study revealed that the determinants of multiple resistance are both chromosomally-borne as well as located on the pPC9 plasmid. Further analysis indicated that pPC9 has recruited antibiotic and biocide resistance genes from environmental microorganisms as well as from opportunistic and true human pathogens. The pPC9 plasmid is not self-transmissible, but can be mobilized by other bacterial plasmids making it capable of spreading antibiotic resistant determinants to new hosts. © 2014 Molina et al.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: KBBE-2007-3-3-02 | Award Amount: 7.36M | Year: 2008

BACSIN is a 16-member consortium with the main focus to improve rational exploitation of the catalytic properties of bacteria for the treatment and prevention of environmental pollution. Current application of bacteria in the environment is hindered by the lack of knowledge on the effects of stresses on cellular activity, most importantly abiotic stresses prevailing on site (e.g., desiccation or nutrient starvation), stresses as a result of pollution itself (e.g., toxicity), and those during strain preparation and formulation. BACSIN proposes four iterative poles of research and technology to overcome this hindrance for subsequent improved microbial usage. The 1st pole will investigate genome-wide catabolic and stress expression in a set of different pollutant degrading bacteria (the BACSINs). Key cellular factors and regulatory networks determining the interplay between stress-survival and pollutant catabolism will be unveiled, and faithful predictive models for cell behaviour produced. The 2nd pole will study stress resistance, survival and activity of BACSINs in real polluted environments, via microcosms and in situ traps, plant roots and leaves, while accentuating possible effects on native communities. The 3d pole will focus on the original microbial communities at contaminated sites, to discover and exploit more optimal stress and survival resistance among resident pollutant-degrading bacteria. We will develop molecular diagnostics tools to screen contaminated sites for catabolic and stress parameters, and decide whether BACSIN complementation should be considered. Promising isolates of resident bacteria will be studied as new BACSINs, to show the usefulness of the diagnosis-isolation-reintroduction approach for enhancing pollutant biodegradation rates. Finally, we will focus on BACSIN formulations, to understand the stresses on bacteria during growth, preservation and resuscitation, and to produce optimally active cells for environmental application.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: KBBE.2011.3.6-03 | Award Amount: 7.77M | Year: 2011

The ST-FLOW Project merges the efforts of 14 leading European research groups for developing material and computational standards that enable the forward-design of prokaryotic systems with a degree of robustness and predictability that is not possible with customary Genetic Engineering. The central issue at stake is the identification and implementation of rules that allow the conversion of given biological parts assembled with a set of principles for physical composition into perfectly predictable functional properties of the resulting devices, modules and entire systems. ST-FLOW focuses on each of the steps that go from assembling a DNA sequence encoding all necessary expression signals in a prokaryotic host (by default, E. coli) all the way to the making of the final product or to the behaviour of single cells and populations. Two complementary approaches will be adopted to solve the conundrum of physical composition vs. biological functionality of thereby engineered devices. In one case (bottom up), large combinatorial libraries of gene expression signals will be merged with suitable reporter systems and the input/output functions examined and parameterized in a high-throughput fashion. The expected outcome of this effort is to establish experience-based but still reliable rules and criteria for the assembly of new devices and systems -following the same physical composition rules or adopting CAD design. Yet, many outliers (combinations that do not follow the rules) are expected, and making sense of them will be the task of the complementary top-down approach. In this case, ST-FLOW will revisit some of gaps in our knowledge of the gene expression flow (transcription, mRNA fate, translation) that need to be addressed for engineering functional devices from first principles. Ethical, legal and societal issues will also be examined in a context of public dialogue and sound science communication.


Fernandez M.,Bio Iliberis Research and Development | Conde S.,Bio Iliberis Research and Development | De La Torre J.,Consejo Superior de Investigaciones Cientificas | Molina-Santiago C.,Consejo Superior de Investigaciones Cientificas | And 2 more authors.
Antimicrobial Agents and Chemotherapy | Year: 2012

Pseudomonas putida KT2440 is a chloramphenicol-resistant bacterium that is able to grow in the presence of this antibiotic at a concentration of up to 25 μg/ml. Transcriptomic analyses revealed that the expression profile of 102 genes changed in response to this concentration of chloramphenicol in the culture medium. The genes that showed altered expression include those involved in general metabolism, cellular stress response, gene regulation, efflux pump transporters, and protein biosynthesis. Analysis of a genome-wide collection of mutants showed that survival of a knockout mutant in the TtgABC resistance-nodulation-division (RND) efflux pump and mutants in the biosynthesis of pyrroloquinoline (PQQ) were compromised in the presence of chloramphenicol. The analysis also revealed that an ABC extrusion system (PP2669/PP2668/PP2667) and the AgmR regulator (PP2665) were needed for full resistance toward chloramphenicol. Transcriptional arrays revealed that AgmR controls the expression of the pqq genes and the operon encoding the ABC extrusion pump from the promoter upstream of open reading frame (ORF) PP2669. Copyright © 2012, American Society for Microbiology. All Rights Reserved.


Fernandez M.,Bio Iliberis Research and Development | Conde S.,Bio Iliberis Research and Development | Duque E.,CSIC - Experimental Station of El Zaidín | Ramos J.-L.,CSIC - Experimental Station of El Zaidín
Microbial Biotechnology | Year: 2013

Pseudomonas putidaKT2440 has the ability to colonize the rhizosphere of a wide range of plants and can reach cell densities in the range of 105-106 cfu g soil-1. Using the IVET technology we investigated which KT2440 genes were expressed in the rhizosphere of four different plants: pine, cypress, evergreen oak and rosemary. We identified 39 different transcriptional fusions containing the promoters of annotated genes that were preferentially expressed in the rhizosphere. Six of them were expressed in the rhizosphere of all the plant types tested, 11 were expressed in more than one plant and the remaining 22 fusions were found to be expressed in only one type of plant. Another 40 fusions were found to correspond to likely promoters that encode antisense RNAs of unknown function, some of which were isolated as fusions from the bacteria recovered in the rhizosphere from all of the plants, while others were specific to one or several of the plants. The results obtained in this study suggest that plant-specific signals are sensed by KT2440 in the rhizosphere and that the signals and consequent gene expression are related to the bacteria's successful establishment in this niche. Pseudomonas putida KT2440 efficiently colonizes the rhizosphere of a wide range of plants; genes specifically activated in the rhizosphere of four different plants (pine, cypress, evergreen oak and rosemary) were investigated using the IVET technology. The results revealed that Pseudomonas responds specifically to plant signals through the activation of common genes and some specific ones for a given plant. © 2013 The Authors. Published by Society for Applied Microbiology and Blackwell Publishing Ltd.


Garcia-Salamanca A.,CSIC - Experimental Station of El Zaidín | Molina-Henares M.A.,CSIC - Experimental Station of El Zaidín | van Dillewijn P.,CSIC - Experimental Station of El Zaidín | Solano J.,Bio Iliberis Research and Development | And 4 more authors.
Microbial Biotechnology | Year: 2013

Maize represents one of the main cultivar for food and energy and crop yields are influenced by soil physicochemical and climatic conditions. To study how maize plants influence soil microbes we have examined microbial communities that colonize maize plants grown in carbonate-rich soil (pH8.5) using culture-independent, PCR-based methods. We observed a low proportion of unclassified bacteria in this soil whether it was planted or unplanted. Our results indicate that a higher complexity of the bacterial community is present in bulk soil with microbes from nine phyla, while in the rhizosphere microbes from only six phyla were found. The predominant microbes in bulk soil were bacteria of the phyla Acidobacteria, Bacteroidetes and Proteobacteria, while Gammaproteobacteria of the genera Pseudomonas and Lysobacter were the predominant in the rhizosphere. As Gammaproteobacteria respond chemotactically to exudates and are efficient in the utilization of plants exudate products, microbial communities associated to the rhizosphere seem to be plant-driven. It should be noted that Gammaproteobacteria made available inorganic nutrients to the plants favouring plant growth and then the benefit of the interaction is common. © 2012 The Authors. Microbial Biotechnology © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.


Fernandez M.,Bio Iliberis Research and Development | Niqui-Arroyo J.S.,Bio Iliberis Research and Development | Conde S.,Bio Iliberis Research and Development | Ramos J.S.,CSIC - Experimental Station of El Zaidín | Duque E.,CSIC - Experimental Station of El Zaidín
Applied and Environmental Microbiology | Year: 2012

In this work, we explore the potential use of the Pseudomonas putida KT2440 strain for bioremediation of naphthalene-polluted soils. Pseudomonas putida strain KT2440 thrives in naphthalene-saturated medium, establishing a complex response that activates genes coding for extrusion pumps and cellular damage repair enzymes, as well as genes involved in the oxidative stress response. The transfer of the NAH7 plasmid enables naphthalene degradation by P. putida KT2440 while alleviating the cellular stress brought about by this toxic compound, without affecting key functions necessary for survival and colonization of the rhizosphere. Pseudomonas putida KT2440(NAH7) efficiently expresses the Nah catabolic pathway in vitro and in situ, leading to the complete mineralization of [14C]naphthalene, measured as the evolution of 14CO2, while the rate of mineralization was at least 2-fold higher in the rhizosphere than in bulk soil. © 2012, American Society for Microbiology.


PubMed | Bio Iliberis Research and Development
Type: Journal Article | Journal: Applied and environmental microbiology | Year: 2012

In this work, we explore the potential use of the Pseudomonas putida KT2440 strain for bioremediation of naphthalene-polluted soils. Pseudomonas putida strain KT2440 thrives in naphthalene-saturated medium, establishing a complex response that activates genes coding for extrusion pumps and cellular damage repair enzymes, as well as genes involved in the oxidative stress response. The transfer of the NAH7 plasmid enables naphthalene degradation by P. putida KT2440 while alleviating the cellular stress brought about by this toxic compound, without affecting key functions necessary for survival and colonization of the rhizosphere. Pseudomonas putida KT2440(NAH7) efficiently expresses the Nah catabolic pathway in vitro and in situ, leading to the complete mineralization of [(14)C]naphthalene, measured as the evolution of (14)CO(2), while the rate of mineralization was at least 2-fold higher in the rhizosphere than in bulk soil.


PubMed | Bio Iliberis Research and Development
Type: Journal Article | Journal: Microbial biotechnology | Year: 2013

Pseudomonas putidaKT2440 has the ability to colonize the rhizosphere of a wide range of plants and can reach cell densities in the range of 10(5) -10(6) cfu g soil(-1) . Using the IVET technology we investigated which KT2440 genes were expressed in the rhizosphere of four different plants: pine, cypress, evergreen oak and rosemary. We identified 39 different transcriptional fusions containing the promoters of annotated genes that were preferentially expressed in the rhizosphere. Six of them were expressed in the rhizosphere of all the plant types tested, 11 were expressed in more than one plant and the remaining 22 fusions were found to be expressed in only one type of plant. Another 40 fusions were found to correspond to likely promoters that encode antisense RNAs of unknown function, some of which were isolated as fusions from the bacteria recovered in the rhizosphere from all of the plants, while others were specific to one or several of the plants. The results obtained in this study suggest that plant-specific signals are sensed by KT2440 in the rhizosphere and that the signals and consequent gene expression are related to the bacterias successful establishment in this niche.

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