Pseudomonas
Bacteria belonging to the Pseudomonas group are common inhabitants of soil and water and can also be found on the surfaces of plants and animals. Pseudomonas bacteria are found in nature in a biofilm or in planktonic form. In the latter form the single cell can display an extremely high motility due to its polar flagella. Pseudomonas bacteria are renowned for their metabolic versatility as they can grow under a variety of growth conditions and do not need any organic growth factors. Typically they are plant pathogens, although several strains are pathogenic to humans.
Biology of Pseudomonas stutzeri 
Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 20 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals.
Multigenic phylogenetic studies on P. stutzeri strains demonstrate that they belong to the same branch, together with related species within the genus. However, it is one of the most genetically diverse species described so far, with many metabolic capabilities. As a consequence, its distribution is almost universal, occupying many ecological niches, including the human body. P. stutzeri is a relevant organism for 3 main topics:
- Bioremediation: P. stutzeri has developed systems to ensure the availability of essential metals and, simultaneously, to handle metal toxicity, by sinthesizing special siderophores that combine with Co, Cu, Fe and Ni;
- Alternative Energy: P. stuzeri is involved in energy production in many natural and artificial habitats (biodigestors) through its ability to hydrolyze polymers by producing different types of amylases, which are necessary in the preparation of the biomass for the biogas or bioalcohol production; and
- Global Carbon Cycling and accumulation of greenhouse gases in the atmosphere: P. stutzeri is the best known denitrifier, playing a key role in the natural production of N2 and NOx in the atmosphere.
The sequencing and comparative genomic analysis of P. stutzeri strains, nowadays includes strains representing up to 6 genomovars of the 18 so far described in the species. All strains have been selected for their physiological properties and as representatives of different genomovars of the species, in detail:
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ZoBell is of marine origin (formerly classified as "P. perfectomarina"), representing the genomovar 2 and considered a model micoorganism in studies of the denitrification process. It is the best denitrifying microorganism studied. Most bioremediation studies have been performed with bacterial strains in aerobic process. Denitrification is an anaerobic process in which several strains of P. stutzeri are able to use aromatic contaminants when oxygen is the limiting factor, using nitrate as terminal electron aceptor.
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JM300 is considered the model organism for natural transformation, and an excellent organism for genetic analysis in the environment and the spread of degradation genes;
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AN10 is a strain isolated from marine sediments highly contaminated by hydrocarbons and has been studied for its ability to mineralize aromatic compounds;
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CCUG 11256 T, the type strain of the species and will be used as a reference and it is of clinical origin. Adaptation of the species to this totally different habitat should will be studied;
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19SMN4 is the reference strain of genomovar 4, isolated from highly contaminated marine sediment in the Mediterranean;
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NF13 strain belongs to the genomovar 3 and was isolated from hydrothermal vents of the deep ocean (2,500 to 2,600 m), grows at low temperatures (for example, 4 ° C). Additionally, its enzymatic activities especially different from the rest of members of the genomovar 3 make it particularly interesting.
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The type strain of Pseudomonas balearica (DSM 6083 T). It is the former genomovar 6 within P. stutzeri and now recognized as a new species within the genus Pseudomonas (Bennasar et al, 1996).
P. stutzeri is the species with the greatest recognized genetic diversity described so far. Elucidation of the mechanisms underlying this diversity will help in understanding speciation. Thus, P. stutzeri is a good model organism to understand bacterial evolution and the adaptation of bacterial strains to contaminated environments for their detoxification. Along the genomic projects, we expect increase our knowledge on the following aspects:
- Determination of the core genes of the species comprising its genetic “backbone”, together with the remaining accessory genes, which defines their adaptation to different habitats, determining the ecotypes of the species;
- Its use for proteomic studies, defining the transcriptome;
- Study of the genomic plasticity, rearrangements of genes, plasmid integrations and deletions, especially under stress conditions. The design and use of microarrays or transcriptome Next Generation Sequencing methods will be very helpful.
- The genome sequence will facilitate the analysis of the interaction between the corresponding bacterial strain and the environment, through in vivo expression technology;
- Understanding the transformation ability of the species to capture genes from the environment, and to gain new physiological properties;
- Assessment of the potential function as a shuttle for controlled introduction of genes into target environments;
- Genome sequencing will provide valuable insights into the mechanisms of lateral gene transfer in natural environments.
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