Analysis of the core genome and pangenome of Pseudomonas putida Zulema Udaondo, 1 Lázaro Molina, 2 Ana Segura, 1 Estrella Duque 1 and Juan L. Ramos 1 * 1 Biotechnology Technological Area, Abengoa Research, Calle Energía Solar 1, Building E, Campus Palmas Altas, 41014, Sevilla, Spain. 2 Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, 18008, Granada, Spain. Summary Pseudomonas putida are strict aerobes that prolifer- ate in a range of temperate niches and are of interest for environmental applications due to their capacity to degrade pollutants and ability to promote plant growth. Furthermore solvent-tolerant strains are useful for biosynthesis of added-value chemicals. We present a comprehensive comparative analysis of nine strains and the first characterization of the Pseudomonas putida pangenome. The core genome of P. putida comprises approximately 3386 genes. The most abundant genes within the core genome are those that encode nutrient transporters. Other con- served genes include those for central carbon metabolism through the Entner–Doudoroff pathway, the pentose phosphate cycle, arginine and proline metabolism, and pathways for degradation of aro- matic chemicals. Genes that encode transporters, enzymes and regulators for amino acid metabolism (synthesis and degradation) are all part of the core genome, as well as various electron transporters, which enable aerobic metabolism under different oxygen regimes. Within the core genome are 30 genes for flagella biosynthesis and 12 key genes for biofilm formation. Pseudomonas putida strains share 85% of the coding regions with Pseudomonas aeruginosa; however, in P. putida, virulence factors such as exotoxins and type III secretion systems are absent. Introduction Pseudomonas putida are members of the Pseudomonadales order of the Gammaproteobacteria class and are chemo-organotrophic aerobic, Gram- negative rods with polar flagella that use respiratory rather than fermentative metabolism (Palleroni, 1984). These microorganisms are widely distributed in environmental niches in all continents, although they are particularly abundant in temperate soils and waters. They have often been found in polluted soils because of their metabolic versatility (Timmis, 2002). A number of P. putida strains grow favourably in plant roots and are used as plant growth-promoting rhizobacteria (PGPR) (Matilla et al., 2011; Roca et al., 2013; Pizarro-Tobías et al., 2014). The PGPR properties of P. putida derive from a number of characteristics, including the ability to solubilize phos- phate, the inhibition of fungal growth through the produc- tion of iron-chelators such as siderophores and the ability to promote root elongation via secretion of indole-acetic acid and other phytohormones. Genes involved in the catabolism of a wide variety of organic compounds, including many naturally occurring products (e.g. metabolites from the partial degradation of lignin), are chromosomally encoded in the P. putida genome. As stated above, some strains of this species colonize the rhizosphere of plants (Molina et al., 2000; Weyens et al., 2010; Li et al., 2013; Roca et al., 2013). This characteris- tic, combined with the ability to degrade an array of com- pounds, provides these strains with a strong potential for bioremediation of contaminated soils in a process known as rhizophytoremediation (van Dillewijn et al., 2009; Segura and Ramos, 2013). Because Pseudomonas putida is easy to culture in laboratory settings (with a duplication time of around 1 h in various culture media) and because there are a wide array of genetic tools avail- able for its manipulation, this microbe has become a ‘workhorse’ and model organism in soil bacteria research (Timmis, 2002). The ability of P. putida to thrive in different niches is the result of its genetic arsenal (genome size around of 6Mb), which contains highly sophisticated genes and pathways that mediate adaptation to changes in the local environment. Understanding the physiological and genetic basis of bacterial responses to diverse energy sources or stressors is crucial for the development of applications such as bioremediation, the control of plant Received 29 May, 2015; revised 4 August, 2015; accepted 6 August, 2015. *For correspondence. E-mail juan.ramos@abengoa.com; Tel. (+34) 954 437 111; Fax (+34) 955 413 371. Environmental Microbiology (2015) doi:10.1111/1462-2920.13015 © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd