Pseudomonas putida KT2440, a saprophytic soil bacterium that colonizes the plant root, is a suitable microorganism for the removal of pollutants and a stable host for foreign genes used in biotransformation processes. Because of its potential use in agriculture and industry, we investigated the conditions for the optimal preservation of the strain and its derivatives for long-term storage. The highest survival rates were achieved with cells that had reached the stationary phase and which had been subjected to freeze-drying in the presence of disaccharides (trehalose, maltose, and lactose) as lyoprotectants. Using fluorescence polarization techniques, we show that cell membranes of KT2440 were more rigid in the stationary phase than in the exponential phase of growth. This is consistent with the fact that cells grown in the stationary phase exhibited a higher proportion of C 17:cyclopropane as a fatty acid than cells in the exponential phase. Mutants for the cfaB gene, which encodes the main C 17:cyclopropane synthase, and for the cfaA gene, which encodes a minor C 17:cyclopropane synthase, were constructed. These mutants were more sensitive to freeze-drying than wild-type cells, particularly the mutant with a knockout in the cfaB gene that produced less than 2% of the amount of C 17:cyclopropane produced by the parental strain.Pseudomonas putida KT2440 is a well-characterized saprophytic member of the family Pseudomonaceae (38) certified by the National Institutes of Health as a secure host for foreign gene cloning (3). This microorganism uses a number of aromatic compounds, amino acids, and organic acids as carbon and energy sources (2, 34, 39), and it is able to adhere to abiotic and biotic surfaces, being an excellent colonizer of the plant roots (26). The complete genome sequence of P. putida KT2440 (27) reveals its nonpathogenic nature and also its potential for applications in agriculture, biocatalysis, bioremediation, and bioplastic production (19,27,30).The availability of complete genome sequences facilitates research with genomics and proteomics, although many of these studies require a collection of mutants large enough to establish unequivocal gene and function relationships to identify regulons and to determine the hierarchy in transcriptional processes. We have constructed an ordered bank of mutants of P. putida (E. Duque [www.artemisa.eez.csic.es]) to facilitate detailed functional genomic studies of this microorganism. Long-term storage conservation of the mutant collection is of critical importance. Freezing at Ϫ80°C is frequently used for high-throughput analyses and to search for defined phenotypes. However, lyophilization is the most appropriate method for the long-term preservation of the clones. Lyophilization involves the use of lyoprotectants and myoinositol has been used with gram-negative bacteria in general (13, 29, 37) and with Pseudomonas in particular (E. Duque, unpublished results). However, upon lyophilization of P. putida KT2440, the recovery rate is on the order of 1 out of 10 4...