Environmental bacteria persist in various habitats, yet little is known about the genes that contribute to growth and survival in their respective ecological niches. Signature-tagged mutagenesis (STM) of Shewanella oneidensis MR-1 coupled with a screen involving incubations of mutant strains in anoxic aquifer sediments allowed us to identify 47 genes that enhance fitness in sediments. Gene functions inferred from annotations provide us with insight into physiological and ecological processes that environmental bacteria use while growing in sediment ecosystems. Identification of the mexF gene and other potential membrane efflux components by STM demonstrated that homologues of multidrug resistance genes present in pathogens are required for sediment fitness of nonpathogenic bacteria. Further studies with a mexF deletion mutant demonstrated that the multidrug resistance pump encoded by mexF is required for resistance to antibiotics, including chloramphenicol and tetracycline. Chloramphenicol-adapted cultures exhibited mutations in the gene encoding a TetR family regulatory protein, indicating a role for this protein in regulating expression of the mexEF operon. The relative importance of mexF for sediment fitness suggests that antibiotic efflux may be a required process for bacteria living in sediment systems.Ecology encompasses the study of organisms and their interactions with one another and with the surrounding environment. In the field of microbiology, observations of these relationships are far less direct than studies of macroscopic organisms, as we cannot readily observe, in a traditional sense, in situ processes that occur at molecular to microscopic levels. Some information can be ascertained from studies that monitor microbial communities (33) or dominant respiratory processes (23), but in situ molecular scale interactions often elude us. While pure culture studies can monitor physiological and molecular changes (e.g., through microarray and proteomic analyses) in response to defined components of a habitat, extrapolation of laboratory results to the real environment is often not possible. From an environmental standpoint, an in situ perspective of bacterial fitness would provide a greater understanding of processes that are of fundamental ecological importance, and the knowledge gained can then be applied toward enhancement of beneficial microbial activities (e.g., bioremediation) or prevention of disruptive activities (e.g., oil well souring).In this study, 47 genes that aid in bacterial ecological fitness in sediments were identified using in situ-based signaturetagged mutagenesis (STM) (12). STM is one technique by which whole genomes are screened for genes that enable bacteria to survive in their natural habitats. Genes involved in general cellular processes of DNA repair, transport, transcriptional regulation, and energy and amino acid metabolism, as well as genes encoding phage-related and transposon-related proteins, were identified as helpful for sediment fitness.Of all the mutants detected, ge...