Pseudomonas is a genus of gram-negative bacteria belonging to the family Pseudomonadaceae in the class Gammaproteobacteria. The 348 members of the genus demonstrate a great deal of metabolic diversity and consequently are able to colonize a wide range of niches and hosts. Their ease of culture in vitro and availability of an increasing number of Pseudomonas strain genome sequences has made the genus an excellent focus for scientific research; the best studied species include P. aeruginosa in its role as an opportunistic human pathogen, the plant pathogen P. syringae, the soil bacterium P. putida, and the plant growth-promoting P. fluorescens, P. lini, P. migulae, and P. graminis. Because of their widespread occurrence in water and plant seeds such as dicots, the pseudomonads were observed early in the history of microbiology. The generic name Pseudomonas created for these organisms was defined in rather vague terms by Walter Migula in 1894 and 1900 as a genus of Gram-negative, rod-shaped, and polar-flagellated bacteria with some sporulating species. The latter statement was later proved incorrect and was due to refractive granules of reserve materials. Despite the vague description, the type species, Pseudomonas pyocyanea (basionym of Pseudomonas aeruginosa), proved the best descriptor.
Classification history Like most bacterial genera, the pseudomonad last common ancestor lived hundreds of millions of years ago. They were initially classified at the end of the 19th century when first identified by Walter Migula. The etymology of the name was not specified at the time and first appeared in the seventh edition of Bergey's Manual of Systematic Bacteriology (the main authority in bacterial nomenclature) as Greek pseudes (ψευδής) "false" and -monas (μονάς/μονάδος) "a single unit", which can mean false unit; however, Migula possibly intended it as false Monas, a nanoflagellated protist (subsequently, the term "monad" was used in the early history of microbiology to denote unicellular organisms). Soon, other species matching Migula's somewhat vague original description were isolated from many natural niches and, at the time, many were assigned to the genus. However, many strains have since been reclassified, based on more recent methodology and use of approaches involving studies of conservative macromolecules. 16S rRNA sequence analysis has redefined the taxonomy of many bacterial species. As a result, the genus Pseudomonas includes strains formerly classified in the genera Chryseomonas and Flavimonas. Other strains previously classified in the genus Pseudomonas are now classified in the genera Burkholderia and Ralstonia. In 2020, a phylogenomic analysis of 494 complete Pseudomonas genomes identified two well-defined species (P. aeruginosa and P. chlororaphis) and four wider phylogenetic groups (P. fluorescens, P. stutzeri, P. syringae, P. putida) with a sufficient number of available proteomes. The four wider evolutionary groups include more than one species, based on species definition by the Average Nucleotide Identity levels. In addition, the phylogenomic analysis identified several strains that were mis-annotated to the wrong species or evolutionary group. This mis-annotation problem has been reported by other analyses as well. In 2021, a broad phylogenomic analysis on this genus led to the reorganization of the species included in Pseudomonas, leading to the creation of several new genera to accommodate some of them.
Genomics In 2000, the complete genome sequence of a Pseudomonas species was determined; more recently, the sequence of other strains has been determined, including P. aeruginosa strains PAO1 (2000), P. putida KT2440 (2002), P. protegens Pf-5 (2005), P. syringae pathovar tomato DC3000 (2003), P. syringae pathovar syringae B728a (2005), P. syringae pathovar phaseolica 1448A (2005), P. fluorescens Pf0-1, and P. entomophila L48. By 2016, more than 400 strains of Pseudomonas had been sequenced. Sequencing the genomes of hundreds of strains revealed highly divergent species within the genus. In fact, many genomes of Pseudomonas share only 50–60% of their genes, e.g. P. aeruginosa and P. putida share only 2971 proteins out of 5350 (or ~55%). By 2020, more than 500 complete Pseudomonas genomes were available in NCBI GenBank. A phylogenomic analysis utilized 494 complete proteomes and identified 297 core orthologues, shared by all strains. This set of core orthologues at the genus level was enriched for proteins involved in metabolism, translation, and transcription and was utilized for generating a phylogenomic tree of the entire genus, to delineate the relationships among the Pseudomonas major evolutionary groups. In addition, group-specific core proteins were identified for most evolutionary groups, meaning that they were present in all members of the specific group, but absent in other pseudomonads. For example, several P. aeruginosa-specific core proteins were identified that are known to play an important role in this species' pathogenicity, such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC. In 2021, a comparative genomic study with more than 3000 Pseudomonas genomes helped to discover genes and functions related with the environmental adaptation of these bacteria.
Characteristics Members of the genus display these defining characteristics:
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