The rhizobacterium Pseudomonas alcaligenes AVO110 exhibits antagonism toward the
phytopathogenic fungus Rosellinia necatrix. This strain efficiently colonizes R. necatrix hyphae and
is able to feed on their exudates. Here, we report the complete genome sequence of P. alcaligenes
AVO110. The phylogeny of all available P. alcaligenes genomes separates environmental isolates,
including AVO110, from those obtained from infected human blood and oyster tissues, which cluster
together with Pseudomonas otitidis. Core and pan-genome analyses showed that P. alcaligenes strains
encode highly heterogenic gene pools, with the AVO110 genome encoding the largest and most
exclusive variable region (~1.6 Mb, 1795 genes). The AVO110 singletons include a wide repertoire of
genes related to biofilm formation, several of which are transcriptionally modulated by R. necatrix
exudates. One of these genes (cmpA) encodes a GGDEF/EAL domain protein specific to Pseudomonas
spp. strains isolated primarily from the rhizosphere of diverse plants, but also from soil and water
samples. We also show that CmpA has a role in biofilm formation and that the integrity of its
EAL domain is involved in this function. This study contributes to a better understanding of the
niche-specific adaptations and lifestyles of P. alcaligenes, including the mycophagous behavior of
strain AVO110
