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We isolated  Pseudomonas putida  ( P. putida ) strain 1A00316 from Antarctica. This bacterium has a high efficiency against  Meloidogyne incognita  ( M. incognita )  in vitro  and under greenhouse conditions. The complete genome of  P. putida  1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16  Pseudomonas  strains revealed that although  P. putida  1A00316 belonged to  P. putida , it was phenotypically more similar to nematicidal  Pseudomonas fluorescens  ( P. fluorescens ) strains. We characterized the diversity and specificity of nematicidal factors in  P. putida  1A00316 with comparative genomics and functional analysis, and found that  P. putida  1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-( l -isoleucyl- l -proline). We show for the first time that cyclo-( l -isoleucyl- l -proline) exhibit nematicidal activity in  P. putida . Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in  P. putida  1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in  P. putida  strain 1A00316.

Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316