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

Abstract

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.

Volatile organic compounds from Paenibacillus polymyxa KM2501-1 control Meloidogyne incognita by multiple strategies

“…Chemical nematicides are the primary means of control for plant parasitic nematodes, but their potential negative impacts on human health and the environment have led to a total ban or greatly restricted the use of such compounds. Researchers have therefore searched for decades for antagonistic microorganisms as an alternative to nematicidal chemicals, and many such fungi and bacteria have been reported 30 , 31 . However, the development of biological nematicides has been constrained by difficulties in commercial production and formulation 32 .…”

Species-Wide Genome Mining of Pseudomonas putida for Potential Secondary Metabolites and Drug-Like Natural Products Characterization

“…The genome sequence analysis suggested the close relationship of P. entomophila with P. putida [52]. Moreover, the P. putida1A00316 is reported to be quite distinct in virulence and metabolism compare to other P. putida strains and exhibit nematicidal activity [53]. Though diverse nematicidal factors are addressed in genome sequence report of P. putida 1A00316 isolate [53], but the entolysin biosynthetic molecular signatures and capabilities of this isolate not discussed.…”

“…Moreover, the P. putida1A00316 is reported to be quite distinct in virulence and metabolism compare to other P. putida strains and exhibit nematicidal activity [53]. Though diverse nematicidal factors are addressed in genome sequence report of P. putida 1A00316 isolate [53], but the entolysin biosynthetic molecular signatures and capabilities of this isolate not discussed. We assume the role of predicted entolysin coding BGC in nematicidal activity of P. putida1A00316 strain.…”

Multiple Modes of Nematode Control by Volatiles of Pseudomonas putida 1A00316 from Antarctic Soil against Meloidogyne incognita

“…Many secondary metabolites of microorganisms have nematicidal activity (NA) and therefore could become substitutes for highly toxic chemical nematicides. Through comparative genomic studies, isolation and purification, the nematicidal compounds alkaline metalloproteinase AprA and two metabolites, hydrogen cyanide and cyclo(L-Pro-L-Ile), were previously identified from Pseudomonas putida strain 1A00316 and shown to have good NA against M. incognita ( Guo et al, 2016 ). Bacillus cereus strain S2 produced sphingosine and showed high NA against M. incognita ( Gao et al, 2016 ).…”