Genome Mining and Predictive Functional Profiling of Acidophilic Rhizobacterium Pseudomonas fluorescens Pt14

Abstract

Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic soil (pH 4.65). Genome sequencing of strain Pt14 was performed using Single Molecule Real Time (SMRT) sequencing to get insights into unique existence of this strain in acidic environment. Complete genome sequence of this strain revealed a chromosome of 5,841,722 bp having 5354 CDSs and 88 RNAs. Phylogenomic reconstruction based on 16S rRNA gene, Average Nucleotide Identity (ANI) values and marker proteins revealed that strain Pt14 shared a common clade with strain A506 and strain SS101. ANI value of strain Pt14 in relation to strain A506 was found 99.23% demonstrating a very close sub-species association at genome level. Further, orthology determination among these three phylogenetic neighbors revealed 4726 core proteins. Functional analysis elucidated significantly higher abundance of sulphur metabolism (>1×) which could be one of the reasons for the survival of strain Pt14 under acidic conditions (pH 4.65). Acidophilic bacteria have capability to oxidize sulphur into sulphuric acid which in turn can make the soil acidic and genome-wide analysis of Pt14 demonstrated that this strain contributes towards making the soil acidic.

Tropical soils are a reservoir for fluorescent Pseudomonas spp. biodiversity

“…Currently, there are 104 genome sequences of strains named as P. fluorescens in the NCBI Genome database. Only eight – P. fluorescens Pt14 (Rani et al ., ), P. fluorescens BRIP34879 (Gardiner et al ., ), P. fluorescens SRM1 (Lo et al ., ), P. fluorescens EGD‐AQ6 (unpublished), P. fluorescens S12 (unpublished), P. fluorescens UM270 (Hernández‐Salmerón et al ., ), P. fluorescens et76 (Aarab et al ., ) and P. fluorescens Ps006 (Gamez et al ., ) – were submitted by institutions from tropical countries (https://www.ncbi.nlm.nih.gov/genome/genomes/150, searched in 02/10/2017). Even considering that the taxonomic classification of these strains may be ambiguous, these data nonetheless exemplify how the diversity of fluorescent Pseudomonas spp.…”