Introduction {#Sec1}
============

Phosphorus, one of the major essential macronutrients for plant growth and development, is usually found in insufficient quantities in soil because of its low solubility and fixation \[[@CR1], [@CR2]\]. Since phosphorus deficiency in agricultural soil is limits plant growth, the release bound phosphorus from soils by microbes is an important aspect that can be used to improve soil fertility for increasing crop yields \[[@CR2]\].

Phosphate-solubilizing microorganisms, a group of soil microorganisms capable of converting insoluble phosphate to soluble forms, have received attention as efficient bio-fertilizers for enhancing the phosphate availability for plants \[[@CR3]\]. As one of the representative phosphate-solubilizing bacteria \[[@CR4]\], rhizosphere-colonizing pseudomonads are of interest owing to the benefits they offer to plants. Besides increasing the phosphate accessibility, they promote plant development by facilitating direct and indirect plant growth promotion through the production of phytohormones and enzymes or through the suppression of soil-borne diseases by inducing systemic resistance in the plants \[[@CR5]--[@CR7]\].

[*Pseudomonas lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ (=[LMG 21974](http://prokaryote.info/strainfinder?id=LMG+21974&forward=false)^T^, [CECT 5822](http://prokaryote.info/strainfinder?id=LMG+21974&forward=false)^T^) with insoluble phosphate-solubilizing activity was isolated from the rhizosphere of grass growing in northern [Spain](https://www.google.com/maps/place/Spain) \[[@CR8]\]. Characteristics of the whole genome sequence and a brief summary of the phenotype for this type strain are presented in this study.

Organism information {#Sec2}
====================

Classification and features {#Sec3}
---------------------------

A 16S rRNA gene sequence of [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ was compared to those of other type strains of the genus [*Pseudomonas*](http://doi.org/10.1601/nm.2552) using BLAST on NCBI \[[@CR9]\]. The 16S rRNA gene sequence showed highest similarity (99 % identity) to that of [*P. graminis*](http://doi.org/10.1601/nm.2617)[DSM 11363^T^](http://doi.org/10.1601/strainfinder?urlappend=%3Fid%3DDSM+11363) \[[@CR10]\], followed by similarity to the 16S rRNA gene sequence of [*P. rhizosphaerae*](http://doi.org/10.1601/nm.2678)[IH5](http://prokaryote.info/strainfinder?id=IH5&forward=false)^T^ (98 % identity) \[[@CR11]\], [*P. protegens*](http://doi.org/10.1601/nm.23137)[CHA0](https://www.dsmz.de/catalogues/details/culture/DSM-19095.html)^T^ (98 % identity) \[[@CR12], [@CR13]\], [*P. rhodesiae*](http://doi.org/10.1601/nm.2679)[CIP 104664](http://prokaryote.info/strainfinder?id=CIP+104664&forward=false)^T^ (97 % identity) \[[@CR14]\], and [*P. argentinensis*](http://doi.org/10.1601/nm.9433)[CH01](http://prokaryote.info/strainfinder?id=CH01&forward=false)^T^ (97 % identity) \[[@CR15]\]. Species showing full-length 16S rRNA gene sequences in BLAST analysis were considered for further phylogenetic analyses. A phylogenetic tree was constructed using the neighbor-joining method \[[@CR16]\], and the bootstrap value was set as 1,000 times random replicate sampling. The consensus phylogenetic neighborhood of [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ within the genus [*Pseudomonas*](http://doi.org/10.1601/nm.2552) is shown in Fig. [1](#Fig1){ref-type="fig"}.Fig. 1A phylogenetic tree constructed using the neighbor-joining method presenting the position of *Pseudomonas lutea* OK2^T^ (shown in bold print with asterisk) relative to the other species within the genus *Pseudomonas*. Only the type strains from the genus *Pseudomonas* presenting full-length 16S rRNA gene sequences were selected from the NCBI database \[[@CR43]\]. The nucleotide sequences of these strains were aligned using CLUSTALW \[[@CR44]\], and a phylogenetic tree was constructed with the MEGA version 6 package \[[@CR45]\] using the neighbor-joining method with 1,000 bootstrap replicates \[[@CR16]\]. The bootstrap values for each species are indicated at the nodes. Scale bar indicates 0.005 nucleotide change per nucleotide position. The strains selected for the analysis of the 16S rRNA gene and their corresponding GenBank accession numbers are as follows: *Pseudomonas rhodesiae* CIP 104664^T^ (NR_024911) \[[@CR14], [@CR46]\]; *Pseudomonas marginalis* ATCC 10844^T^ (NR_112072) \[[@CR47], [@CR48]\]; *Pseudomonas veronii* CIP 104663^T^ (NR_028706) \[[@CR49]\]; *Pseudomonas tolaasii* ATCC 33618^T^ (NR_115613) \[[@CR47], [@CR50]\]; *Pseudomonas fluorescens* CCM 2115^T^ (NR_115715) \[[@CR47], [@CR51]\]; *Pseudomonas libanensis* CIP 105460^T^ (NR_024901) \[[@CR52]\]; *Pseudomonas synxantha* IAM 12356^T^ (NR_043425) \[[@CR47], [@CR53]\]; *Pseudomonas kilonensis* 520-20^T^ (NR_028929) \[[@CR54]\]; *Pseudomonas protegens* CHA0^T^ (NR_114749) \[[@CR13], [@CR55]\]; *Pseudomonas saponiphila* DSM 9751^T^ (NR_116905) \[[@CR56], [@CR57]\]; *Pseudomonas syringae* ATCC 19310^T^ (NR_115612) \[[@CR47], [@CR58]\]; *Pseudomonas asturiensis* LPPA 221^T^ (NR_108461) \[[@CR59]\]; *Pseudomonas graminis* DSM 11363^T^ (NR_026395) \[[@CR10]\]; *Pseudomonas rhizosphaerae* IH5^T^ (NR_029063) \[[@CR11]\]; *Pseudomonas putida* IAM 1236^T^ (NR_043424) \[[@CR47], [@CR60]\]; *Pseudomonas monteilii* CIP 104883^T^ (NR_112073) \[[@CR61]\]; *Pseudomonas stutzeri* ATCC 17588^T^ (NR_103934) \[[@CR47], [@CR62]\]; *Pseudomonas benzenivorans* DSM 8628^T^ (NR_116904) \[[@CR56], [@CR57]\]; *Pseudomonas flavescens* B62^T^ (NR_025947) \[[@CR63]\]; and *Pseudomonas argentinensis* CH01^T^ (NR_043115) \[[@CR15]\]

[*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ is a motile, strictly aerobic, non-spore forming, gram-negative bacterium that belongs to the family [*Pseudomonadaceae*](http://doi.org/10.1601/nm.2551) of the class [*Gammaproteobacteria*](http://doi.org/10.1601/nm.2068) \[[@CR8]\]. The cells are rod-shaped with a diameter of approximately 0.75 μm and a length of 1.2--1.6 μm (Fig. [2](#Fig2){ref-type="fig"}). The strain produces yellow, translucent, circular convex colonies of 1--2 mm diameter on plates containing YED-P medium (per liter: 7.0 g of glucose, 3.0 g of yeast extract, 3.0 g of bicalcium phosphate, and 17.0 g of agar) within 2 days at 25 °C \[[@CR8]\]. [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ is capable of oxidizing glucose in media containing ammonium nitrate as a nitrogen source and hydrolyzes aesculin \[[@CR8]\]. The strain OK2^T^ is positive for catalase, but negative for oxidase, gelatinase, caseinase, urease, β-galactosidase, arginine dehydrolase, tryptophan deaminase, and indole/H~2~S \[[@CR8]\]. Further, it can utilize galactose, ribose, mannose, glycerol, D-fructose, D-xylose, D-/L-arabinose, D-/L-arabitol, D-/L-fucose, L-lyxose, melibiose, inositol, mannitol, adonitol, xylitol, caprate, malate, gluconate, 2-ketogluconate, and citrate as sole carbon sources, but cannot utilize maltose, lactose, sucrose, trehalose, cellobiose, starch, glycogen, inulin, sorbitol, D-tagatose, D-raffinose, L-xylose, L-sorbose, L-rhamnose, N-acetylglucosamine, salicin, and erythritol \[[@CR8]\]. Unlike other pseuodomonads, the strain OK2^T^ does not produce fluorescent pigments \[[@CR8]\].Fig. 2Scanning electron micrograph of *Pseudomonas lutea* OK2^T^. The image was taken under a Field Emission Scanning Electron Microscope (FE-SEM, SU8220; Hitachi, Japan) at an operating voltage of 5.0 kV. The scale bar represents 10.0 μm

### Chemotaxonomic data {#Sec4}

The important non-polar fatty acids present in [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ include hexadecenoic acid (16:1, 39.0 %), hexadecanoic acid (16:0, 29.0 %), and octadecenoic acid (18:1, 18.6 %). In addition, the strain OK2^T^ has hydroxy fatty acids such as 3-hydroxydodecanoic acid (3-OH 12:0, 3.3 %), 2-hydroxydodecanoic acid (2-OH 12:0, 2.7 %), and 3-hydroxydecanoic acid (3-OH 10:0, 2.4 %) \[[@CR8]\]. The whole-cell fatty acid profile of this strain is similar to that observed in other representative strains of the genus [*Pseudomonas*](http://doi.org/10.1601/nm.2552), such as [*P. graminis*](http://doi.org/10.1601/nm.2617) \[[@CR10]\] and [*P. rhizosphaerae*](http://doi.org/10.1601/nm.2678) \[[@CR11]\]. The general characteristics of the strain are summarized in Table [1](#Tab1){ref-type="table"}.Table 1Classification and general features of *Pseudomonas lutea* OK2^T^ \[[@CR18]\]MIGS IDPropertyTermEvidence code^a^ClassificationDomain *Bacteria*TAS \[[@CR64]\]Phylum *Proteobacteria*TAS \[[@CR65]\]Class *Gammaproteobacteria*TAS \[[@CR66], [@CR67]\]Order *Pseudomonadales*TAS \[[@CR47], [@CR68], [@CR69]\]Family *Pseudomonadaceae*TAS \[[@CR47], [@CR70]\]Genus *Pseudomonas*TAS \[[@CR47], [@CR71]--[@CR73]\]Species *Pseudomonas lutea*TAS \[[@CR8]\]Type strain OK2^T^ (=LMG 21974^T^, CECT 5822^T^)TAS \[[@CR8]\]Gram stainNegativeTAS \[[@CR8], [@CR74]\]Cell shapeRod-shapedTAS \[[@CR8], [@CR74]\]MotilityMotileTAS \[[@CR8], [@CR74]\]SporulationNoneTAS \[[@CR8], [@CR74]\]Temperature rangeMesophilicNASOptimum temperature25°CTAS \[[@CR8]\]pH range7.0--7.5NASCarbon sourceHeterotrophicTAS \[[@CR75]\]MIGS-6HabitatSoilTAS \[[@CR8]\]MIGS-6.3SalinityNot reportedMIGS-22Oxygen requirementAerobicTAS \[[@CR8], [@CR74]\]MIGS-15Biotic relationshipsFree livingNASMIGS-14PathogenicityNon-pathogenMIGS-4Geographic locationSpain; northern SpainTAS \[[@CR8]\]MIGS-5Sample collection2003NASMIGS-4.1LatitudeNot reportedMIGS-4.2LongitudeNot reportedMIGS-4.4AltitudeNot reported^a^Evidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project \[[@CR76]\]

Genome sequencing information {#Sec5}
=============================

Genome project history {#Sec6}
----------------------

[*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ was selected as a novel-phosphate solubilizing strain for the genome-sequencing project of agriculturally useful microbes undertaken at Kyungpook National University. Genome sequencing was performed in September 2014, and the results of the Whole Genome Shotgun project have been deposited at DDBJ/EMBL/GenBank under the accession number [JRMB00000000](http://www.ncbi.nlm.nih.gov/nuccore/JRMB00000000). The version described in this study is the first version, indicated as [JRMB00000000](http://www.ncbi.nlm.nih.gov/nuccore/JRMB00000000).1. The information obtained from the genome sequencing project is registered on the Genome Online Database \[[@CR17]\] with the GOLD Project ID Gp0107463. A summary of this information and its association with the Minimum Information about a Genome Sequence (MIGS) version 2.0 compliance \[[@CR18]\] are presented in Table [2](#Tab2){ref-type="table"}.Table 2Project informationMIGS IDPropertyTermMIGS-31Finishing qualityDraftMIGS-28Libraries used10-kb SMRT-bell libraryMIGS-29Sequencing platformsPacBio RS IIMIGS-31.2Fold coverage67.58 ×MIGS-30AssemblersRS HGAP Assembly Protocol \[[@CR20]\] in SMRT analysis pipeline v.2.2.0MIGS-32Gene calling methodNCBI Prokaryotic Genome Annotation Pipeline \[[@CR77]\]; GeneMarkS+ \[[@CR78]\]Locus TagLT42Genbank IDJRMB00000000Genbank Date of ReleaseSeptember 29, 2014GOLD IDGp0107463BIOPROJECTPRJNA261881MIGS-13Source material identifierLMG 21974^T^, CECT 5822^T^Project relevanceAgriculture

Growth conditions and genomic DNA preparation {#Sec7}
---------------------------------------------

The strain was cultured in tryptic soy broth (Difco Laboratories Inc., [Detroit, MI](https://www.google.com/maps/place/Detroit,+Michigan,+United+States)) at 30 °C on a rotary shaker at 200 rpm. Genomic DNA was isolated using a QIAamp® DNA Mini Kit (Qiagen, [Valencia](http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=195854), [CA](https://www.google.com/maps/place/Valencia,+California,+United+States)) according to the manufacturer\'s standard protocol. The quantity and purity of the extracted genomic DNA were assessed using a Picodrop Microliter UV/Vis Spectrophotometer (Thermo Fisher Scientific Inc., [Waltham, MA](https://www.google.com/maps/place/Waltham,+Massachusetts,+United+States)) and Qubit® 2.0 Fluorometer (Fisher Scientific Inc., [Pittsburgh, PA](https://www.google.com/maps/place/Pittsburgh,+Pennsylvania,+United+States)), respectively.

Genome sequencing and assembly {#Sec8}
------------------------------

The isolated genomic DNA of [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ was sequenced using the SMRT DNA sequencing platform and the Pacific Biosciences RS II sequencer with P4 polymerase-C2 sequencing chemistry (Pacific Biosciences, [Menlo Park, CA](https://www.google.com/maps/place/Menlo+Park,+California,+United+States)) \[[@CR19]\]. After shearing the genomic DNA, a 10-kb insert SMRT-bell library was prepared and loaded on two SMRT cells. During the 90 min of movie time, 654,270,150 read bases were generated from 300,584 reads. All the obtained bases were filtered to remove any reads shorter than 100 bp or those having accuracy values less than 0.8. Subsequently, 461,880,761 nucleotides were obtained from 116,562 reads, with a read quality of 0.843. These bases were assembled *de novo* using the RS HGAP assembly protocol version 3.3 on the SMRT analysis platform version 2.2.0 \[[@CR20]\]. The HGAP analysis yielded five contigs corresponding to five scaffolds, with a 67.58-fold coverage. The maximum contig length and N50 contig length were identical: 2,839,280 bp. The total length of the [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ genome was found to be 5,647,497 bp.

Genome annotation {#Sec9}
-----------------

The protein coding sequences were determined using the NCBI PGAP version 2.8 (rev. 447021) \[[@CR21]\]. Additional gene prediction and functional annotation analyses were performed on the RAST server \[[@CR22]\] and IMG-ER pipeline, respectively, by the Department of Energy-Joint Genome Institute \[[@CR23]\].

Genome properties {#Sec10}
=================

The average G + C content of the genome was 60.15 %. The genome was predicted to encode 4,941 genes including 4,846 protein-coding genes and 95 RNA genes (24 rRNAs, 70 tRNAs, and 1 ncRNA). Putative functions were assigned to 4,102 of the protein-coding genes, and 3,507 genes (approximately 70.98 %) were assigned to the COG functional categories. The most abundant COG category was \"Amino acid transport and metabolism\" (10.36 %), followed by \"General function prediction only\" (8.71 %), "Transcription\" (8.34 %), and "Signal transduction mechanisms" (6.52 %). The category for "Mobilome: prophages, transposons" (0.92 %) was also classified with functional genes for transposase (LT42_00515, LT42_05870, LT42_07855, LT42_10965, LT42_14240, LT42_14330, LT42_18595, LT42_19270, LT42_21870, LT42_21925), integrase (LT42_17205), terminase (LT42_06460, LT42_17145, LT42_17150), and plasmid stabilization protein (LT42_19025, LT42_24175). The genome statistics of strain OK2^T^ are presented in Table [3](#Tab3){ref-type="table"} and Fig. [3](#Fig3){ref-type="fig"}. The gene distribution within the COG functional categories is presented in Table [4](#Tab4){ref-type="table"}.Table 3Genome statisticsAttributeValue% of TotalGenome size (bp)5,647,497100.00DNA coding (bp)4,778,15384.61DNA G + C (bp)3,397,08760.15DNA scaffolds5100.00Total genes4,941100.00Protein coding genes4,84698.08RNA genes951.92Pseudo genes2394.84Genes in internal clusters1,40226.64Genes with function prediction4,10283.02Genes assigned to COGs3,50770.98Genes with Pfam domains4,02681.48Genes with signal peptides4859.82Genes with transmembrane helices1,02620.77CRISPR repeats00.00Fig. 3Graphical circular map of the *Pseudomonas lutea* OK2^T^ genome. The circular map was generated using the BLAST Ring Image Generator program \[[@CR79]\]. From the inner circle to the outer circle: Genetic regions; GC content (*black*); and GC skew (*purple*/*green*)Table 4Number of genes associated with general COG functional categoriesCodeValue% ageDescriptionJ2315.75Translation, ribosomal structure and biogenesisA10.02RNA processing and modificationK3358.34TranscriptionL1213.01Replication, recombination and repairB20.05Chromatin structure and dynamicsD340.85Cell cycle control, Cell division, chromosome partitioningV731.82Defense mechanismsT2626.52Signal transduction mechanismsM2285.68Cell wall/membrane biogenesisN1333.31Cell motilityU972.41Intracellular trafficking and secretionO1523.78Posttranslational modification, protein turnover, chaperonesC2486.17Energy production and conversionG2566.37Carbohydrate transport and metabolismE41610.36Amino acid transport and metabolismF852.12Nucleotide transport and metabolismH1984.93Coenzyme transport and metabolismI1824.53Lipid transport and metabolismP2345.83Inorganic ion transport and metabolismQ982.44Secondary metabolites biosynthesis, transport and catabolismR3508.71General function prediction onlyS2125.28Function unknown-143429.02Not in COGsThe total is based on the total number of protein coding genes in the genome

Insights from the genome sequence {#Sec11}
=================================

Microorganisms that show phosphate-solubilizing activity are generally known to be involved in either of the following two biochemical mechanisms: production of organic acids for the acidification of external surroundings for plants and production of enzymes for direct solubilization \[[@CR24], [@CR25]\]. Genes encoding functional enzymes with these biochemical properties were predicted using the KO database via IMG-ER pipeline \[[@CR26], [@CR27]\]. The genome of [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ was annotated with several genes involved in phosphate solubilization. For example, *ldhA* (D-lactate dehydrogenase, KO:[K03778](http://www.genome.jp/dbget-bin/www_bget?ko:K03778)) and *icd* (isocitrate dehydrogenase, KO:[K00031](http://www.genome.jp/dbget-bin/www_bget?ko:K00031)) were found to be involved in the production of organic acids, and *phoD* (alkaline phosphatase D, KO:[K01113](http://www.genome.jp/dbget-bin/www_bget?ko:K01113)) was involved in direct phosphate solubilization. Direct oxidation of glucose to gluconic acid by a periplasmic membrane-bound glucose dehydrogenase is also known to be one of the major metabolic steps for phosphate solubilization in pseudomonads \[[@CR6]\]. In relation to this process, the *gcd* gene coding for a cofactor pyrroloquinoline quinone-dependent glucose dehydrogenase (=quinoprotein glucose dehydrogenase, KO:[K00117](http://www.genome.jp/dbget-bin/www_bget?ko:K00117)) was revealed (Table [5](#Tab5){ref-type="table"}). Phosphate solubilization is normally a complex phenomenon depending on conditions such as bacterial, nutritional, physiological, and growth variations \[[@CR2]\]. Given that phosphate solubilization can occur through various microbial processes/mechanisms \[[@CR28]\], the predicted genes on the genome being described could compositely contribute to this activity.Table 5Putative genes related to functional enzymes for potential PGPR effects predicted from the genome sequence of *Pseudomonas lutea* OK2^T^Function IDNamePhosphate solubilization KO:K01113alkaline phosphatase D \[EC:3.1.3.1\] (*phoD*) KO:K03778\*D-lactate dehydrogenase \[EC:1.1.1.28\] (*ldhA*) \* KO:K00031isocitrate dehydrogenase \[EC:1.1.1.42\] (*icd*) KO:K01647citrate synthase \[EC:2.3.3.1\] (*gltA*) KO:K00117quinoprotein glucose dehydrogenase \[EC:1.1.5.2\] (*gcd*)Antibiotic resistance KO:K17836\*beta-lactamase class A (penicillinase) \[EC:3.5.2.6\] (*penP*) \* KO:K08218MFS transporter, PAT family, beta-lactamase induction signal transducer AmpG (*ampG*) KO:K03806beta-lactamase expression regulator, N-acetyl-anhydromuramyl-L-alanine amidase AmpD protein (*ampD*) KO:K03807Membrane protein required for beta-lactamase induction, AmpE protein (*ampE*) KO:K05365penicillin-binding protein 1B \[EC:2.4.1.129 3.4.-.-\] (*mrcB*) KO:K05366penicillin-binding protein 1A \[EC:2.4.1.-3.4.-.-\] (*mrcA*) KO:K05367penicillin-binding protein 1C \[EC:2.4.1.-\] (*pbpC*) KO:K05515penicillin-binding protein 2 (*mrdA*) KO:K07552MFS transporter, DHA1 family, bicyclomycin/chloramphenicol resistance protein (*bcr*) KO:K08223MFS transporter, FSR family, fosmidomycin resistance protein (*fsr*) KO:K05595\*multiple antibiotic resistance protein (*marC*) \* KO:K18138multidrug efflux pump (*acrB*, *mexB*, *adeJ*, *smeE*, *mtrD*, *cmeB*) KO:K07799putative multidrug efflux transporter MdtA (*mdtA*) KO:K07788RND superfamily, multidrug transport protein MdtB (*mdtB*) KO:K07789RND superfamily, multidrug transport protein MdtC (*mdtC*)Toxins KO:K11068membrane damaging toxins Type II toxin, pore-forming toxin hemolysin III (*hlyIII*)Metal ion resistance KO:K07213copper chaperone KO:K07245putative copper resistance protein D (*pcoD*) KO:K07665two-component system, OmpR family, copper resistance phosphate regulon response regulator CusR (*cusR*) KO:K06189magnesium and cobalt transporter (*corC*) KO:K08970\*nickel/cobalt exporter (*rcnA*) \* KO:K06213magnesium transporter (*mgtE*) KO:K16074zinc transporter (*zntB*) KO:K09815zinc transport system substrate-binding protein (*znuA*) KO:K09816zinc transport system permease protein (*znuB*) KO:K09823Fur family transcriptional regulator, zinc uptake regulator (*zur*) KO:K03893arsenical pump membrane protein (*arsB*) KO:K11811\*arsenical resistance protein ArsH (*arsH*) \*Siderophore KO:K02362enterobactin synthetase component D \[EC:2.7.8.-\] (*entD*) KO:K16090catecholate siderophore receptor (*fiu*)Attachment and colonization in the plant rhizosphere KO:K04095\*cell filamentation protein (*fic*) \* KO:K06596\*chemosensory pili system protein ChpA (sensor histidine kinase/response regulator) (*chpA*) \* KO:K02655, K02656, K02662, K02663, K02664, K02665, K02666, K02671, K02672, K02673, K02674, K02676, K02650\*, K02652, K02653type IV pilus assembly protein\
PilE (*pilE*), PilF (*pilF*), PilM (*pilM*), PilN (*pilN*), PilO (*pilO*), PilP (*pilP*), PilQ (*pilQ*), PilV (*pilV*), PilW (*pilW*), PilX (*pilX*), PilY1 (*pilY1*), PilZ (*pilZ*), PilA (*pilA*)\*, PilB (*pilB*), PilC (*pilC*) KO:K08086, K02280pilus assembly protein\
FimV (*fimV*), CpaC (*cpaC*) KO:K02657, K02658twitching motility two-component system response regulator PilG (*pilG*), PilH (*pilH*) KO:K02659, K02660, K02669, K02670\*twitching motility protein\
PilI (*pilI*), PilJ (*pilJ*), PilT (*pilT*), PilU (*pilU*) \*Secretion system KO:K03196\*, K03198\*, K03199\*, K03200\*, K03203\*, K03204\*, K03205\*type IV secretion system protein\
VirB11 (*virB11*) \*, VirB3 (*virB3*) \*, VirB4 (*virB4*) \*, VirB5 (*virB5*) \*, VirB8 (*virB8*) \*, VirB9 (*virB9*) \*, VirD4 (*virD4*) \* KO:K11891\*, K11892\*, K11893\*, K11894\*, K11895\*, K11896\*, K11900\*, K11901\*type VI secretion system protein\
ImpL (*impL*) \*, ImpK (*impK*) \*, ImpJ (*impJ*) \*, ImpI (*impI*) \*, ImpH (*impH*) \*, ImpG (*impG*) \*, ImpC (*impC*) \*, ImpB (*impB*) \* KO:K11903\*, K11904\*type VI secretion system secreted protein\
Hcp (*hcp*) \*, VgrG (*vgrG*) \* KO:K11905\*type VI secretion system protein\* KO:K11906\*, K11907\*, K11910\*type VI secretion system protein\
VasD (*vasD*) \*, VasG (*vasG*) \*, VasJ (*vasJ*) \*Plant hormone auxin biosynthesis KO:K01696tryptophan synthase \[EC:4.2.1.20\] (*trpB*) KO:K00766anthranilate phosphoribosyltransferase \[EC:2.4.2.18\] (*trpD*) KO:K01817phosphoribosylanthranilate isomerase \[EC:5.3.1.24\] (*trpF*)^a^Based on the function profiles obtained from the KO database \[[@CR25], [@CR26]\], under the IMG-ER pipeline \[[@CR23]\]\*Predicted only in the genome sequence of *P. lutea* OK2^T^ (IMG Genome ID 2593339262) upon comparison with the complete genome sequence of *P. rhizosphaerae* IH5^T^ (=DSM 16299^T^, IMG Genome ID 2593339263) \[[@CR34]\]

[*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ is also expected to possess functional traits related to plant growth promotion \[[@CR29]--[@CR32]\]. As shown in Table [5](#Tab5){ref-type="table"}, genes coding for functional enzymes with various PGPR effects such as "antibiotic resistance", "metal ion resistance", "toxin production", "siderophore production", "attachment and colonization in the plant rhizosphere", and "plant hormone auxin production" were revealed. Although *nif* gene clusters involved in nitrogen-fixing activity were not found in the strain OK2^T^, a gene encoding for the nitrogen-fixation protein NifU (KO:[K04488](http://www.genome.jp/dbget-bin/www_bget?ko:K04488)) was identified \[[@CR33]\].

Within the genus [*Pseudomonas*](http://doi.org/10.1601/nm.2552)*sensu stricto*, [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ is presented as a group phylogenetically closest to [*P. graminis*](http://doi.org/10.1601/nm.2617)[DSM 11363](https://www.dsmz.de/catalogues/details/culture/DSM-11363.html)^T^ \[[@CR10]\] and [*P. rhizosphaerae*](http://doi.org/10.1601/nm.2678) IH5^T^ \[[@CR11]\] (shown in Fig. [1](#Fig1){ref-type="fig"}). The majority of the genes in [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ were predicted based on the genome of [*P. rhizosphaerae*](http://doi.org/10.1601/nm.2678) IH5^T^ (=[DSM 16299](https://www.dsmz.de/catalogues/details/culture/DSM-16299.html)^T^, IMG Genome ID 2593339263) \[[@CR34]\]. However, genes such as *ldhA* (D-lactate dehydrogenase, KO:[K03778](http://www.genome.jp/dbget-bin/www_bget?ko:K03778)), *penP* (beta-lactamase class A, KO:[K17836](http://www.genome.jp/dbget-bin/www_bget?ko:K17836)), *marC* (multiple antibiotic resistance protein, KO:[K05595](http://www.genome.jp/dbget-bin/www_bget?ko:K05595)), *rcnA* (nickel/cobalt exporter, KO:[K08970](http://www.genome.jp/dbget-bin/www_bget?ko:K08970)), *arsH* (arsenical resistance protein ArsH, KO:[K11811](http://www.genome.jp/dbget-bin/www_bget?ko:K11811)), *fic* (cell filamentation protein, KO:[K04095](http://www.genome.jp/dbget-bin/www_bget?ko:K04095)), and *chpA* (chemosensory pili system protein ChpA, KO:[K06596](http://www.genome.jp/dbget-bin/www_bget?ko:K06596)) and the gene clusters coding for enzymes with type IV secretion systems were only annotated in OK2^T^. Furthermore, pertinent gene clusters for type VI secretion systems, known as a complex multicomponent secretion machine, with bacterial competitions \[[@CR35]--[@CR37]\] were only predicted in the strain OK2^T^. The type VI secretion system may be related to possible features of bacterial motility/adaptation/competition in the strain. Although the strain [*P. graminis*](http://doi.org/10.1601/nm.2617)[DSM 11363](https://www.dsmz.de/catalogues/details/culture/DSM-11363.html)^T^ had similar general features and biochemical properties as strain OK2^T^, its genome sequence is not yet available.

Average Nucleotide Identity calculations \[[@CR38]\] were used to compare the genomes of [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ and other sequenced [*Pseudomonas*](http://doi.org/10.1601/nm.2552) species (Table [6](#Tab6){ref-type="table"}). The strain was found to be most closely related to [*Pseudomonas syringae*](http://doi.org/10.1601/nm.10982)[ATCC 19310](http://www.atcc.org/Products/All/19310.aspx)^T^ (77.31 % identity), followed by [*Pseudomonas kilonensis*](http://doi.org/10.1601/nm.2627) 520-20^T^ (76.96 % identity). These values are under the acceptable range of species cutoff values of 95--96 % \[[@CR39]\], indicating that [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ is different from other sequenced [*Pseudomonas*](http://doi.org/10.1601/nm.2552) species.Table 6Average nucleotide identity of the genome sequence of different *Pseudomonas* species with that of OK2^T^StrainAverage Nucleotide Identity (%)*Pseudomonas syringae* ATCC 19310^T^77.31*Pseudomonas kilonensis* 520-20^T^76.96*Pseudomonas protegens* CHA0^T^76.86*Pseudomonas veronii* CIP 104663^T^76.72*Pseudomonas libanensis* CIP 105460^T^76.48*Pseudomonas fluorescens* CCM 2115^T^76.45*Pseudomonas synxantha* IAM 12356^T^76.39*Pseudomonas rhizosphaerae* IH5^T^76.39*Pseudomonas putida* IAM 1236^T^75.59*Pseudomonas monteilii* CIP 104883^T^75.39*Pseudomonas stutzeri* ATCC 17588^T^73.85

Conclusions {#Sec12}
===========

We presented here the first genome sequence of [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^, a phosphate-solubilizing bacterium isolated from the rhizosphere of grass in northern [Spain](https://www.google.com/maps/place/Spain) \[[@CR8]\]. This study showed that [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ has potential traits including phosphate-solubilizing capability, making it as an effective pseudomonad-PGPR.

Considering a variety of complex conditions that occur in rhizospheres \[[@CR40]\], the environmental adaptability of PGPR in *in situ* rhizosphere became an important factor for improved plant growth-promoting capacity. In addition, initial studies focusing on the functional properties of PGPR \[[@CR31], [@CR32]\] have led to interest in the comparative analyses of pan-/core-genomes of these bacteria, which are of ecological importance for elucidating the fundamental genotypic features of PGPR under diverse rhizosphere conditions \[[@CR41], [@CR42]\]. The genetic information obtained for [*P. lutea*](http://doi.org/10.1601/nm.8794) OK2^T^ will improve our understanding of the genetic basis of phosphate-solubilizing pseudomonad-PGPR activities and further provide insights into the practical applications of the strain as a biocontrol agent in the field of agriculture.

HGAP

:   Hierarchical genome assembly process

IMG-ER

:   Integrated microbial genomes-expert review

KO

:   Kyoto encyclopedia of genes and genomes Orthology

PGAP

:   Prokaryotic genome annotation pipeline

PGPR

:   Plant growth-promoting rhizobacteria

RAST

:   Rapid annotation using subsystems technology

SMRT

:   Single molecule real-time

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (NRF-2015R1D1A1A01057187).

Authors' contributions {#FPar1}
======================

YK performed the genomic sequencing, genomic analyses, phenotypic characterization of the bacterium, and drafted the manuscript. GP performed the genomic analyses and drafted the manuscript. JHS conceived the study, participated in its design and coordination, and drafted the manuscript. All the authors have read and approved the final manuscript.

Competing interests {#FPar2}
===================

The authors declare that they have no competing interests.
