Genome Sequence of Novoherbaspirillum sp. UKPF54, a Plant Growth-Promoting Rhizobacterial Strain with N2O-Mitigating Abilities, Isolated from Paddy Soil

Novoherbaspirillum sp. strain UKPF54, a plant growth-promoting rhizobacterium with the ability to mitigate nitrous oxide emission from agriculture soils, has been successfully isolated from paddy soil in Kumamoto, Japan. Here, we report the whole-genome sequence of this strain.

H erbaspirillum spp. are endophytic diazotrophs which can colonize sugarcane, rice, maize, sorghum, red clover, and other crops (1)(2)(3). Some Herbaspirillum sp. strains and their close relatives, such as Novoherbaspirillum sp. strains, are known to promote plant growth, suggesting that they are important resource species for the development of biofertilizers (1)(2)(3). Novoherbaspirillum sp. strain UKPF54, previously called Herbaspirillum sp. strain UKPF54, was isolated from the rhizosphere of paddy soil in Kumamoto, Japan (4). It simultaneously promotes the growth of pasture plants and mitigates nitrous oxide emissions from soils (3,5).
Novoherbaspirillum sp. UKPF54 was grown in 5 ml NBNS culture medium (briefly, 5 g liter Ϫ1 peptone and 3 g liter Ϫ1 beef extract containing 0.3 mM NaNO 3 and 4 mM sodium succinate [pH 7.0]) at 28°C and 220 rpm. The genomic DNA was extracted using a DNeasy blood and tissue kit (Qiagen, Germany). A SMRTbell library with a 20-kb insert size was constructed with the template prep kit 1.0 and the BluePippin size selection system, according to the manual. The genome was sequenced with the PacBio RS II DNA sequencing system using SMRT Cell 8Pac v3 and DNA polymerase binding kit P6 reagents. To remove the PacBio short reads, the RS HGAP assembly software (v3.0) was applied, with default parameters (6). When 5= and 3= ends were connected, the contig was assembled into a single circular DNA molecule. The circular DNA molecule had a mean subread length of 8,279 bp, an N 50 value of raw sequences of 11,260 bp, and a total of 1,453,750,364 bases and 175,579 reads. Novoherbaspirillum sp. UKPF54 contains a chromosome of 4,718,988 bp with a GϩC content of 61.89%. The sequencing depth reached 198ϫ.
Genes were predicted using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP, revision 4.8) with the best-placed reference protein set (GeneMarkS2ϩ) (7,8). In addition, BlastKOALA (9) against the "species_prokaryotes" database was used for functional annotation and KEGG pathway mapping. A total of 4,307 protein-coding sequences, 56 tRNAs, 9 rRNAs, 4 noncoding RNAs (ncRNAs), and 50 pseudogenes were discovered. The predicted functional genes consisted of 11 genes of the ABC transporters, 10 genes of the two-component system, and 5 genes of bacterial chemotaxis. The functional genes contained candidate genes associated with nitrogen metabolism and plant growth promotion (Table 1).
We analyzed the secondary metabolism cluster of the complete genome with antiSMASH v5.0.0 (10). The results showed that four secondary metabolite gene clusters relevant to the production of active substances were predicted. Moreover, two nonribosomal peptide synthetase (NRPS)-like fragment gene clusters and one beta-lactonecontaining protease inhibitor (betalactone) gene cluster were predicted.
Overall, the whole-genome sequence is of critical importance to reveal the molecular mechanisms for the promotion of plant growth and the mitigation of nitrous oxide from agricultural soils by Novoherbaspirillum sp. UKPF54, thereby providing fundamental support to develop biofertilizer applications with this strain.
Data availability. The whole-genome sequence of Novoherbaspirillum sp. UKPF54 has been deposited in GenBank under the accession number CP040128. The raw reads have been deposited in the Sequence Read Archive (SRA) under the accession number SRR8943564.

ACKNOWLEDGMENTS
This study was financially supported by the National Natural Science Foundation of China (grants 41771291 and 31972503), the Natural Science Foundation of the Higher Education Institutions of Jiangsu Province (grant 18KJB210007), and the Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture (grant XTE1828), China, and