Whole genome sequencing data of the submerged macrophytes growth promoting and aerobic denitrifying bacterium Bacillus velezensis NBNZ-0060

The Bacillus velezensis strain NBNZ-0060 was isolated from the bottom sediment samples of the lake Jin in Wuhan, China. This strain is an aerobic denitrifying bacterium and able to promote growth of submerged macrophytes. The 3,929,784 bp entire genome contains 3,781 coding sequences (CDS), 27 rRNAs, 85 tRNAs, 5 ncRNAs, with an average G + C content of 46.5%. The average nucleotide identity and digital DNA-DNA values between strain NBNZ-0060 and Bacillus velezensis NRRL B-41580T were 98.28% and 84.5%, respectively. The genome data have been deposited in NCBI with the accession number CP133277.1.


Value of the Data
• The genome data of Bacillus velezensis NBNZ-0060 can provide insights for the understanding of submerged macrophytes growth promotion potential.• The experimental data and genome information may benefit researchers in the remediation of high nitrogen-contaminated sediments in lakes through the combined effect of microbes and submerged plants.• The genome data could be useful for comparative genomic research of Bacillus strains with bioremediation capability.

Data Description
Bacillus velezensis NBNZ-0060 was obtained from sediment samples collected in the bottom of Jin Lake, China.The pot experiment of Vallisneria natans (Lour.)Hara growth in sediment enriched with nitrogen shows that strain NBNZ-0060 improved the survival rate by 225.0%, leaf length by 147.0%, root length by 132.0%, and fresh weight by 234.2%, respectively ( Table 1 ).Furthermore, strain NBNZ-0060 exhibited a nitrate nitrogen removal capability of 75.8 ±2.7% after 24 hours of incubation at 100 mg/L nitrate under low oxygen conditions (cultivation without shaking).Table 2 summarizes genomic characteristics of B. velezensis NBNZ-0060.The chromosome of strain NBNZ-0060 is 3,929,784 bp in length, with a G + C content of 46.50%, and contains 3,781 CDS, 85 tRNA genes, 27 rRNA genes, as determined by NCBI Prokaryotic Genome Annotation Pipeline (PGAP) [2] .Fig. 1 shows a circular map of the NBNZ-0060 genome.The RAST server classified approximately 49% of the genome sequences into 26 of the 27 subsystems, yielding a total of 460 subsystems, as illustrated in Fig. 2 .Based on the RAST annotation, the most abundant subsystem feature was metabolism of amino acids and derivatives (426 CDSs), followed by carbohydrates (399 CDSs), protein metabolism (281 CDSs) and vitamins metabolism (230 CDSs).66 CDSs and 32 CDSs were assigned to the respiration and nitrogen metabolism respectively, which might be associated with denitrification in deep water.No discernible sequences were identified that could be applied to the photosynthesis subsystem.
Table 3 provides a concise overview of the potential genes associated with the indole-3acetic acid (IAA) production in the NBNZ-0060 genome, with a focus on their role in promoting  plant growth.The distribution of these genes primarily occurred within the indole-3-pyruvate pathway, tryptamine pathway, indole-3-acetonitrile pathway, and other related pathways [4] .In addition, a total of 12 biosynthetic gene clusters (BGCs) were identified, 7 of which matched known clusters with 86% ∼100% similarity of bacillibactin, bacilysin, surfactin, macrolactin H, bacillaene, fengycin and difficidin, which exhibit varying degrees of antifungal and bacterial activity ( Table 4 ) [6] .The remaining 5 BGCs with unknown products were predicted to encode saccharide (7% similarity), Class II lanthipeptides, type III polyketide synthase and terpenes ( Table 4 ).The potential functions of these BGCs in the plant growth promotion could be further investigated.

Sample collection and bacterial isolation
Strain NBNZ-0060 was obtained from sediment samples.The samples were collected from the benthic region of Jin Lake (114.1917°N, 30.6516 °E, Wuhan, China) during the month of May in the year 2021.A previously reported data involved the collection of a total of 25 sediment samples, each weighing between one and two kilos [1] .A dilution factor of 10 was applied to the sample by adding 1 g of the sample to 10 mL of sterile distilled water.Following this, the solutions with diluted gradients were uniformly spread onto lysogeny broth (LB) agar plates and incubated at 30 °C for two days.The purification process involved subjecting individual colonies to repeated streaking on LB plates, yielding the isolation of strain NBNZ-0060 as a single pure colony.

Pot experiment of submerged macrophytes
The experiment was conducted using 30-cm high, 20-cm diameter plexiglass buckets with a 5-cm high layer of high nitrogen contaminated sediment (total nitrogen > 20 0 0 mg/kg, collected from Jin Lake) and a 20-cm high layer of overlying water.Each bucket contained three seedlings of commercially available Vallisneria natans (Lour.)Hara, the initial height, and root length of which were cut and normalized to 5 cm, while the new weight of each treatment group remained relatively constant before planting.In each experimental group, ten seedlings were included.The containers were kept in a greenhouse at a constant temperature of 25 °C and under light conditions of 14 h:10 h cycle.A volume of 1 mL of bacterial solution (1 * 10 8 CFU/mL, grow in LB medium) was added to each container for the experimental group, while the control group received 1 mL of blank LB medium.The treatments was applied once a week for a total of three times.Following the completion of the entire 60-day experiment, number of surviving seedlings, fresh weight, leaf length, and root length of the seedlings in each group were measured and recorded.All strains with superscript capital T used for comparison were the type strains.

Nitrate removal characteristics of strain NBNZ-0060
Denitrification medium (DM) were used for the nitrate removal experiment, containing 3.75 g glucose, 0.607 g NaNO 3 , 0.1 g MgSO 4 •7H 2 O, 3.00 g KH 2 PO 4 , 7.00 g K 2 HPO 4 , and 0.05 g FeSO 4 •7H 2 O per liter, pH 7.2.Following an overnight cultivation in LB medium, strain NBNZ-0060 was inoculated at 1% into DM medium with 100 mg/L nitrate and incubated at 30 °C for 24 h without shaking.Then the culture were collected to measure the bacterial density (OD 600 nm ) and the concentrations of nitrate, using the supernatant fluid after centrifugation.A medium that did not contain incubated bacteria served as the blank control treatment and each experiment was replicated in triplicate.Nitrate was measured by phenol disulfonic acid photometry method.

Whole genome sequencing and assembly
Purified colonies of NBNZ-0060 were inoculated into LB medium and cultivated until reaching the mid-logarithmic growth phase, at 30 °C, 220 rpm.Subsequently, genomic DNA isolation was performed using the Blood & Cell Culture DNA Kits (QIAGEN, Germany), following the guidelines provided by the manufacturer.The purity and concentration of DNA samples were assessed using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and Qubit® DNA Assay Kit in Qubit ® 2.0 Flurometer (Life Technologies, CA, USA).The monitoring of DNA degradation and contamination was conducted using 1% agarose gels.
For long-read sequencing, size-select of the genomic DNA sample were performed using the PippinHT system (Sage Science, USA).The DNA library was generated utilizing a ligation sequencing kit (SQK-LSK-109; Oxford Nanopore Technologies, Ltd. [ONT], Oxford, UK) without the application of DNA fragmentation.Subsequently, the library was subjected to sequencing using a Nanopore PromethION sequencer instrument (ONT) employing a R9.4.1 flow cell (FLO-MIN106).The process of base-calling and barcode segmentation, as well as the removal of adapter sequences from the raw sequences, was carried out using Guppy v.4.4.2 [11] .A total of 123,200 reads were produced, including 1,306,272,863 bp, which had an average length of 10,602.86bp with a N50 value of 23,163 bp.For short-reads sequencing, the genomic DNA sample described above underwent fragmentation using sonication, utilizing the Covaris LE220 focused ultrasonicator (USA), yielding a size of 350bp.Subsequently, purification was carried out using AM-Pure XP magnetic beads (Beckman, Germany).A paired-end DNA library was created using the Truseq Nano DNA HT Sample preparation Kit (Illumina USA) in accordance with the guidelines provided by the manufacturer.The sequencing procedure was conducted on an Illumina No-vaSeq 60 0 0 equipment (Illumina, USA), using 150 nucleotide length reads.The raw data underwent processing using the FASTQ preprocessing software fastp v.0.23.2 [12] in order to remove adapters and low-quality data, yielding a total of 4,686,608 short reads, with a combined length of 1,405,982,400 bp.The assembly of the high-quality long-and short-read sequences was performed using Unicycler v.0.5.0 [13] , yielding the generation of entire and circularized chromosomes.The average coverage is 361x.

Fig. 2 .
Fig. 2. Subsystem category distribution of Bacillus velezensis NBNZ-0060 generated using the tool kit of the Rapid Annotation using Subsystem Technology (RASTtk).The bar chart shows the subsystem coverage in percentage (the blue bar corresponds to the percentage of proteins not identified).The pie chart shows the distribution of the 27 most abundant subsystem categories.

Table 1
Effect of strain NBNZ-0060 on the survival number and biomass of Vallisneria natans (Lour.)Hara.

Table 3
Putative genes involved in tryptophan dependent IAA production of Bacillus velezensis NBNZ-0060.

Table 5
Taxonomic affiliation of Bacillus velezensis NBNZ-0060 based on ANI and dDDH values.