De novo genome assembly of Bacillus altitudinis 19RS3 and Bacillus altitudinis T5S-T4, two plant growth-promoting bacteria isolated from Ilex paraguariensis St. Hil. (yerba mate)

Abstract

Plant growth-promoting bacteria (PGPB) are a heterogeneous group of bacteria that can exert beneficial effects on plant growth directly or indirectly by different mechanisms. PGPB-based inoculant formulation has been used to replace chemical fertilizers and pesticides. In our previous studies, two endophytic endospore-forming bacteria identified as Bacillus altitudinis were isolated from roots of Ilex paraguariensis St. Hil. seedlings and selected for their plant growth-promoting (PGP) properties shown in vitro and in vivo. The purposes of this work were to assemble the genomes of B. altitudinis 19RS3 and T5S-T4, using different assemblers available for Windows and Linux and to select the best assembly for each strain. Both genomes were also automatically annotated to detect PGP genes and compare sequences with other genomes reported. Library construction and draft genome sequencing were performed by Macrogen services. Raw reads were filtered using the Trimmomatic tool. Genomes were assembled using SPAdes, ABySS, Velvet, and SOAPdenovo2 assemblers for Linux, and Geneious and CLC Genomics Workbench assemblers for Windows. Assembly evaluation was done by the QUAST tool. The parameters evaluated were the number of contigs ≥ 500 bp and ≥ 1000 bp, the length of the longest contig, and the N50 value. For genome annotation PROKKA, RAST, and KAAS tools were used. The best assembly for both genomes was obtained using Velvet. The B. altitudinis 19RS3 genome was assembled into 15 contigs with an N50 value of 1,943,801 bp. The B. altitudinis T5S-T4 genome was assembled into 24 contigs with an N50 of 344,151 bp. Both genomes comprise several genes related to PGP mechanisms, such as those for nitrogen fixation, iron metabolism, phosphate metabolism, and auxin biosynthesis. The results obtained offer the basis for a better understanding of B. altitudinis 19RS3 and T5S-T4 and make them promissory for bioinoculant development.

Isolation and identification of plant growth‐promoting rhizobacteria from tall fescue rhizosphere and their functions under salt stress

“…Among all strains, Bacillus zanthoxyli and Bacillus altitudinis were the most potent in promoting tall fescue growth under salt condition on account of their better tolerance to salt, their fast growth rate in the salt environment, IAA secreting ability, phosphorus dissolving ability, and potassium dissolving ability. Several reports are in agreement with our results regarding their effectiveness as PGPR (Cortese et al, 2021; Khan et al, 2019). For instance, it is reported that Bacillus altitudinis reduces low‐phosphorus stress and high‐salinity stress in wheat by producing soluble phosphatases and phytases (Yue et al, 2019).…”

Colonization ofBacillus altitudinison the Compatible Soybean Varieties to Provide Seed Rot Resistance

“…B. altitudinis was first isolated from extreme UV-stressed air samples collected in the stratosphere [73]. It has been identified as an endophyte in various plants, including soybean [74] and others [75, 76, 77, 78, 79, 80, 81]. Several strains of B. altitudinis have shown biocontrol capabilities, such as cotton Verticillium wilt [75], grape downy mildew [78], kiwi fruit root-knot nematodes [82], soybean Phytophthora damping-off [74] and sweet potato black rot [80].…”

Alterations in Gut Archaea Composition and Their Bacterial Interactions Linked to Hypertension

“…Metagenomic sequencing datasets obtained from ENA public database and in-house metagenomic sequencing data were quality filtered by using trimmomatic v_0.33 software to remove low quality sequences [15]. Human sequences were removed after alignment with a reference genome (hg38 database) using Bowtie2 v_2.2.4, with default settings [16].…”