Hybrid genome assembly and annotation of Paenibacillus pasadenensis strain R16 reveals insights on endophytic life style and antifungal activity

Abstract

Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one. In this study, we have characterized the genome of Paenibacillus pasadenensis, strain R16, recently investigated for its antifungal activities and plant-associated features. An hybrid assembly approach was used integrating the very precise reads obtained by Illumina technology and long fragments acquired with Oxford Nanopore Technology (ONT) sequencing. De novo genome assembly based solely on Illumina reads generated a relatively fragmented assembly of 5.72 Mbp in 99 ungapped sequences with an N50 length of 544 Kbp; hybrid assembly, integrating Illumina and ONT reads, improved the assembly quality, generating a genome of 5.75 Mbp, organized in 6 contigs with an N50 length of 3.4 Mbp. Annotation of the latter genome identified 4987 coding sequences, of which 1610 are hypothetical proteins. Enrichment analysis identified pathways of particular interest for the endophyte biology, including the chitin-utilization pathway and the incomplete siderophore pathway which hints at siderophore parasitism. In addition the analysis led to the identification of genes for the production of terpenes, as for example farnesol, that was hypothesized as the main antifungal molecule produced by the strain. The functional analysis on the genome confirmed several plant-associated, plant-growth promotion, and biocontrol traits of strain R16, thus adding insights in the genetic bases of these complex features, and of the Paenibacillus genus in general.

Isolation, identification, and characterization of phosphate solubilizing bacteria, Paenibacillus sp., from the soil of Danum Valley Tropical Rainforest, Sabah, Malaysia

“…Nevertheless, with very limited information on its phosphatase enzymes, many strains of Paenibacillus sp. have been previously used as biofertilizer with a consortium of bacterial species and its functional traits was only based on its genome analysis (Khalid et al 2009;Shtark et al 2010;Passera et al 2018). Nevertheless, no studies have been reported on the catalytic and structural properties of phosphatase.…”

Genome Mining and Characterization of Biosynthetic Gene Clusters in Two Cave Strains of Paenibacillus sp.

“…The terpene biosynthetic pathway is unknown in the genus Paenibacillus sp. The partial hypothetical pathway was proposed by Passera et al (2018) for Paenibacillus pasadenensis strain R16, which was reported to produce sesquiterpenoid farnesol. The antibacterial activities of sesquiterpenoids and different terpenes against Gram-positive and Gram-negative bacteria have been determined previously ( Mahizan et al, 2019 ).…”

Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IVPaenibacillus larvaegenotypes reveals a wide range of virulence factors

“…Thus, the genus Paenibacillus has recently been the subject of scientific reviews [1][2][3]. In an attempt to generate additional data on the relatively poorly understood Paenibacillus taxon, detailed studies have been performed to identify and characterize Paenibacillus isolates to facilitate their utilization [4,5]. In addition to the diverse beneficial Paenibacillus species, important pathogens of beneficial insects are also members of this genus [1,6].…”