Bacillus is a phylogenetically heterogeneous taxon, and
Paenibacillus was classified as a new genus in 1993 (
1–3). The rod-shaped cells are motile, have peritrichous flagella, and show variable Gram staining. They form ellipsoidal endospores (
4). Species of this genus are known to produce hormones that stimulate plant growth, like cytokinin (
5), and antibiotic peptides as well as different (
6) hydrolyzing enzymes, which are responsible for antagonistic behavior against many plant pathogens. Thus, many species of the genus have been described as plant growth-promoting bacteria.
Paenibacillus sp. P22 was isolated by Ulrich et al. (
7) from the poplar hybrid 741 [
Populus alba × (
P. davidiana +
P. simonii) ×
P. tomentosa] (
8). The phylogenetic analysis of the strain was based on 16S rRNA gene sequencing and showed that
Paenibacillus sp. P22 has strong 16S rRNA gene sequence similarity to
Paenibacillus humicus (99.5%) (
7). Former experiments have shown that
in vitro grown explants of hybrid 741 inoculated with
Paenibacillus sp. P22 exhibited significantly more root growth and root length than noninoculated explants (
7). The pure culture of the bacterial strain was grown under aerobic conditions on tryptic soy broth agar plates. The DNA extraction was performed with a DNA GeneJET gel extraction kit according to the manufacturer's instructions. Application of the 454 GS FLX Titanium sequencing technology and sequencing of an 8-kb paired-end library resulted in 561,213 reads and 61,143,112 nucleotides. In an Ion Torrent PGM sequencing approach, 1,978,332 reads and 343,311,791 nucleotides were gathered. Consensus assembly using MIRA (
9) yielded 5,443,257 bp in 297 contigs (>300 bp), with an overall GC content of 58%. Coding sequences (CDS) were predicted based on an in-house workflow that integrates
ab initio predictions from Glimmer (
10), Genemark (
11), Prodigal (
12), and Critica (
13) with homology information derived from a BLAST search against NCBI nr (
14). Noncoding RNAs were identified by tRNAscanSE (
15), RNAmmer (
16), and Infernal (
17). Predicted CDS were compared to the databases InterPro (
18), Swissprot (
19), and trEMBL (
19) for functional annotation and mapped to KEGG pathways.
The genome of
Paenibacillus sp. P22 contains 5,224 protein-coding genes, 65 tRNAs, and 1 16S rRNA. Presence of tRNAs for all 20 proteinogenic amino acids as well as 31 out of 31 phylogenetic marker proteins (AMPHORA2 software) (
20) that are essential in prokaryotes indicates an estimated completeness of the genome of about 99%. Further investigation of the metabolic capabilities of
Paenibacillus sp. P22 yielded two particularly interesting findings. We found a gene encoding a nitrogenase (EC 1.19.6.1) for nitrogen fixation coinciding with the observation that
Paenibacillus sp. P22 is able to grow without nitrogen in the medium (
21). Accordingly, metabolite profiles of poplar plants which were inoculated with
Paenibacillus sp. P22 showed a strongly altered C/N homeostasis as a result of the endophyte-plant interaction (
21). Genes of the auxine-pathway were also detected, suggesting growth-promoting effects by hormone secretion. This finding was indeed confirmed by the detection of auxin in a metabolite profile of a
Paenibacillus sp. P22 culture.