Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes

Abstract

We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ70-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.

Describing Paenibacillus mucilaginosus strain N3 as an efficient plant growth promoting rhizobacteria (PGPR)

“…Over the period of last 10 years, new Paenibacillus strains are identified as nitrogen fixers (Xie et al, 2014). Lu, Xue, Cao, Yang, and Hu (2014) reported various strains of P. mucilaginosus could fix nitrogen and suggested its potential application in agriculture.…”

“…However, over the period of last 10 years, few strains of Paenibacillus were rediscovered as nitrogen fixers which helped them to prove superiority over other extensively studied PGPR. Few nitrogen-fixing Paenibacillus strains include P. polymyxa, P. macerans, P. durus, P. peoriae, P. borealis, P. brasilensis, P. graminis, P. odorifer, P. wynnii, P. massiliensis, and P. sabinae (Beneduzi et al, 2010;Xie et al, 2014). Thus, there is a huge scope in isolating new stains of Paenibacillus and studying them for their plantgrowth-promoting traits which can help them to characterize as cogent PGPR.…”

Current knowledge and perspectives of Paenibacillus: a review

“…More than 20 Paenibacillus species can fix nitrogen [25], with single species comprising both diazotrophic and non-diazotrophic strains [26, 27]. The nif gene cluster is highly conserved among nitrogen-fixing Paenibacillus , with most clusters containing 9 genes within 10.5–12 kb, and exhibiting over 80% identity [25].…”

Endophytes-assisted biocontrol: novel insights in ecology and the mode of action of Paenibacillus

“…One of the most likely potential contributing factors accounting for differences between the behavior of Bacillus and Paenibacillus spp. relates to their ability to fix nitrogen (Jin et al 2011;Xie et al 2014). This is a common and widespread feature of Paenibacillus but was also shown for several rhizosphere-associated Bacillus strains (Ding et al 2005).…”