Complete Genome Sequence of the Nitrogen-Fixing and Rhizosphere-Associated Bacterium Pseudomonas stutzeri Strain DSM4166

Abstract

We present here the analysis of the whole-genome sequence of Pseudomonas stutzeri strain DSM4166, a diazotrophic isolate from the rhizosphere of a Sorghum nutans cultivar. To our knowledge, this is the second genome to be sequenced for P. stutzeri. The availability and analysis of the genome provide insight into the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in interactions with host plants.

GENOME ANNOUNCEMENT

Pseudomonas stutzeri is a Gram-negative soil bacterium that belongs to the group of nonfluorescent Pseudomonas bacteria (7, 8, 10). These bacteria are known for their ability to oxidize a large variety of organic compounds and to occupy diverse ecological niches (2, 9). Some strains have received particular attention because of specific properties, such as degradation of aromatic compounds, denitrification, and nitrogen fixation (6). Members of the species are used as model organisms for studying the denitrification process. It is also an opportunistic pathogen in clinical settings, although infections are rare (1). P. stutzeri has been assigned at least nine genomovars, reflecting a remarkable degree of physiological and genetic diversity (4). Strain DSM 4166 (formerly strain CMT.9.A) was isolated from the rhizosphere of a “high-fixing” Sorghum nutans cultivar in Germany (5). This strain exhibits the unusual feature, for a Pseudomonas strain, of fixing nitrogen.

The genome was sequenced using a Roche/454 GS FLX sequencer by a whole-genome shotgun strategy which obtained 432,459 reads, totaling ∼134 Mb, ∼29-fold coverage of the genome. The reads were assembled into 84 contigs using the Newbler assembler (Roche). The order of contigs was confirmed by genomic PCR, and the gaps were closed by conventional Sanger sequencing of the amplicons. Open reading frames (ORFs) were predicted by the Glimmer 3 software program (3), and functional annotations were carried out by a BLASTP search against GenBank's nonredundant protein database (NR) and manual curation. tRNA genes were identified by the tRNAscan-SE software program.

P. stutzeri DSM4166 has a 61.74%-GC circular chromosome of 4,689,946 bp with no plasmid. The DSM4166 genome is predicted to contain 59 tRNA genes and 4 rRNA operons. The genome size is similar to that of P. stutzeri A1501 (11) and smaller than those of other sequenced Pseudomonas species. A 66.8% proportion (2,770) of the DSM4166 genes had counterparts in the P. stutzeri A1501 genome, exhibiting the highest overall similarity to A1501 compared to other species. Both the two P. stutzeri strains can fix nitrogen and contain a nif island with similar gene organization. The A1501 island contains 59 genes, all of which are conserved in DSM4166 except for only one gene, PST1312, encoding a thiopurine S-methyltransferase. The ability to fix nitrogen within the Pseudomonas genus has been long debated, but in recent years several Pseudomonas strains that can fix nitrogen have been identified (6). The origin of the nitrogen-fixing genes in the Pseudomonas genus can be explained by a plausible lateral gene transfer acquisition. This hypothesis seems to be supported by nifH phylogenies and further by our present data. In addition to nitrogen-fixing ability, the genome contains at least 42 genes encoding the denitrification apparatus' core structures. The genome also contains genes involved in nitrogen fixation, denitrification, chemotaxis, and other functions that presumably give the bacterium an advantage in root colonization.

Nucleotide sequence accession number.

The complete nucleotide genome sequence of P. stutzeri DSM4166 has been deposited in GenBank under accession number CP002622.