NEW YORK (GenomeWeb News) – An international group of researchers has sequenced the genome of a nitrogen-fixing, root-associated bacterial species.
In a paper published online this week in the Proceedings of the National Academy of Sciences, Chinese and French researchers report sequencing the genome of a diazotrophic Pseudomonas stutzeri strain that lives in the soil in and around plant roots. In the process, it uses nitrogenase enzymes to convert dinitrogen to ammonia, which can be used by plants. The team also started teasing apart genes that were shared with other Pseudomonas species and those that were unique to P. stutzeri.
“The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants,” Qi Jin, a molecular virologist and genetic engineer at the Chinese Academy of Medical Sciences in Beijing, and colleagues wrote. “[M]oreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture.”
The team sequenced the 4,567,418 base pair P. stutzeri A1501 genome to about seven-fold coverage using whole-genome shotgun sequencing. The genome contains an estimated 4,146 protein coding genes. About half of these, some 1,977, are similar to genes found in five other Pseudomonas species, suggesting this may represent the core Pseudomonas genome. Interestingly, genes related to nitrogenase function are located on a so-called nitrogen fixation island that is about 49 kilobases in size and houses 59 genes.
They also used microarrays to gauge transcription status across the A1501 genome. For instance, most of the genes found in the nitrogen-fixation island were up-regulated in response to nitrogen fixation conditions, but down-regulated when excess nitrogen was available.
The bug contained hundreds of genes coding transporters along with several suspected to mediate osmotolerance. The team also found genes that may be help P. stutzeri survive in soil and colonize plant roots, though they noted that more work is necessary to pinpoint the exact role of these genes.
“[T]he availability of the A1501 genome sequence provides insights into the evolution of nitrogen-fixing organisms and opens up new perspectives for molecular interaction between the microbe and host plant,” Jin and colleagues concluded.