Publications

4578

We report here the near-complete genome sequence of “ Candidatus Spirobacillus cienkowskii,” a spiral-shaped, red-pigmented uncultivated bacterial pathogen of Daphnia spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen.

Abstract Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.

Specific scopeThis Standard describes the procedures for inspection of places of production of plants for planting which are susceptible to ‘Candidatus Phytoplasma pyri’. The scope of a place of production inspection may be for export, for internal country movements of materials or as an element of a national survey. Further inspections would be needed to determine freedom of a country or area from the pest concerned. This Standard does not cover eradication or containment measures in infested areas or measures needed to establish and maintain pest‐free places of production within areas where the pest is known to occur. It provides more detailed guidance to supplement EPPO Standard PM 3/76 (1) Trees of Malus, Pyrus, Cydonia and Prunus spp. – inspection of places of production.