bAerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with "Candidatus Nitrosoarchaeum koreensis" and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail. N itrification, the microbial oxidation of NH 3 (ammonia) to NO 3 Ϫ (nitrate), is one of the key processes of the global nitrogen cycle. The first and rate-limiting step of nitrification is the oxidation of NH 3 to NO 2 Ϫ (nitrite). Until recently, aerobic ammonia oxidation was attributed to only a small subset of the Proteobacteria; most freshwater and terrestrial ammonia-oxidizing bacteria (AOB) belong to a distinct group in the Betaproteobacteria, while a few marine AOB species belong to the Gammaproteobacteria (29,32,33). The AOB have a chemolithoautotrophic metabolism, oxidizing NH 3 to NO 2 Ϫ via the intermediate NH 2 OH (hydroxylamine) and fixing carbon from CO 2 (carbon dioxide) via the Calvin cycle (1).Recently, genes encoding ammonia monooxygenase (amoA), the first enzyme in the process of ammonia oxidation, were discovered together with archaeal 16S rRNA genes in a metagenomic study (60) and a soil fosmid library (57). At the same time, Nitrosopumilus maritimus, the first archaeal ammonia oxidizer, was isolated in pure culture from a saltwater aquarium (30). Ammoniaoxidizing archaea (AOA) in pure and enrichment cultures have essentiallythesamemetabolismasAOB;theyoxidizeNH 3 stoichiometrically to NO 2 Ϫ and fix carbon from bicarbonate (HCO 3 Ϫ ) (15,20,30,36,43,56). However, the genomes of N. maritimus and "Candidatus Nitrosoarchaeum limnia" revealed differences between AOA and AOB, such as the use of the 3-hydroxypropionat...

No abstract

No abstract

The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt and causes significant crop loss in the Solanaceae family. The pathogen first infects roots, which are a critical source of resistance in tomato (Solanum lycopersicum L.). Roots of both resistant and susceptible plants are colonized by the pathogen, yet rootstocks can provide significant levels of resistance. Currently, mechanisms of this 'root-mediated resistance' remain largely unknown. To identify the molecular basis of this resistance, we analyzed the genome-wide transcriptional response of roots of resistant 'Hawaii 7996' and susceptible 'West Virginia 700' (WV) tomatoes at multiple timepoints after inoculation with R. solanacearum. We found that defense pathways in roots of the resistant Hawaii 7996 are activated earlier and more strongly than roots of susceptible WV. Further, auxin signaling and transport pathways are suppressed in roots of the resistant variety. Functional analysis of an auxin transport mutant in tomato revealed a role for auxin pathways in bacterial wilt. Together, our results suggest that roots mediate resistance to R. solanacearum through genome-wide transcriptomic changes that result in strong activation of defense genes and alteration of auxin pathways.

No abstract