Publications

4482

‘Candidatus Liberibacter solanacearum’ is a plant pathogen associated with diseases affecting several crops of the Solanaceae and Apiaceae families. Two ‘Ca. L. solanacearum’ haplotypes (LsoA and LsoB) infect solanaceous crops in North America and are transmitted by the tomato psyllid Bactericera cockerelli. Although both ‘Ca. L. solanacearum’ haplotypes cause zebra chip in potato, the diseases associated with each haplotype in tomato (Solanum lycopersicum) have not been described. ‘Ca. L. solanacearum’-infected tomato plants exhibit symptoms resembling those of permanent yellowing disease (known in Mexico as “permanente del tomate”) and sometimes called psyllid yellows. In this study, the symptoms associated with each ‘Ca. L. solanacearum’ haplotype in tomato were compared, and the bacterial abundance in different nodes of the plants was measured by quantitative polymerase chain reaction. Surprisingly, both plant phenotype and bacterium distribution were different between LsoA- and LsoB-infected plants. Plants infected with LsoB died prematurely, whereas those infected with LsoA did not. Across the measured time points, LsoB abundance in infected plants was consistent with previous reports describing a sink to source gradient, while such gradient was only observed in LsoA-infected plants early after infection. This is the first report describing the differences in symptoms in tomato associated with two ‘Ca. L. solanacearum’ haplotypes, LsoA and LsoB.

A draft genome sequence is presented for a strain of “ Candidatus Phytoplasma asteris” affecting canola plants in Saskatoon, Canada. This phytopathogenic bacterium was determined to be a 16SrI strain and features 16S rRNA-encoding gene sequence heterogeneity.

This study on d -galacturonate metabolism by open, mixed-culture enrichments under anaerobic, d -galacturonate-limited chemostat conditions shows a stable and efficient fermentation of d -galacturonate into acetate as the dominant organic fermentation product. This fermentation stoichiometry and population analyses provide a valuable baseline for interpretation of the conversion of pectin-rich agricultural feedstocks by mixed microbial cultures. Moreover, the results of this study provide a reference for studies on the microbial metabolism of d -galacturonate under different cultivation regimes.

ABSTRACT Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus “ Candidatus Nitrotoga” are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure “ Ca . Nitrotoga” culture was available. Here we obtained the first “ Ca . Nitrotoga” isolate from activated sludge. This organism, “ Candidatus Nitrotoga fabula,” prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous “ Ca . Nitrotoga” enrichments, which were described as cold-adapted NOB. “ Ca . Nitrotoga fabula” also showed an unusually high tolerance to nitrite (activity at 30 mM NO 2 − ) and nitrate (up to 25 mM NO 3 − ). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent K m ( K m (app) ) of ~89 µM nitrite and a V max of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of “ Ca . Nitrotoga fabula” were reconstructed from the closed genome. “ Ca . Nitrotoga fabula” possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in “ Ca . Nitrotoga” and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, “ Ca . Nitrotoga fabula” uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable “ Ca . Nitrotoga fabula” to survive nitrite depletion and colonize new niches. IMPORTANCE Nitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus “ Candidatus Nitrotoga” and performed a detailed physiological and genomic characterization of this organism (“ Candidatus Nitrotoga fabula”). Differences between key phenotypic properties of “ Ca . Nitrotoga fabula” and those of previously enriched “ Ca . Nitrotoga” members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that “ Ca . Nitrotoga” are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in “ Ca . Nitrotoga fabula” expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.