UC Santa Barbara

Ammonia-oxidizing organisms are key contributors to the nitrogen cycle, yet little is known about their genomic adaptations to saline or alkaline conditions. This study combines physiological characterization and comparative genomics of ammonia-oxidizing bacteria (AOB) with a metagenomics to better understand potential adaptations to salt and high pH environments. Halotolerant AOB possess numerous adaptations that help regulate the osmotic stress caused by varying salt and pH conditions including osmolyte biosynthesis pathways and an inventory of transporters that helps regulate the electrochemical gradient imposed. Genomic analysis of Nitrosomonas sp. ANs5, an extremely alkalitolerant species within the Nitrosomonas lineage, identified multiple genomic features predicted to facilitate osmotic and pH homeostasis, including biosynthesis of compatible solutes and the presence of a V-type ATPase, unique within the Nitrosomonas. Ammonia-oxidizing enrichment cultures were established from an isolated hypersaline brine pool at the Carpinteria Salt Marsh, in which attempts to isolate the novel MAG, Nitrosomonas sp. CSM, were unsuccessful although the enrichment demonstrated faster growth at 800mM NaCl than 600 mM NaCl. Comparative genomic analysis revealed the combination of transporter and osmolyte biosynthesis adaptations that contribute to salt and pH tolerance across reference and newly sequenced AOB. Metagenomic read mapping indicated that halotolerant AOB co-inhabit environments where freshwater or halophilic AOB are distributed. These results demonstrate some AOB are adapted to saline and alkaline environments and provides insight into the adaptations that permit their activity in extreme environments.