PT  - JOURNAL ARTICLE
AU  - Paul Carini
AU  - Christopher L. Dupont
AU  - Alyson E. Santoro
TI  - Correlated expression of archaeal ammonia oxidation machinery across disparate environmental and culture conditions
AID  - 10.1101/175141
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 175141
4099  - http://biorxiv.org/content/early/2017/08/11/175141.short
4100  - http://biorxiv.org/content/early/2017/08/11/175141.full
AB  - Although marine metatranscriptomes suggest planktonic ammonia-oxidizing thaumarchaea are among the most active microbes in marine waters1-4, we understand little about how thaumarchaeal expression patterns relate to substrate utilization and activity. Here, we characterize the global transcriptional response of a marine ammonia-oxidizing thaumarchaeon, ‘Candidatus Nitrosopelagicus brevis’ str. CN25, to ammonia limitation. We further describe the genome and transcriptome of Ca. N. brevis str. U25, a new thaumarchaeal strain capable of oxidizing ammonia derived from urea. Ammonium limitation in CN25 resulted in reduced expression of transcripts coding for core ammonia oxidation proteins, and increased expression of a gene coding an Hsp20-like chaperone. Despite significantly different transcript abundances across treatments, amoAB, nirK and both ammonium transporter genes were always among the most abundant transcripts, regardless of growth state. Ca. N. brevis str. U25 cells growing on urea expressed a urea transporter 139-fold more than the urease catalytic subunit ureC, indicating that the expression of urea acquisition machinery is favored over urease genes during exponential growth. Gene co-expression networks derived from transcriptomes from CN25 and U25 cultures and ten thaumarchaea-enriched metatranscriptomes revealed a high degree of correlated gene expression across disparate environmental conditions. We show nirK is tightly co-expressed with amoABC, suggesting a central role for NirK in ammonia oxidation. These findings demonstrate how transcriptomes from microbial cultures can be used to contextualize and identify gene expression relationships that are otherwise enigmatic.