Oxidation of urea‐derived nitrogen by thaumarchaeota‐dominated marine nitrifying communities

Tolar, Bradley B.; Wallsgrove, Natalie J.; Popp, Brian N.; Hollibaugh, James T.

doi:10.1111/1462-2920.13457

Cited by 62 publications

(74 citation statements)

References 58 publications

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“…Rates of nitrification and coupled urea hydrolysisnitrification were similar, and suggest that urea could be an important source of NH 3 fueling nitrification in the mesopelagic as has been recently shown in mesopelagic waters over the Antarctic Shelf (Tolar et al 2016). Our experiments cannot resolve whether this transformation is being carried out by a single group of organisms, or a consortium of ureahydrolyzing microbes and ammonia oxidizers, as was recently proposed (Koch et al 2015).…”

Section: Discussionmentioning

confidence: 51%

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

Santoro

Saito

Goepfert

et al. 2017

Limnology & Oceanography

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Thaumarchaea are among the most abundant microbial groups in the ocean, but controls on their abundance and the distribution and metabolic potential of different subpopulations are poorly constrained. Here, two ecotypes of ammonia-oxidizing thaumarchaea were quantified using ammonia monooxygenase (amoA) genes across the equatorial Pacific Ocean. The shallow, or water column "A" (WCA), ecotype was the most abundant ecotype at the depths of maximum nitrification rates, and its abundance correlated with other biogeochemical indicators of remineralization such as NO 3 : Si and total Hg. Metagenomes contained thaumarchaeal genes encoding for the catalytic subunit of the urease enzyme (ureC) at all depths, suggesting that members of both WCA and the deep, water column "B" (WCB) ecotypes may contain ureC. Coupled urea hydrolysisammonia oxidation rates were similar to ammonia oxidation rates alone, suggesting that urea could be an important source of ammonia for mesopelagic ammonia oxidizers. Potential inducement of metal limitation of both ammonia oxidation and urea hydrolysis was demonstrated via additions of a strong metal chelator. The water column inventory of WCA was correlated with the depth-integrated abundance of WCB, with both likely controlled by the flux of sinking particulate organic matter, providing strong evidence of vertical connectivity between the ecotypes. Further, depth-integrated amoA gene abundance and nitrification rates were correlated with particulate organic nitrogen flux measured by contemporaneously deployed sediment traps. Together, the results refine our understanding of the controls on thaumarchaeal distributions in the ocean, and provide new insights on the relationship between material flux and microbial communities in the mesopelagic.

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Section: Discussionmentioning

confidence: 51%

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

Santoro

Saito

Goepfert

et al. 2017

Limnology & Oceanography

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“…Our finding that ureC was not highly expressed in exponentially growing cells also helps to explain previous field observations of low ureC expression and suggests the abundance of ureC transcripts may be a poor molecular biomarker of active urea‐based nitrification. For example, ureC expression and urea‐based nitrification were found to be only weakly correlated across several environments (Tolar et al ., ), in contrast to high correlation between amoA expression and ammonia oxidation rates (Smith et al ., ). Similarly, although ureC genes were detected in Arctic samples collected across seasons, corresponding ureC transcripts were only sporadically detected and at low abundances (Pedneault et al ., ).…”

Section: Resultsmentioning

confidence: 97%

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

Carini

Dupont

Santoro

2018

Environmental Microbiology

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Thaumarchaea are ubiquitous in marine habitats where they participate in carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea are active microbes in marine waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization and activity. Here, we report the global transcriptional response of the marine ammonia-oxidizing thaumarchaeon 'Candidatus Nitrosopelagicus brevis' str. CN25 to ammonia limitation using RNA-Seq. We further describe the genome and transcriptome of Ca. N. brevis str. U25, a new strain capable of urea utilization. Ammonia limitation in CN25 resulted in reduced expression of transcripts coding for ammonia oxidation proteins, and increased expression of a gene coding an Hsp20-like chaperone. Despite significantly different transcript abundances across treatments, two ammonia monooxygenase subunits (amoAB), a nitrite reductase (nirK) and both ammonium transporter genes were always among the most abundant transcripts, regardless of growth state. Ca. N. brevis str. U25 cells expressed a urea transporter 139-fold more than the urease catalytic subunit ureC. Gene coexpression networks derived from culture transcriptomes and 10 thaumarchaea-enriched metatranscriptomes revealed a high degree of correlated gene expression across disparate environmental conditions and identified a module of coexpressed genes, including amoABC and nirK, that we hypothesize to represent the core ammonia oxidation machinery.

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“…Our finding that ureC was not highly expressed in exponentially growing cells also helps to explain previous field observations of low ureC expression, and suggests the abundance of ureC transcripts may be a poor molecular biomarker of active urea-based nitrification. For example, ureC expression and urea-based nitrification were found to be only weakly correlated across several environments (Tolar, Wallsgrove, et al ., 2016), in contrast to high correlation between amoA expression and ammonia oxidation rates (J. M. Smith et al ., 2014). Similarly, in Arctic samples collected across seasons, ureC genes were detected, yet ureC transcripts were only sporadically detected and at low abundances (Pedneault et al ., 2014).…”

Section: Resultsmentioning

confidence: 99%

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

Carini¹,

Dupont²,

Santoro³

2017

Preprint

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Oxidation of urea‐derived nitrogen by thaumarchaeota‐dominated marine nitrifying communities

Cited by 62 publications

References 58 publications

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

Patterns of thaumarchaeal gene expression in culture and diverse marine environments

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