Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter

Christman, Glenn D.; Cottrell, Matthew T.; Popp, Brian N.; Gier, Elizabeth; Kirchman, David L.

doi:10.1128/aem.01907-10

Cited by 103 publications

(100 citation statements)

References 58 publications

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“…The copy numbers of archaeal amoA and 16S rRNA genes were highly correlated, and the ratio between these genes was on average 3 and 1 in Arctic and Antarctic water samples, respectively (Fig. 4 and SI Appendix, Tables S4 and S5), in agreement with previous reports from the Chukchi Sea (37) and off the Antarctic Peninsula (28). Our results thus indicate that a genetic potential for ammonia oxidation is widespread in polar MGI Archaea.…”

Section: Quantification Of Amoa and Urec Gene Abundances In Arctic Andsupporting

confidence: 91%

“…Therefore, we believe that our finding that polar Thaumarchaeota do not contribute significantly to the uptake of labile monomers such as leucine is more representative for the low to moderate productivity conditions found in most polar marine waters. Reports of archaeal amoA genes in polar environments (28), and recent evidence of active nitrification in Arctic winter waters (31,37), suggest that polar Thaumarchaeota may be nitrifiers. To test whether polar Thaumarchaeota were growing autotrophically, we measured their activity in bicarbonate uptake.…”

Section: Resultsmentioning

confidence: 99%

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Role for urea in nitrification by polar marine Archaea

Alonso‐Sáez

Waller

Mende

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

248

231

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Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.amoA | ureC | Beaufort Sea | Ross Sea | Amundsen Sea

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Section: Quantification Of Amoa and Urec Gene Abundances In Arctic Andsupporting

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Role for urea in nitrification by polar marine Archaea

Alonso‐Sáez

Waller

Mende

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

248

231

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“…Therefore, active nitrification mediated by microbes under the sea ice could be occurring, oxidizing NH 4 + and producing N 2 O as a byproduct of this reaction, especially bearing in mind that sea ice melt can release NH 4 + (Tovar-Sánchez et al, 2010). Indeed, previous experiments in the coastal Arctic Ocean have shown the presence of ammonia-oxidizing Betaproteobacteria and Crenarchaea, and potentially high nitrification rates with higher values in the winter compared with the summer, due to competition with phytoplankton for NH 4 + concentrations (Christman et al, 2011).…”

Section: Pml and Haloclinementioning

confidence: 99%

Climate relevant trace gases (N2O and CH4) in the Eurasian Basin (Arctic Ocean)

Verdugo

Damm

Snoeijs

et al. 2016

Deep Sea Research Part I: Oceanographic Research Papers

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A B S T R A C TThe concentration of greenhouse gases, including nitrous oxide (N 2 O), methane (CH 4 ), and compounds such as total dimethylsulfoniopropionate (DMSP t ), along with other oceanographic variables were measured in the icecovered Arctic Ocean within the Eurasian Basin (EAB). The EAB is affected by the perennial ice-pack and has seasonal microalgal blooms, which in turn may stimulate microbes involved in trace gas cycling. Data collection was carried out on board the LOMROG III cruise during the boreal summer of 2012. Water samples were collected from the surface to the bottom layer (reaching 4300 m depth) along a South-North transect (SNT), from 82.19°N, 8.75°E to 89.26°N, 58.84°W, crossing the EAB through the Nansen and Amundsen Basins. The Polar Mixed Layer and halocline waters along the SNT showed a heterogeneous distribution of N 2 O, CH 4 and DMSP t , fluctuating between 42-111 and 27-649% saturation for N 2 O and CH 4, respectively; and from 3.5 to 58.9 nmol L −1 for DMSP t . Spatial patterns revealed that while CH 4 and DMSP t peaked in the Nansen Basin, N 2 O was higher in the Amundsen Basin. In the Atlantic Intermediate Water and Arctic Deep Water N 2 O and CH 4 distributions were also heterogeneous with saturations between 52% and 106% and 28% and 340%, respectively. Remarkably, the Amundsen Basin contained less CH 4 than the Nansen Basin and while both basins were mostly under-saturated in N 2 O. We propose that part of the CH 4 and N 2 O may be microbiologically consumed via methanotrophy, denitrification, or even diazotrophy, as intermediate and deep waters move throughout EAB associated with the overturning water mass circulation. This study contributes to baseline information on gas distribution in a region that is increasingly subject to rapid environmental changes, and that has an important role on global ocean circulation and climate regulation.

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“…There has been a widespread effort to determine the distribution of AOA in nearly all major oceanic regions (Lam et al, 2007;Beman et al, 2008;Church et al, 2010;Santoro et al, 2010;Christman et al, 2011;Alonso-Sáez et al, 2012;Baker et al, 2012;Sintes et al, 2013). Substantial evidence now exists that AOA have a primary role in determining the distribution and magnitude of nitrification in the sea (Mincer et al, 2007;Beman et al, 2008;Church et al, 2010;Hollibaugh et al, 2010;Newell et al, 2011;Santoro et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Differential contributions of archaeal ammonia oxidizer ecotypes to nitrification in coastal surface waters

et al. 2014

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The occurrence of nitrification in the oceanic water column has implications extending from local effects on the structure and activity of phytoplankton communities to broader impacts on the speciation of nitrogenous nutrients and production of nitrous oxide. The ammonia-oxidizing archaea, responsible for carrying out the majority of nitrification in the sea, are present in the marine water column as two taxonomically distinct groups. Water column group A (WCA) organisms are detected at all depths, whereas Water column group B (WCB) are present primarily below the photic zone. An open question in marine biogeochemistry is whether the taxonomic definition of WCA and WCB organisms and their observed distributions correspond to distinct ecological and biogeochemical niches. We used the natural gradients in physicochemical and biological properties that upwelling establishes in surface waters to study their roles in nitrification, and how their activityascertained from quantification of ecotype-specific ammonia monooxygenase (amoA) genes and transcripts-varies in response to environmental fluctuations. Our results indicate a role for both ecotypes in nitrification in Monterey Bay surface waters. However, their respective contributions vary, due to their different sensitivities to surface water conditions. WCA organisms exhibited a remarkably consistent level of activity and their contribution to nitrification appears to be related to community size. WCB activity was less consistent and primarily constrained to colder, high nutrient and low chlorophyll waters. Overall, the results of our characterization yielded a strong, potentially predictive, relationship between archaeal amoA gene abundance and the rate of nitrification.

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Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter

Cited by 103 publications

References 58 publications

Role for urea in nitrification by polar marine Archaea

Role for urea in nitrification by polar marine Archaea

Climate relevant trace gases (N2O and CH4) in the Eurasian Basin (Arctic Ocean)

Differential contributions of archaeal ammonia oxidizer ecotypes to nitrification in coastal surface waters

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