A simple and precise method for measuring ammonium in marine and freshwater ecosystems

Holmes, Robert M.; Aminot, Alain; Kérouel, Roger; Hooker, Bethanie A; Peterson, Bruce J.

doi:10.1139/f99-128

Cited by 1,113 publications

(600 citation statements)

References 19 publications

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“…Water samples were collected by a pumpcast-CTD in high-resolution intervals, or by Go-Flo bottles on a CTD-rosette system. NH 4 ϩ was analyzed onboard fluorometrically (46), and NO 2 Ϫ and NO 3 Ϫ with an autoanalyzer in a shore-based laboratory. Sulfide concentration was measured onboard spectrophotometrically (47).…”

Section: Methodsmentioning

confidence: 99%

Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea

Lam

Jensen

Lavik

et al. 2007

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

504

485

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Active expression of putative ammonia monooxygenase gene subunit A (amoA) of marine group I Crenarchaeota has been detected in the Black Sea water column. It reached its maximum, as quantified by reverse-transcription quantitative PCR, exactly at the nitrate maximum or the nitrification zone modeled in the lower oxic zone. Crenarchaeal amoA expression could explain 74.5% of the nitrite variations in the lower oxic zone. In comparison, amoA expression by ␥-proteobacterial ammonia-oxidizing bacteria (AOB) showed two distinct maxima, one in the modeled nitrification zone and one in the suboxic zone. Neither the amoA expression by crenarchaea nor that by ␤-proteobacterial AOB was significantly elevated in this latter zone. Nitrification in the suboxic zone, most likely microaerobic in nature, was verified by 15 ammonia-oxidizing bacteria ͉ amoA gene expression ͉ marine group ͉ Crenarchaeota ͉ marine nitrogen loss N itrification, the stepwise oxidation of ammonium to nitrite and then nitrate, is a key process in marine nitrogen cycling. It is responsible for the formation of the large deep-sea nitrate reservoir. It connects the recycling of organic nitrogen to the ultimate nitrogen loss from the oceans, because its products are substrates for denitrification and anaerobic ammonium oxidation (anammox), the only two presently known nitrogen loss processes. In productive waters such as upwelling regions, high fluxes of organic matter and thus remineralization create strong subsurface oxygen minima, enabling denitrification (1-4) or anammox (5-8) to occur. Nitrogen losses from these oxygen minimum zones (OMZs) are estimated to account for 30-50% of total nitrogen loss from the oceans (9, 10). Because remineralization also releases large amounts of ammonium, high nitrification rates are often associated with these OMZs (11), implying that nitrification may play an important role in promoting marine nitrogen loss.The Black Sea is the largest marine anoxic basin in the world. A 20-to 40-m-thick suboxic transitional zone, characterized by low oxygen (Ͻ5 M) and undetectable sulfide, persists throughout the basin between the surface oxic layer and the sulfidic anoxic deep water (Ն100 m) (12, 13). The exact depth zonation varies according to the location within the basin because of circulation and gyre formation, but similar concentrations of chemical species can be traced along isopycnals or density ( t ) surfaces throughout the basin (12). Therefore, the Black Sea provides an ideal model system to study nitrogen cycling processes along oxygen gradients. Nitrification has been reported in the lower oxic zone (14) and so has nitrogen loss via anammox in the suboxic zone (15). Nevertheless, the identity and abundance of the responsible nitrifiers, or any coupling between nitrification and nitrogen losses, remain poorly documented.The first and rate-limiting step of nitrification is aerobic ammonia oxidation. It is a microbially mediated reaction. For decades, only specific groups of ␤-and ␥-proteobacteria have been found to exh...

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Section: Methodsmentioning

confidence: 99%

Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea

Lam

Jensen

Lavik

et al. 2007

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

504

485

View full text Add to dashboard Cite

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“…The concentrations of nitrogen species (ammonia, nitrite, and nitrate) were determined colorimetrically as described previously (Grasshoff et al 1999;Holmes et al 1999;Zhang and Fischer 2006). Cells for deoxyribonucleic acid (DNA) extraction were collected by filtering 1 to 3 liters of seawater through 0.22 mm pore size Sterivex cartridge filters (Millipore).…”

Section: Methodsmentioning

confidence: 99%

Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary

Urakawa

Martens‐Habbena

Huguet

et al. 2014

Limnology & Oceanography

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A combination of molecular and activity measures was used to explore seasonal patterns of distribution, activity, and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in relationship to ammonia availability in Hood Canal, a fjord within the Puget Sound, Washington State estuary system. A greater contribution of AOA to nitrification, relative to AOB, was supported by complementary quantification of transcripts of a gene (amoA) coding for one subunit of the ammonia monooxygenase, quantification of intact glycerol dialkyl glycerol tetraether lipids, and kinetic modeling. High AOA : AOB ratios and nitrification rates measured by 15 NH z 4 dilution technique were associated with low concentrations of ammonia, whereas transient increases in AOB were most closely associated with regionally and seasonally elevated concentrations of ammonia in the water column. Additionally, single cell nitrification rates and transcript numbers were calculated for AOA and AOB populations. Together these observations offer additional ecological support for the idea that niche separation of AOA and AOB is in part determined by ammonia concentrations in estuarine ecosystems.

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“…Duplicate samples for NH + 4 determination (50 ml) were analyzed immediately according to Holmes et al (1999) using a Turner Designs fluorometer. Samples for DON and dissolved organic phosphorus (DOP; 30 mL) were filtered through pre-combusted (450 • C, 6 h) GF/F filters (Whatman), and analyzed by the wet oxidation procedure (Pujo-Pay and Raimbault, 1994).…”

Section: Chemical and Biological Analysismentioning

confidence: 99%

Dissolved Compounds Excreted by Copepods Reshape the Active Marine Bacterioplankton Community Composition

et al. 2017

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Copepods are important suppliers of bioreactive compounds for marine bacteria through fecal pellet production, sloppy feeding, and the excretion of dissolved compounds. However, the interaction between copepods and bacteria in the marine environment is poorly understood. We determined the nitrogen and phosphorus compounds excreted by copepods fed with two natural size-fractionated diets (<20-and 20-150-µm) in the upwelling zone of central/southern Chile in late summer and spring. We then assessed the biogeochemical response of the bacterial community and its structure, in terms of total and active cells, to enrichment by copepod-excreted dissolved compounds. Results revealed that copepods actively excreted nitrogen and phosphorus compounds, mainly in the form of ammonium and dissolved organic phosphorus (DOP), reaching excretion rates of 2.6 and 0.05 µmol L −1 h −1 , respectively. In both periods, the maximum excretion rates were associated with the 20-150-µm size fraction, but particularly during spring, when a higher organic matter quality was observed in excretion products compared to late summer. There were higher excretion rates of dissolved free amino acids (DFAAs) from copepods fed with the <20-µm size fraction, mainly histidine (HIS) in late summer and glutamic acid (GLU) in spring. A shift in the composition of the active bacterial community was observed between periods and treatments, which was associated with the response of the common seawater surface phyla Proteobacteria and Bacteroidetes. The specific bacterial activity (16S rRNA:rDNA) suggested a different response to the two size-fractionated diets. In late summer, Betaproteobacteria and Bacteroidetes were stimulated by the treatment enriched with excretion products derived from the 20-150-µm and <20-µm size fractions, respectively. In spring, Alphaproteobacteria were active in the treatment enriched with the excretion products of copepods fed with the <20-µm size fraction, whereas they were inhibited in the treatment enriched with excretion products in the 20-150-µm size fraction. Our findings indicate that different Valdés et al. Copepod Excretion and Bacterial Community Structure copepod diets can have a significant impact on the quantity and quality of their excretion compounds, which can subsequently generate shifts in the active bacterial composition. The bacterial response is probably associated with common-opportunistic sea surface microbes that are adapted to rapidly reacting to environmental offers.

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A simple and precise method for measuring ammonium in marine and freshwater ecosystems

Cited by 1,113 publications

References 19 publications

Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea

Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea

Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary

Dissolved Compounds Excreted by Copepods Reshape the Active Marine Bacterioplankton Community Composition

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