A simple and precise method for measuring ammonium in marine and freshwater ecosystems
01 Oct 1999-Canadian Journal of Fisheries and Aquatic Sciences (NRC Research Press Ottawa, Canada)-Vol. 56, Iss: 10, pp 1801-1808
TL;DR: A fluorometric method is presented that gives precise measurements of ammonium over a wide range of concentrations and salinities emphasizing submicromolar levels and not only solves analytical problems but also substantially simplifies sample collection and preservation.
Abstract: The accurate measurement of ammonium concentrations is fundamental to understanding nitrogen biogeochemistry in aquatic ecosystems. Unfortunately, the commonly used indophenol blue method often yie...
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TL;DR: Oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon ‘Candidatus Nitrosopumilus maritimus’ strain SCM1 support the hypothesis that nitrification is more prevalent in the marine nitrogen cycle than accounted for in current biogeochemical models.
Abstract: The discovery of ammonia oxidation by mesophilic and thermophilic Crenarchaeota and the widespread distribution of these organisms in marine and terrestrial environments indicated an important role for them in the global nitrogen cycle. However, very little is known about their physiology or their contribution to nitrification. Here we report oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon 'Candidatus Nitrosopumilus maritimus' strain SCM1. Unlike characterized ammonia-oxidizing bacteria, SCM1 is adapted to life under extreme nutrient limitation, sustaining high specific oxidation rates at ammonium concentrations found in open oceans. Its half-saturation constant (K(m) = 133 nM total ammonium) and substrate threshold (
1,389 citations
TL;DR: It is shown that dissolved inorganic carbon consumption of a natural plankton community maintained in mesocosm enclosures at initial CO2 partial pressures increases with rising CO2, and the observed responses have implications for a variety of marine biological and biogeochemical processes, and underscore the importance of biologically driven feedbacks in the ocean to global change.
Abstract: The oceans have absorbed nearly half of the fossil-fuel carbon dioxide (CO2) emitted into the atmosphere since pre-industrial times1, causing a measurable reduction in seawater pH and carbonate saturation2. If CO2 emissions continue to rise at current rates, upper-ocean pH will decrease to levels lower than have existed for tens of millions of years and, critically, at a rate of change 100 times greater than at any time over this period3. Recent studies have shown effects of ocean acidification on a variety of marine life forms, in particular calcifying organisms4, 5, 6. Consequences at the community to ecosystem level, in contrast, are largely unknown. Here we show that dissolved inorganic carbon consumption of a natural plankton community maintained in mesocosm enclosures at initial CO2 partial pressures of 350, 700 and 1,050 μatm increases with rising CO2. The community consumed up to 39% more dissolved inorganic carbon at increased CO2 partial pressures compared to present levels, whereas nutrient uptake remained the same. The stoichiometry of carbon to nitrogen drawdown increased from 6.0 at low CO2 to 8.0 at high CO2, thus exceeding the Redfield carbon:nitrogen ratio of 6.6 in today’s ocean7. This excess carbon consumption was associated with higher loss of organic carbon from the upper layer of the stratified mesocosms. If applicable to the natural environment, the observed responses have implications for a variety of marine biological and biogeochemical processes, and underscore the importance of biologically driven feedbacks in the ocean to global change.
784 citations
TL;DR: Because anammox is a major nitrogen loss in marine suboxic waters, such nitrification–anammox coupling potentially occurring also in oceanic oxygen minimum zones would act as a short circuit connecting regenerated ammonium to direct nitrogen loss, thus reducing the presumed direct contribution from deep-sea nitrate.
Abstract: 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 gamma-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 beta-proteobacterial AOB was significantly elevated in this latter zone. Nitrification in the suboxic zone, most likely microaerobic in nature, was verified by (15)NO(2)(-) and (15)N(15)N production in (15)NH(4)(+) incubations with no measurable oxygen. It provided a direct local source of nitrite for anammox in the suboxic zone. Both ammonia-oxidizing crenarchaea and gamma-proteobacterial AOB were important nitrifiers in the Black Sea and were likely coupled to anammox in indirect and direct manners respectively. Each process supplied about half of the nitrite required by anammox, based on (15)N-incubation experiments and modeled calculations. Because anammox is a major nitrogen loss in marine suboxic waters, such nitrification-anammox coupling potentially occurring also in oceanic oxygen minimum zones would act as a short circuit connecting regenerated ammonium to direct nitrogen loss, thus reducing the presumed direct contribution from deep-sea nitrate.
551 citations
TL;DR: Direct quantification of ammonia oxidation rates by 15N labeling, and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase subunit A (amoA) genes, in the Gulf of California represent compelling evidence for an archaeal role in oceanic nitrification.
Abstract: Nitrification plays an important role in marine biogeochemistry, yet efforts to link this process to the microorganisms that mediate it are surprisingly limited. In particular, ammonia oxidation is the first and rate-limiting step of nitrification, yet ammonia oxidation rates and the abundance of ammonia-oxidizing bacteria (AOB) have rarely been measured in tandem. Ammonia oxidation rates have not been directly quantified in conjunction with ammonia-oxidizing archaea (AOA), although mounting evidence indicates that marine Crenarchaeota are capable of ammonia oxidation, and they are among the most abundant microbial groups in the ocean. Here, we have directly quantified ammonia oxidation rates by 15N labeling, and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase subunit A (amoA) genes, in the Gulf of California. Based on markedly different archaeal amoA sequence types in the upper water column (60 m) and oxygen minimum zone (OMZ; 450 m), novel amoA PCR primers were designed to specifically target and quantify 'shallow' (group A) and 'deep' (group B) clades. These primers recovered extensive variability with depth. Within the OMZ, AOA were most abundant where nitrification may be coupled to denitrification. In the upper water column, group A tracked variations in nitrogen biogeochemistry with depth and between basins, whereas AOB were present in relatively low numbers or undetectable. Overall, 15NH4+ oxidation rates were remarkably well correlated with AOA group A amoA gene copies (r2=0.90, P<0.001), and with 16S rRNA gene copies from marine Crenarchaeota (r2=0.85, P<0.005). These findings represent compelling evidence for an archaeal role in oceanic nitrification.
405 citations
Cites methods from "A simple and precise method for mea..."
...From each sample bottle, aliquots were taken for analysis of nutrient concentrations (Strickland and Parsons, 1972; Holmes et al., 1999) and, with the exception of the samples from 0 to 100 m in the Carmen Basin, the remaining volume was filtered through 142 mm diameter 0.2 mm Durapore filters…...
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...From each sample bottle, aliquots were taken for analysis of nutrient concentrations (Strickland and Parsons, 1972; Holmes et al., 1999) and, with the exception of the samples from 0 to 100 m in the Carmen Basin, the remaining volume was filtered through 142 mm diameter 0....
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TL;DR: New efforts to evaluate river restoration projects that use channel reconfiguration as a methodology for improving stream ecosystem structure and function are finding little evidence for measurable ecological improvement.
Abstract: River restoration is an increasingly common approach utilized to reverse past degradation of freshwater ecosystems and to mitigate the anticipated damage to freshwaters from future development and resource-extraction activities. While the practice of river restoration has grown exponentially over the last several decades, there has been little empirical evaluation of whether restoration projects individually or cumulatively achieve the legally mandated goals of improving the structure and function of streams and rivers. New efforts to evaluate river restoration projects that use channel reconfiguration as a methodology for improving stream ecosystem structure and function are finding little evidence for measurable ecological improvement. While designed channels may have less-incised banks and greater sinuousity than the degraded streams they replace, these reach-scale efforts do not appear to be effectively mitigating the physical, hydrological, or chemical alterations that are responsible for the loss of sensitive taxa and the declines in water quality that typically motivate restoration efforts. Here we briefly summarize this new literature, including the collection of papers within this Invited Feature, and provide our perspective on the limitations of current restoration.
388 citations
Cites methods from "A simple and precise method for mea..."
...Ammonium analysis was performed using the OPA fluorometric technique (Holmes et al. 1999) using a field fluorometer (10-AU, Turner Designs, Sunnyvale, California, USA)....
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References
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3,465 citations
TL;DR: The role and identity of the "catalyst" for the Berthelot reaction are examined in detail in detail as mentioned in this paper, and a new procedure for ammonia analysis which is superior in both sensitivity and precision to the other published procedures is presented.
Abstract: An investigation of the mechanism of the Berthelot reaction has led to an increased understanding of the many conflicts in the literature concerning the reaction's use for the analytical determination of ammonia. Monochloramine is shown to be the first intermediate, and the kinetics of its formation and decomposition are presented. The identical visible spectra obtained for a series of indophenols synthesized in the course of this research and the blue complexes formed when phenol or a substituted phenol was used in the Berthelot reaction confirmed that indophenol is the final product of the reaction. Conditions which lead to the formation of final products other than indophenol have been observed and are also discussed. The role and identity of the ''catalyst'' for the Berthelot reaction are examined in detail. Finally, a new procedure for ammonia analysis which is superior in both sensitivity and precision to the other published procedures is presented.
754 citations
TL;DR: In this article, a modified version of the ammonia diffusion method is used to measure 15 N −NH4+ in marine, estuarine and fresh waters. But, the method is not applicable to all types of water and it allows measurements with lower ammonium concentrations than has previously been possible.
362 citations
TL;DR: In this article, the authors investigated the response of the riverine food web to additions of the limiting nutrient, phosphorus, in a pristine tundra river for four consecutive sum-mers and found that the response was modified by a strong "top-down" feedback of insects grazing on epilithic algae and by competitive exclusion of black flies by caddisflies.
Abstract: Phosphorus fertilization of a pristine tundra river for four consecutive sum- mers dramatically changed biological processes and populations at all trophic levels. At the primary producer level, both algal biomass and productivity increased and chlorophyll accumulated on the river bottom in the first two summers. Diatom community composition changed little in spite of large chlorophyll changes. However, an increase in grazing insects prevented chlorophyll buildup in the third and fourth summers. Some microbial processes were also stimulated by the increased photosynthesis caused by fertilization. Total respiration of the epilithon, acetate uptake, and decomposition of lignin monomers were all stimulated but only in light-grown epilithon. When epilithon was grown in the dark in the fertilized region of the river, there was no increased respiration. Also, phosphorus did not stimulate the decomposition of Carex litter. Although insects grew more rapidly in the fertilized section of the river, there were community interactions that kept total insect production from appreciable change. The four most abundant large insects did increase their growth rates in response to phosphorus addition and there were increases in populations of Baetis lapponicus and Brachycentrus americanus. These increases were offset by the decline in abundance of the dominant species, the black fly Prosimulium martini, perhaps caused by competition for space from Brachycentrus. Growth of both young-of-the-year and adult grayling (Thymallus arcticus) was strongly stimulated by phosphorus addition in years 3 and 4 (not tested in years 1 and 2). Carbon and nitrogen stable isotope tracers indicated that the measured increases in insect and fish growth were largely attributable to increases in the production of epilithic algae. Overall, the results indicate a strong "bottom-up" response of the riverine food web to additions of the limiting nutrient, phosphorus. The response was modified in later years, however, by a strong "top-down" feedback of insects grazing on epilithic algae and by competitive exclusion of black flies by caddisflies.
333 citations
TL;DR: In this article, a segmented flow analysis was used for routine determination of ammonia in sea and estuarine waters, based on the reaction of ammonia with orthophtaldialdehyde (OPA) and sulfite.
288 citations