A simplified resorcinol method for direct spectrophotometric determination of nitrate in seawater

Zhang, Jiazhong; Fischer, Charles J.

doi:10.1016/j.marchem.2005.09.008

Cited by 80 publications

(39 citation statements)

References 16 publications

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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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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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“…Nitrate þ nitrite, nitrite and ammonium on a foam sample were measured according to Zhang and Fischer (2006), GriesseIlosvay method (Strickland and Parsons, 1968) and ISO 7150/1:1984(E). The ISO method is based on spectrometric measurement of a compound formed by reaction of ammonium with salicylate and hypochlorite ions in the presence of sodium nitrosopentacyanoferrate (III) at about 655 nm.…”

Section: Nutrient Analysismentioning

confidence: 99%

Circumstantial evidence in support of org-I as a component of the marine aerosol arising from a study of marine foams

Truesdale

Žic

Garnier

et al. 2012

Estuarine, Coastal and Shelf Science

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This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues.Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. a b s t r a c tA study of foams formed on the marine Lake Mir, Croatia, and elsewhere on the same coast demonstrates, for the first time, that they are fractionated (enrichened) in org-I by up to 630 times relative to the water from which they form. The results are consistent with an I/C mole ratio for in-situ organic matter. Foams created artificially in the laboratory from natural samples of water from Lake Mir were similarly fractionated, although to a lesser degree. These differences were effectively removed when enrichments were expressed as molar ratios, e.g., P tot /I tot , rather than straightforward concentrations. This similarity in the behaviour to enrichment for organic forms of I, N and P suggests that the time over which foams age is a major determinant of the enrichment they display. It is argued that this period allows time for the seawater occluded in the interstitial spaces between bubbles, to drain away. Since foam production is ubiquitous over the oceans it seems likely that this process local to coastal environments is much more common than at first might appear to be the case. The paper explains how this work provides circumstantial evidence that the bubble-bursting mechanism current since the 1960s may well provide the iodine which appears to be missing in many modelling calculations based upon an atmospheric system dependant upon sorption of the species IO upon the marine aerosol.

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“…Vertical profiles of temperature, salinity, chlorophyll a, and dissolved oxygen were measured using the buoy-equipped sensors. The concentrations of nitrogen species (ammonia, nitrite, and nitrate) were determined as described previously (15,16,46). Cells for DNA extraction were collected on 0.22-m-pore-size Sterivex cartridge filters (Millipore Corp., Bedford, MA) or on 0.22-m-pore-size polycarbonate filters (diameter, 25 mm; GTTP; Millipore) by filtration of 50 to 500 ml seawater.…”

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confidence: 99%

High Abundance of Ammonia-OxidizingArchaeain Coastal Waters, Determined Using a Modified DNA Extraction Method

Urakawa

Martens‐Habbena

Stahl

2010

Appl Environ Microbiol

130

104

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. Appropriate controls to verify this basic assumption are rarely included. Here three different DNA extractions, performed with two commercial kits (FastDNA and UltraClean) and a standard phenol-chloroform method, and two alternative filtration methods (Sterivex and 25-mm-diameter polycarbonate filters) were evaluated, using the addition of Nitrosopumilus maritimus cells to track the recovery of DNA from marine Archaea. After the comparison, a simplified phenol-chloroform extraction method was developed and shown to be significantly superior, in terms of both the recovery and the purity of DNA, to other protocols now generally applied to environmental studies. The simplified and optimized method was used to quantify ammonia-oxidizing Archaea at different depth intervals in a fjord (Hood Canal) by quantitative PCR. The numbers of Archaea increased with depth, often constituting as much as 20% of the total bacterial community.Efficient DNA extraction from environmental samples is fundamental to many culture-independent characterizations (10). Thus, there was an early and concerted effort to establish appropriate methods of DNA extraction from different types of environmental samples (14,19,25,30,34,43,47). DNA extraction efficiency is particularly important for quantitative PCR (qPCR), because poor DNA extraction efficiency results in the underestimation of gene copy numbers in the samples examined (6, 42).Most methodological developments addressed DNA extraction from soil and sediment samples, with fewer comparative studies of the efficiency of collection and extraction from water samples (4, 13, 40). In part, a methodological focus on soils reflected the simplicity of filtration to collect aquatic populations and the generally good recovery of DNA from the Gramnegative bacteria making up a significant fraction of aquatic communities. However, small Archaea are now known to constitute a substantial fraction of the prokaryotic populations in marine and terrestrial systems (2,7,9,20,26,31,33,45). Since the archaeal cell wall and membrane structures are distinct from those of bacteria, there is no assurance that commonly used extraction methods are adequate. With increasing reliance on commercially available bead-beating-type DNA extraction kits, these methods are now often used for different water samples (1, 5-7, 14, 19, 36). Although most protocols incorporate mechanical disruption to ensure more-uniform extraction than is possible by using methods that rely entirely on enzymatic digestion and/or chemical disruption (4,13,40), the suitability of these protocols for the concerted analysis of archaeal and bacterial populations has not been fully evaluated.In the studies reported here, the recently isolated marine archaeon Nitrosopumilus maritimus strain SCM1 (22) was therefore used as a reference standard for evaluation of the commonly employed DNA extraction methods by using qPCR. This archaeon was then used as a reference for the development of a simple, rapid, and efficient method of extracting DNA from both ar...

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A simplified resorcinol method for direct spectrophotometric determination of nitrate in seawater

Cited by 80 publications

References 16 publications

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

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

Circumstantial evidence in support of org-I as a component of the marine aerosol arising from a study of marine foams

High Abundance of Ammonia-OxidizingArchaeain Coastal Waters, Determined Using a Modified DNA Extraction Method

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