High‐resolution pore‐water sampling with a gel sampler

Krom, Michael D.; Davison, Patrick J.; Zhang, H.; Davison, William

doi:10.4319/lo.1994.39.8.1967

Cited by 122 publications

(89 citation statements)

References 8 publications

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“…DET gel probes , Krom et al 1994) were used to determine pore-water ΣNO 3 concentrations in Box Cores 7 and 9. Prior to deployment, the DET probes were conditioned in artificial seawater and deoxygenated by sparging with N 2 for 24 h. For Box Core 7, the DET gel probe was inserted into a 10 cm diameter sub-core that had been removed from the box core.…”

Section: Methodsmentioning

confidence: 99%

“…After processing the core, the Nalgene bottles were briefly removed from the glove box for centrifugation at 3000 rpm for 10 min to extract the pore-water, and returned immediately into the glove box. Supernatants from the bottles were then filtered (0.45 µm; Nuclepore) into 30 ml Nunc vials, from which aliquots were pipetted into pore-water storage vials pre-filled with the appropriate preservative (Table 1).DET gel probes , Krom et al 1994) were used to determine pore-water ΣNO 3 concentrations in Box Cores 7 and 9. Prior to deployment, the DET probes were conditioned in artificial seawater and deoxygenated by sparging with N 2 for 24 h. For Box Core 7, the DET gel probe was inserted into a 10 cm diameter sub-core that had been removed from the box core.…”

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confidence: 99%

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Anoxic nitrification in marine sediments

Mortimer¹,

Harris²,

Krom³

et al. 2004

Mar. Ecol. Prog. Ser.

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Nitrate peaks are found in pore-water profiles in marine sediments at depths considerably below the conventional zone of oxic nitrification. These have been interpreted to represent nonsteady-state effects produced by the activity of nitrifying bacteria, and suggest that nitrification occurs throughout the anoxic sediment region. In this study, ΣNO3 peaks and molecular analysis of DNA and RNA extracted from anoxic sediments of Loch Duich, an organic-rich marine fjord, are consistent with nitrification occurring in the anoxic zone. Analysis of ammonia oxidiser 16S rRNA gene fragments amplified from sediment DNA indicated the abundance of autotrophic ammonia-oxidising bacteria throughout the sediment depth sampled (40 cm), while RT-PCR analysis indicated their potential activity throughout this region. A large non-steady-state pore-water ΣNO3 peak at ~21 cm correlated with discontinuities in this ammonia-oxidiser community. In addition, a subsurface nitrate peak at ~8 cm below the oxygen penetration depth, correlated with the depth of a peak in nitrification rate, assessed by transformation of 15 N-labelled ammonia. The source of the oxidant required to support nitrification within the anoxic region is uncertain. It is suggested that rapid recycling of N is occurring, based on a coupled reaction involving Mn oxides (or possibly highly labile Fe oxides) buried during small-scale slumping events. However, to fully investigate this coupling, advances in the capability of high-resolution pore-water techniques are required. KEY WORDS: Anoxic nitrification · Diffusive Equilibrium in Thin films (DET) · 16sRNAResale or republication not permitted without written consent of the publisher Mar Ecol Prog Ser 276: [37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52] 2004 anaerobic oxidation of ammonia may also be carried out by β-proteobacterial ammonia oxidising bacteria (Schmidt & Bock 1997. Recent work has suggested that ammonium oxidation coupled to the reduction of manganese ('anoxic nitrification') may occur in continental shelf sediments (Luther et al. 1997, Hulth et al. 1999, Anschutz et al. 2000, Hyacinthe et al. 2001, Deflandre et al. 2002.Field evidence suggests that anammox is a significant process, accounting for up to 50% of N 2 production in the marine environment (Thamdrup & Dalsgaard 2002, Dalsgaard et al. 2003, Kuypers et al. 2003. In contrast, the importance of anoxic nitrification is the subject of debate. Luther et al. (1997) calculated that this reaction might account for 90% of N 2 formation in continental margin, whereas Thamdrup & Dalsgaard (2000) found it to be an insignificant process in Mn-rich sediments of the Skagerrak. Anoxic nitrification is difficult to measure, particularly in situ, and hence more work is required to quantify its global significance.In general, evidence for the existence of anoxic nitrification pathways in marine sediments has been provided by geochemical data, including profiles of porewater and solid-phase constituents (e.g. Anschutz et al. 2000, Hya...

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Anoxic nitrification in marine sediments

Mortimer¹,

Harris²,

Krom³

et al. 2004

Mar. Ecol. Prog. Ser.

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“…The gels were cast from 40 ml acrylamide (15%, wt/vol), 20 ml N,N-methylenebisacrylamide (2%, wt/vol), 0.75 ml dipotassium peroxodisulfate (0.11 M), and 60 l tetramethylethylenediamine. Dipotassium peroxodisulfate rather than ammonium peroxodisulfate was used to avoid interference by the excess NH 4 ϩ leaching from the gel (25). After hydration in deionized water (freshwater sediment, quartz sand) or in NaCl solution with a salinity of 25 (marine sediment), the gels were 2 mm thick.…”

mentioning

confidence: 99%

“…Polyacrylamide gel probes were constructed and assembled as described previously (25). The gels were cast from 40 ml acrylamide (15%, wt/vol), 20 ml N,N-methylenebisacrylamide (2%, wt/vol), 0.75 ml dipotassium peroxodisulfate (0.11 M), and 60 l tetramethylethylenediamine.…”

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confidence: 99%

Combined Gel Probe and Isotope Labeling Technique for Measuring Dissimilatory Nitrate Reduction to Ammonium in Sediments at Millimeter-Level Resolution

Stief

Behrendt

Lavik

et al. 2010

Appl Environ Microbiol

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Dissimilatory NO 3؊ reduction in sediments is often measured in bulk incubations that destroy in situ gradients of controlling factors such as sulfide and oxygen. Additionally, the use of unnaturally high NO 3 ؊ concentrations yields potential rather than actual activities of dissimilatory NO 3 ؊ reduction. We developed a technique to determine the vertical distribution of the net rates of dissimilatory nitrate reduction to ammonium (DNRA) with minimal physical disturbance in intact sediment cores at millimeter-level resolution. This allows DNRA activity to be directly linked to the microenvironmental conditions in the layer of NO 3 ؊ consumption. The water column of the sediment core is amended with 15 NO 3 ؊ at the in situ 14 NO 3 ؊ concentration. A gel probe is deployed in the sediment and is retrieved after complete diffusive equilibration between the gel and the sediment pore water. The gel is then sliced and the NH 4 ؉ dissolved in the gel slices is chemically converted by hypobromite to N 2 in reaction vials. The isotopic composition of N 2 is determined by mass spectrometry. We used the combined gel probe and isotopic labeling technique with freshwater and marine sediment cores and with sterile quartz sand with artificial gradients of 15 NH 4 ؉ . The results were compared to the NH 4 ؉ microsensor profiles measured in freshwater sediment and quartz sand and to the N 2 O microsensor profiles measured in acetylene-amended sediments to trace denitrification.Nitrate accounts for the eutrophication of many humanaffected aquatic ecosystems (19,21). Sediment bacteria may mitigate NO 3 Ϫ pollution by denitrification and anaerobic ammonium oxidation (anammox), which produce N 2 (13, 18). However, inorganic nitrogen is retained in aquatic ecosystems when sediment bacteria reduce NO 3 Ϫ to NH 4 ϩ by dissimilatory nitrate reduction to ammonium (DNRA) (5,12,16,39). Hence, DNRA contributes to rather than counteracts eutrophication (23). DNRA may be the dominant pathway of dissimilatory NO 3 Ϫ reduction in sediments that are rich in electron donors, such as labile organic carbon and sulfide (4,8,17,38,55). High rates of DNRA are thus found in sediments affected by coastal aquaculture (8, 36) and settling algal blooms (16).DNRA, denitrification, and the chemical factors that control the partitioning between them (e.g., sulfide) should ideally be investigated in undisturbed sediments. The redox stratification of sediments involves vertical concentration gradients of pore water solutes. These gradients are often very steep, and their measurement requires high-resolution techniques, such as microsensors (26, 42) and gel probes (9, 54). If, for instance, the influence of sulfide on DNRA and denitrification is to be investigated, one wants to know exactly the sulfide concentration in the layers of DNRA and denitrification activity, as well as the flux of sulfide into these layers. This information can easily be obtained using H 2 S and pH microsensors (22,43). It is less trivial to determine the vertical distribution of DNRA...

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“…In comparison with suction samplers, peepers (dialysis cells) (Hesslein 1976;Emerson et al 1984;Brandl and Hanselmann 1991;Urban et al 1997) and the gel sampler (Krom et al 1994;Mortimer et al 1999) both rely on diffusion equilibration to extract sediment pore water and can give a significantly higher depth resolution of a few mm (gel sampler) to 1 cm (peeper). The peeper (typically 30-60 cm long with a cross section of 8 ϫ 2 cm) consists of an array of cells filled with deionized water or filtered seawater and covered by a dialysis or similar membrane.…”

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confidence: 99%

A high‐resolution pore water sampler for sandy sediments

Berg

McGlathery

2001

Limnology & Oceanography

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In this paper, we present a new technique for collecting pore‐water samples in coarse‐to fine‐grained sandy sediments. We have used the technique both for in situ sampling and for pore‐water extraction from sediment cores brought back to the laboratory, in both cases with a depth resolution as fine as 1 cm. The key device is a long, thin (~2 mm) stainless steel tube with a specially designed tip that functions as a filter. Pore‐water samples are collected by inserting the tube into the sediment at the desired depth and applying a light suction from a syringe connected to the tube. The sample is injected immediately into a vial through a syringe filter and stored for later analysis. The technique has some clear advantages over other methods that are used commonly in sandy sediments. In comparison with lysimeters or sippers, it gives pore‐water samples with a much higher depth resolution, which often is needed to accurately estimate fluxes across the sediment‐water interface or transformation rates of solutes within the sediments. In comparison with dialysis cells or peepers, the new technique gives measurements that truly represent the time of collection. This can be crucial when non‐steady‐state systems are studied. Furthermore, disturbance of the sediment is minimal because of the small dimension of the tube. This is especially important in vegetated sediments, in which the deployment of larger conventional samplers is likely to cause significant disturbance. Finally, sample extraction is less laborious than other techniques, requiring only one site visit and typically <1 min of sampling time per sample. In laboratory tests using a dye tracer, we showed that pore water was drawn evenly toward the tube tip from all directions in the surrounding sediment. On the basis of these results, we provide guidelines for choosing the appropriate sampling depth intervals as a function of the sample size. Data from representative pore‐water profiles are presented for PO432 from vegetated coarse‐grained carbonate sediments in the Bahamas and NH4+1 from fine‐grained unvegetated sands in a temperate coastal lagoon in Virginia.

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High‐resolution pore‐water sampling with a gel sampler

Cited by 122 publications

References 8 publications

Anoxic nitrification in marine sediments

Anoxic nitrification in marine sediments

Combined Gel Probe and Isotope Labeling Technique for Measuring Dissimilatory Nitrate Reduction to Ammonium in Sediments at Millimeter-Level Resolution

A high‐resolution pore water sampler for sandy sediments

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