Rhizon sampling of porewaters near the sediment‐water interface of aquatic systems

Seeberg‐Elverfeldt, Jens; Schlüter, Michael; Feseker, Tomas; Kölling, Martin

doi:10.4319/lom.2005.3.361

Cited by 560 publications

(353 citation statements)

References 29 publications

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“…The total organic carbon (TOC) content was measured on corresponding samples after HCl (10%) acid digestion to remove the carbonate on the same analyzer (Elementar VARIO EL III). The pH values were determined with the MultiLab 540 (WTW, Germany) in pore water, which was extracted by applying Rhizons into undisturbed active layer samples according to the method of Seeberg-Elverfeldt et al [51]. Cell counts of MOB were obtained based on fluorescence in situ hybridization with the MOB-specific probes Mg705/Mg84 (type I MOB) and Ma450 (type II MOB) [15] according to a protocol described recently [37].…”

Section: Soil and Pore Water Analysismentioning

confidence: 99%

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

et al. 2008

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With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.

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Section: Soil and Pore Water Analysismentioning

confidence: 99%

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

et al. 2008

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“…Parallel cores were recovered for geochemical analyses and porewater was extracted directly after recovery by using Rhizon samplers (Rhizosphere Research Products B.V, Wageningen, The Netherlands) (Seeberg et al 2005). Porewater samples for Fe 2C and Mn 2C were acidified with 1% (v/v) nitric acid (65% suprapure, Merck, M€ unchen, Germany).…”

Section: Porewater Analysismentioning

confidence: 99%

Potentially Active Iron, Sulfur, and Sulfate Reducing Bacteria in Skagerrak and Bothnian Bay Sediments

Reyes

Schneider

Thürmer

et al. 2017

Geomicrobiology Journal

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In many marine surface sediments, the reduction of manganese (Mn) and iron (Fe) oxides is obscured by sulfate reduction, which is regarded as the predominant anaerobic microbial respiration process. However, many dissimilatory sulfate and sulfur reducing microorganisms are known to utilize alternative electron acceptors such as metal oxides. In this study, we tested whether sulfate and sulfur reducing bacteria are linked to metal oxide reduction based on biogeochemical modeling of porewater concentration profiles of Mn 2C and Fe 2C in Bothnian Bay (BB) and Skagerrak (SK) sediments. Steady-state modeling of Fe 2C and Mn 2C porewater profiles revealed zones of net Fe (0-9 cm BB; »10 and 20 cm SK) and Mn (0-5 cm BB; 2-8 cm SK) species transformations. 16S rRNA pyrosequencing analysis of the in-situ community showed that Desulfobacteraceae, Desulfuromonadaceae and Desulfobulbaceae were present in the zone of Fereduction of both sediments. Rhodobacteraceae were also detected at high relative abundance in both sediments. BB sediments appeared to harbor a greater diversity of potential Fe-reducers compared to SK. Additionally, when the upper 10 cm of sediment from the SK was incubated with lepidocrocite and acetate, Desulfuromonas was the dominant bacteria. Real-time quantitative polymerase chain reaction (qPCR) results showed decreasing dsrA gene copy numbers with depth coincided with decreased Fe-reduction activity. Our results support the idea that sulfur and sulfate reducing bacteria contribute to Fe-reduction in the upper centimeters of both sediments.

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“…With core top water removed, porewaters were extracted from sediments cores at 1 to 2 cm depth intervals using Rhizon samplers (Seeberg-Elverfeldt et al 2005). The MOM-type Rhizon samplers (Rhizosphere Research Products B.V., 50 mm long, 2.5 mm diameter, 0.15 lm pore size) were inserted at right angles through PVC tape that covered the predrilled holes in the core tube walls, and attached via luer-lock fittings to nitrile-free syringes (20 ml, BD Discardit).…”

Section: Sampling Of Sediments Porewaters and Seawatermentioning

confidence: 99%

Stability of dissolved and soluble Fe(II) in shelf sediment pore waters and release to an oxic water column

et al. 2017

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Shelf sediments underlying temperate and oxic waters of the Celtic Sea (NW European Shelf) were found to have shallow oxygen penetrations depths from late spring to late summer (2.2-5.8 mm below seafloor) with the shallowest during/after the spring-bloom (mid-April to mid-May) when the organic carbon content was highest. Sediment porewater dissolved iron (dFe,\0.15 lm) mainly ([85%) consisted of Fe(II) and gradually increased from 0.4 to 15 lM at the sediment surface to *100-170 lM at about 6 cm depth. During the late spring this Fe(II) was found to be mainly present as soluble Fe(II) ([85% sFe, \0.02 lm). Sub-surface dFe(II) maxima were enriched in light isotopes (d 56 Fe -2.0 to -1.5%), which is attributed to dissimilatory iron reduction (DIR) during the bacterial decomposition of organic matter. As porewater Fe(II) was oxidised to insoluble Fe(III) in the surface sediment layer, residual Fe(II) was further enriched in light isotopes (down to -3.0%). Ferrozine-reactive Fe(II) was found in surface porewaters and in overlying core top waters, and was highest in the late spring period. Shipboard experiments showed that depletion of bottom water Responsible Editor: Martin Solan.Electronic supplementary material The online version of this article (doi:10.1007/s10533-017-0309-x) contains supplementary material, which is available to authorized users. 49-67 DOI 10.1007/s10533-017-0309-x oxygen in late spring can lead to a substantial release of Fe(II). Reoxygenation of bottom water caused this Fe(II) to be rapidly lost from solution, but residual dFe(II) and dFe(III) remained (12 and 33 nM) after [7 h. Iron(II) oxidation experiments in core top and bottom waters also showed removal from solution but at rates up to 5-times slower than predicted from theoretical reaction kinetics. These data imply the presence of ligands capable of complexing Fe(II) and supressing oxidation. The lower oxidation rate allows more time for the diffusion of Fe(II) from the sediments into the overlying water column. Modelling indicates significant diffusive fluxes of Fe(II) (on the order of 23-31 lmol m -2 day -1 ) are possible during late spring when oxygen penetration depths are shallow, and pore water Fe(II) concentrations are highest. In the water column this stabilised Fe(II) will gradually be oxidised and become part of the dFe(III) pool. Thus oxic continental shelves can supply dFe to the water column, which is enhanced during a small period of the year after phytoplankton bloom events when organic matter is transferred to the seafloor. This input is based on conservative assumptions for solute exchange (diffusion-reaction), whereas (bio)physical advection and resuspension events are likely to accelerate these solute exchanges in shelf-seas.

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Rhizon sampling of porewaters near the sediment‐water interface of aquatic systems

Cited by 560 publications

References 29 publications

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

Potentially Active Iron, Sulfur, and Sulfate Reducing Bacteria in Skagerrak and Bothnian Bay Sediments

Stability of dissolved and soluble Fe(II) in shelf sediment pore waters and release to an oxic water column

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