GLORIA — GEOMAR Library Ocean Research Information Access

1

Electronic Resource

A nitrate-selective microelectrode based on a lipophilic derivative of iodocobalt(III)salen (1999)

Verschuren, P. G. ; van der Baan, Juul L. ; Blaauw, Rolf ; [et al.]

Springer

Fresenius' journal of analytical chemistry 364 (1999), S. 595-598

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ISSN: 1432-1130

Source: Springer Online Journal Archives 1860-2000

Topics: Chemistry and Pharmacology

Notes: Abstract The synthesis of iodo{2,2′-[1,2-octadecanediylbis(nitrilomethylidyne)]diphenolato}cobalt is described. Liquid membrane microelectrodes based on this carrier exhibit Nernstian behaviour with a selectivity sequence according to the Hofmeister series: I– 〉 NO3 – 〉 NO2 – 〉 Cl– 〉 HCO3 – 〉 AcO–. The selectivity coefficient of nitrate over nitrite and chloride amounts to –1.6 and –2.7, respectively. The detection limit for nitrate in water amounts to 10–5.2 mol/L. A nitrate profile measured in a nitrifying biofilm is presented as a practical application.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002160051392

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2

Electronic Resource

Effects of biofilm structures on oxygen distribution and mass transport (1994)

de Beer, Dirk ; Stoodley, Paul ; Roe, Frank ; [et al.]

New York, NY [u.a.] : Wiley-Blackwell

Biotechnology and Bioengineering 43 (1994), S. 1131-1138

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ISSN: 0006-3592

Keywords: confocal microscopy ; microelectrodes ; cell clusters ; pores ; Chemistry ; Biochemistry and Biotechnology

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology

Notes: Aerobic biofilms were found to have a complex structure consisting of microbial cell clusters (discrete aggregates of densely packed cells) and interstitial voids. The oxygen distribution was strongly correlated with these strutures. The voids facilitated oxygen transport from the bulk liquid through the biofilm, supplying approximately 50% of the total oxygen consumed by the cells. The mass transport rate from the bulk liquid is influenced by the biofilm structure; the observed exchange surface of the biofilm is twice that calculated for a simple planar geometry. The oxygen diffusion occurred in the direction normal to the cluster surfaces, the horizontal and vertical components of the oxygen gradients were of equal importance. Consequently, for calculations of mass transfer rates a three-dimensional model is necessary. These findings imply that to accurately describe biofilm activity, the relation between the arrangement of structural components and mass transfer must be undrstood. © 1994 John Wiley & Sons, Inc.

Additional Material: 8 Ill.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1002/bit.260431118

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3

Electronic Resource

Liquid flow in heterogeneous biofilms (1994)

de Beer, Dirk ; Stoodley, Paul ; Lewandowski, Zbigniew

New York, NY [u.a.] : Wiley-Blackwell

Biotechnology and Bioengineering 44 (1994), S. 636-641

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ISSN: 0006-3592

Keywords: biofilm ; hydrodynamics ; mass transport ; particle tracking ; Chemistry ; Biochemistry and Biotechnology

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology

Notes: Liquid flow was studied in aerobic biofilms, consisting of microbial cell clusters (discrete aggregates of densely packed cells) and interstitial voids. Fluorescein microinjection was used as a qualitative technique to determine the presence of flow in cell clusters and voids. Flow velocity profiles were determined by tracking fluorescent latex spheres using confocal microscopy. Liquid was flowing through the voids and was stagnant in the cell clusters. Consequently, in voids both diffusion and convection may contribute to mass transfer, whereas in cell clusters diffusion is the dominant factor. The flow velocity in the biofilm depended on the average flow velocity of the bulk liquid. The velocity profiles in biofilms were linear and the velocity was zero at the substratum surface. The velocity gradients within biofilms were 50% of that near walls without biofilm coverage. The influence of the biofilm roughness on the flow velocity profiles was similar to that caused by rigid roughness elements. © 1994 John Wiley & Sons, Inc.

Additional Material: 5 Ill.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1002/bit.260440510

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4

Electronic Resource

Measurement of local diffusion coefficients in biofilms by microinjection and confocal microscopy (1997)

de Beer, Dirk ; Stoodley, Paul ; Lewandowski, Zbigniew

New York, NY [u.a.] : Wiley-Blackwell

Biotechnology and Bioengineering 53 (1997), S. 151-158

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ISSN: 0006-3592

Keywords: biofilms ; biofilm structure ; diffusivity ; mass transport in biofilms ; Chemistry ; Biochemistry and Biotechnology

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology

Notes: A new technique for the determination of local diffusion coefficients in biofilms is described. It is based on the microinjection of fluorescent dyes and quantitative analysis of the subsequent plume formation using confocal laser microscopy. The diffusion coefficients of fluorescein (MW 332), TRITC-IgG (MW 150000) and phycoerythrin (MW 240000) were measured in the cell clusters and interstitial voids of a heterogeneous biofilm. The diffusivities measured in the voids were close to the theoretical values in water. Fluorescein had the same diffusivity in cell clusters, voids, and sterile medium. TRITC-IgG did not diffuse in cell clusters, presumably due to binding to the cell cluster matrix. After treatment of the biofilm with bovine serum albumin, binding capacity decreased and the diffusion coefficient could be measured. The diffusivity of phycoerythrin in cell clusters was impeded by 41%, compared to interstitial voids. From the diffusion data of phycoerythrin it was further calculated that the cell cluster matrix had the characteristics of a gel with 0.6 nm thick fibers and pore diameters of 80 nm. © 1997 John Wiley & Sons, Inc.

Additional Material: 4 Ill.

Type of Medium: Electronic Resource

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5

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Measurements of microbial processes, dissolution, water and porewater chemistry during experiments on two coral reef sediments (2017)

Fink, Artur ; den Haan, Joost ; Chennu, Arjun ; [et al.]

PANGAEA

In: Supplement to: Fink, Artur; den Haan, Joost; Chennu, Arjun; Uthicke, Sven; de Beer, Dirk (2017): Ocean Acidification Changes Abiotic Processes but Not Biotic Processes in Coral Reef Sediments. Frontiers in Marine Science, 4, https://doi.org/10.3389/fmars.2017.00073

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Publication Date: 2023-03-09

Description: Two coral reef sediments have been subjected to OA scenarios in the laboratory. Sediments from Magnetic Island (year 2014, 3 pCO2 treatments) were investigated under diffusive conditions in flumes. Parameters studied were: oxygen fluxes, porewater pH and oxygen concentrations. Sulfate reduction rates and pigment concentrations as a measure for microphytobenthos abundance were measured at the end of the experiment. Sediments from Davies Reef (year 2015, 2 pCO2 treatments) were studied under advective conditions using stirred chambers. Microphytobenthos growth over the experimental period was studied using hyperspectral imaging. Porewater pH profiles were measured in different regions of the chambers. Fluxes of oxygen, total alkalinity (as a measure of CaCO3 dissolution), dissolved organic carbon and nutrients were measured using incubations. Pigment concentrations were measured at the end of the experiment as a measure for microphytobenthos abundance and to calibrate the hyperspectral imaging results. In both experiments, elevated pCO2 did not affect biotic processes. Elevated pCO2 caused an increase in dissolution of the Davies Reef sediments. The porewater pH measurements indicated that this is likely caused by the dissolution of high-magnesium calcites.

Keywords: Benthos; BIOACID; Biological Impacts of Ocean Acidification; Biomass/Abundance/Elemental composition; Bottles or small containers/Aquaria (〈20 L); Coast and continental shelf; Community composition and diversity; Entire community; Laboratory experiment; OA-ICC; Ocean Acidification International Coordination Centre; Other metabolic rates; Primary production/Photosynthesis; Rocky-shore community; South Pacific; Tropical

Type: Dataset

Format: application/zip, 10 datasets

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Environmental data from coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea (2016)

Raulf, Felix F ; Fabricius, Katharina Elisabeth ; Uthicke, Sven ; [et al.]

PANGAEA

In: Supplement to: Raulf, Felix F; Fabricius, Katharina Elisabeth; Uthicke, Sven; de Beer, Dirk; Abed, Raeid M M; Ramette, Alban (2015): Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea. Environmental Microbiology, 17(10), 3678-3691, https://doi.org/10.1111/1462-2920.12729

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Publication Date: 2023-03-14

Description: Natural CO2 venting systems can mimic conditions that resemble intermediate to high pCO2 levels as predicted for our future oceans. They represent ideal sites to investigate potential long-term effects of ocean acidification on marine life. To test whether microbes are affected by prolonged exposure to pCO2 levels, we examined the composition and diversity of microbial communities in oxic sandy sediments along a natural CO2 gradient. Increasing pCO2 was accompanied by higher bacterial richness and by a strong increase in rare members in both bacterial and archaeal communities. Microbial communities from sites with CO2 concentrations close to today's conditions had different structures than those of sites with elevated CO2 levels. We also observed increasing sequence abundance of several organic matter degrading types of Flavobacteriaceae and Rhodobacteraceae, which paralleled concurrent shifts in benthic cover and enhanced primary productivity. With increasing pCO2, sequences related to bacterial nitrifying organisms such as Nitrosococcus and Nitrospirales decreased, and sequences affiliated to the archaeal ammonia-oxidizing Thaumarchaeota Nitrosopumilus maritimus increased. Our study suggests that microbial community structure and diversity, and likely key ecosystem functions, may be altered in coastal sediments by long-term CO2 exposure to levels predicted for the end of the century.

Keywords: Aluminium; Calcium; Carbon, organic, total; Carbon, total; DATE/TIME; Depth, bathymetric; DEPTH, sediment/rock; Dobu; EsaAla; Event label; Iron; LATITUDE; LONGITUDE; Magnesium; Manganese; Nitrogen, total; pH; Phosphorus; Potassium; Rubidium; Sample ID; Silicon; South Pacific; Strontium; Sulfur, total; Titanium; Upa-Upasina

Type: Dataset

Format: text/tab-separated-values, 198 data points

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7

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Chlorophyll and true-color maps of sediments from the intertidal zones in Winyah Bay, South Carolina, USA and List, Sylt, Germany (2015)

Chennu, Arjun ; Volkenborn, Nils ; de Beer, Dirk ; [et al.]

PANGAEA

In: Supplement to: Chennu, Arjun; Volkenborn, Nils; de Beer, Dirk; Wethey, David S; Woodin, Sarah A; Polerecky, Lubos (2015): Effects of bioadvection by Arenicola marina on microphytobenthos in permeable sediments. PLoS ONE, 10(7), e0134236, https://doi.org/10.1371/journal.pone.0134236

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Publication Date: 2023-01-13

Description: We used hyperspectral imaging to study short-term effects of bioturbation by lugworms (Arenicola marina) on the surficial biomass of microphytobenthos (MPB) in permeable marine sediments. Within days to weeks after the addition of a lugworm to a homogenized and recomposed sediment, the average surficial MPB biomass and its spatial heterogeneity were, respectively, 150 - 250% and 280% higher than in sediments without lugworms. The surficial sediment area impacted by a single medium-sized lugworm (~4 g wet weight) over this time-scale was at least 340 cm**2. While sediment reworking was the primary cause of the increased spatial heterogeneity, experiments with lugworm-mimics together with modeling showed that bioadvective porewater transport from depth to the sediment surface, as induced by the lugworm ventilating its burrow, was the main cause of the increased surficial MPB biomass. Although direct measurements of nutrient fluxes are lacking, our present data show that enhanced advective supply of nutrients from deeper sediment layers induced by faunal ventilation is an important mechanism that fuels high primary productivity at the surface of permeable sediments even though these systems are generally characterized by low standing stocks of nutrients and organic material.

Type: Dataset

Format: application/zip, 2 datasets

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Benthic cyanobacterial mat (BCM) abundance on samples from the coast of Curacao (2015)

Brocke, Hannah J ; Polerecky, Lubos ; de Beer, Dirk ; [et al.]

PANGAEA

In: Supplement to: Brocke, Hannah J; Polerecky, Lubos; de Beer, Dirk; Weber, Miriam; Claudet, Joachim; Nugues, Maggy M (2015): Organic Matter Degradation Drives Benthic Cyanobacterial Mat Abundance on Caribbean Coral Reefs. PLoS ONE, 10(5), e0125445, https://doi.org/10.1371/journal.pone.0125445

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Publication Date: 2023-01-14

Description: Benthic cyanobacterial mats (BCMs) are impacting coral reefs worldwide. However, the factors and mechanisms driving their proliferation are unclear. We conducted a multi-year survey around the Caribbean island of Curaçao, which revealed highest BCM abundance on sheltered reefs close to urbanised areas. Reefs with high BCM abundance were also characterised by high benthic cover of macroalgae and low cover of corals. Nutrient concentrations in the water-column were consistently low, but markedly increased just above substrata (both sandy and hard) covered with BCMs. This was true for sites with both high and low BCM coverage, suggesting that BCM growth is stimulated by a localised, substrate-linked release of nutrients from the microbial degradation of organic matter. This hypothesis was supported by a higher organic content in sediments on reefs with high BCM coverage, and by an in situ experiment which showed that BCMs grew within days on sediments enriched with organic matter (Spirulina). We propose that nutrient runoff from urbanised areas stimulates phototrophic blooms and enhances organic matter concentrations on the reef. This organic matter is transported by currents and settles on the seabed at sites with low hydrodynamics. Subsequently, nutrients released from the organic matter degradation fuel the growth of BCMs. Improved management of nutrients generated on land should lower organic loading of sediments and other benthos (e.g. turf and macroalgae) to reduce BCM proliferation on coral reefs.

Type: Dataset

Format: application/zip, 7 datasets

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Oxygen, pH and calcium dynamics and fluxes at the thallus surface under ambient (8.1) and low (7.8) seawater pH and across a range of irradiances (2016)

Hofmann, Laurie C ; Koch, Marguerite ; de Beer, Dirk

PANGAEA

In: Supplement to: Hofmann, Laurie C; Koch, Marguerite; de Beer, Dirk (2016): Biotic control of surface pH and evidence of light-induced H+ pumping and Ca2+-H+ exchange in a tropical crustose coralline alga. PLoS ONE, 11(7), e0159057, https://doi.org/10.1371/journal.pone.0159057

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Publication Date: 2023-01-13

Description: Presently, an incomplete mechanistic understanding of tropical reef macroalgae photosynthesis and calcification restricts predictions of how these important autotrophs will respond to global change. Therefore, we investigated the mechanistic link between inorganic carbon uptake pathways, photosynthesis and calcification in a tropical crustose coralline alga (CCA) using microsensors. We measured pH, oxygen (O2), and calcium (Ca2+) dynamics and fluxes at the thallus surface under ambient (8.1) and low (7.8) seawater pH (pHSW) and across a range of irradiances. Acetazolamide (AZ) was used to inhibit extracellular carbonic anhydrase (CAext), which mediates hydrolysis of HCO3-, and 4,4' diisothiocyanatostilbene-2,2'-disulphonate (DIDS) that blocks direct HCO3- uptake by anion exchange transport. Both inhibited photosynthesis, suggesting both diffusive uptake of CO2 via HCO3- hydrolysis to CO2 and direct HCO3- ion transport are important in this CCA. Surface pH was raised approximately 0.3 units at saturating irradiance, but less when CAext was inhibited. Surface pH was lower at pHSW 7.8 than pHSW 8.1 in the dark, but not in the light. The Ca2+ fluxes were large, complex and temporally variable, but revealed net Ca2+ uptake under all conditions. The temporal variability in Ca2+ dynamics was potentially related to localized dissolution during epithallial cell sloughing, a strategy of CCA to remove epiphytes. Simultaneous Ca2+ and pH dynamics suggest the presence of Ca2+/H+ exchange. Rapid light-induced H+ surface dynamics that continued after inhibition of photosynthesis revealed the presence of a light-mediated, but photosynthesis-independent, proton pump. Thus, the study indicates metabolic control of surface pH can occur in CCA through photosynthesis and light-inducible H+ pumps. Our results suggest that complex light-induced ion pumps play an important role in biological processes related to inorganic carbon uptake and calcification in CCA.

Keywords: DATE/TIME; Date/time end; File name; File size; Uniform resource locator/link to file

Type: Dataset

Format: text/tab-separated-values, 28 data points

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Chlorophyll and true-color maps of sediment from the intertidal zone in Winyah Bay, South Carolina, USA, with links to maps in HDF5 format (1.4 GB) (2015)

Chennu, Arjun ; Volkenborn, Nils ; de Beer, Dirk ; [et al.]

PANGAEA

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Publication Date: 2023-01-13

Keywords: Baruch; MULT; Multiple investigations; Winyah Bay, South Carolina, USA

Type: Dataset

Format: application/octet-stream, 1.4 GBytes

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