Soil characteristics and abundance of archaea in samples from the Ross Sea Region, Antarctica

The objective of this study was to examine the presence and diversity of Archaea within mineral and ornithogenic soils from 12 locations across the Ross Sea region. Archaea were not abundant but DNA sufficient for producing 16S rRNA gene clone libraries was extracted from 18 of 51 soil samples, from four locations. A total of 1452 clones were analysed by restriction fragment length polymorphism and assigned to 43 operational taxonomic units from which representatives were sequenced. Archaea were primarily restricted to coastal mineral soils which showed a predominance of Crenarchaeota belonging to group 1.1b (>99% of clones). These clones were assigned to six clusters (A through F), based on shared identity to sequences in the GenBank database. Ordination indicated that soil chemistry and water content determined archaeal community structure. This is the first comprehensive study of the archaeal community in Antarctic soils and as such provides a reference point for further investigation of microbial function in this environment.

Metabolism of mesozooplankton in the North-Eastern Aegean Sea during SES_GR2 in October 2008

The dataset is based on samples taken during October 2008 in the North-Eastern Aegean Sea. NH4 excretion rate: Mesozooplankton is collected by vertical tows within the Black sea water body mass layer in the NE Aegean, using a WP-2 200 µm net equipped with a large non-filtering cod-end (10 l). Macrozooplankton organisms are removed using a 2000 µm net. A few unsorted animals (approximately 100) are placed inside 8 bottles of 350 or 650 ml filled with GF/F or 0.2 µm Nucleopore filtered seawater and then on a wheell at dim light and maintaining the in situ temperature. 4 bottles without animals are used as control. After 24hours bottles are opened and water samples taken for NH4 chemical analysis. Then the bottle content is filtered on pre-combusted preweighted CF/F filters, which are then dried at 60 C and weighted. Calculations are made as described by Ikeda et al. (2000). Samples for the NH4 determination were collected in pre-cleaned 50 ml Duran bottles and analysed onboard immediately after collection. Ammonium concentration was measured on a Perkin Elmer Lambda 25 UV/VIS Spectrometer according to the method of Koroleff (1970). PO4 excretion rate: Mesozooplankton is collected by vertical tows within the Black sea water body mass layer in the NE Aegean, using a WP-2 200 µm net equipped with a large non-filtering cod-end (10 l). Macrozooplankton organisms are removed using a 2000 µm net. A few unsorted animals (approximately 100) are placed inside 8 bottles of 350 or 650 ml filled with GF/F or 0.2 µm Nucleopore filtered seawater and then on a wheell at dim light and maintaining the in situ temperature. 4 bottles without animals are used as control. After 24hours bottles are opened and water samples taken for PO4 chemical analysis. Then the bottle content is filtered on pre-combusted preweighted CF/F filters, which are then dried at 60 C and weighted. Calculations are made as described by Ikeda et al. (2000). Samples for the determination of PO4 were collected in pre-cleaned 50 ml polyethylene volumetric tubes and analysed on board immediately after collection. PO4 concentration was measured on a Perkin Elmer Lambda 25 UV/VIS Spectrometer following the protocol of Murphy and Riley (1962). O2 consumption rate: Mesozooplankton is collected by vertical tows within the Black sea water body mass layer in the NE Aegean, using a WP-2 200 µm net equipped with a large non-filtering cod-end (10 l). Macrozooplankton organisms are removed using a 2000 µm net. A few unsorted animals (approximately 100) are placed inside 8 bottles of 350 or 650 ml filled with GF/F or 0.2 µm Nucleopore filtered seawater and then on a wheell at dim light and maintaining the in situ temperature. 4 bottles without animals are used as control. After 24hours bottles are opened and water samples taken for O2 chemical analysis. Then the bottle content is filtered on pre-combusted preweighted CF/F filters, which are then dried at 60 C and weighted. Calculations are made as described by Ikeda et al. (2000). For the dissolved O2 determination, the samples were fixed immediately after collection and analysed with the Winkler method as modified by Carpenter (1965a and 1965b). Carbon specific CO2 respiration rate: O2 consumption rate was converted to CO2 production using a RQ value of 0.87 (Mayzaud et al. 2005). Conversion of mesozooplankton dry weight to carbon was done using the % of carbon content measured in the same station from the SESAME dataset of zooplankton biomass. Carbon specific NH4 excretion rate: Conversion of mesozooplankton dry weight to carbon was done using the % of carbon content measured in the same station from the SESAME dataset of zooplankton biomass. Carbon specific PO4 excretion rate: Conversion of mesozooplankton dry weight to carbon was done using the % of carbon content measured in the same station from the SESAME dataset of zooplankton biomass.

High-resolution in situ oxygen microprofiles, porewater and solid phase geochemistry from the Crimean shelf (Black Sea) from Maria S. Merian cruise MSM15/1

The outer western Crimean shelf of the Black Sea is a natural laboratory to investigate effects of stable oxic versus varying hypoxic conditions on seafloor biogeochemical processes and benthic community structure. Bottom-water oxygen concentrations ranged from normoxic (175 µmol O2/L) and hypoxic (< 63 µmol O2/L) or even anoxic/sulfidic conditions within a few kilometers' distance. Variations in oxygen concentrations between 160 and 10 µmol/L even occurred within hours close to the chemocline at 134 m water depth. Total oxygen uptake, including diffusive as well as fauna-mediated oxygen consumption, decreased from 15 mmol/m**2/d on average in the oxic zone, to 7 mmol/m**2/d on average in the hypoxic zone, correlating with changes in macrobenthos composition. Benthic diffusive oxygen uptake rates, comprising respiration of microorganisms and small meiofauna, were similar in oxic and hypoxic zones (on average 4.5 mmol/m**2/d), but declined to 1.3 mmol/m**2/d in bottom waters with oxygen concentrations below 20 µmol/L. Measurements and modeling of porewater profiles indicated that reoxidation of reduced compounds played only a minor role in diffusive oxygen uptake under the different oxygen conditions, leaving the major fraction to aerobic degradation of organic carbon. Remineralization efficiency decreased from nearly 100 % in the oxic zone, to 50 % in the oxic-hypoxic zone, to 10 % in the hypoxic-anoxic zone. Overall, the faunal remineralization rate was more important, but also more influenced by fluctuating oxygen concentrations, than microbial and geochemical oxidation processes.

Measurements of trace metal abundances and isotopes in carbonate sediments, Exuma, Bahamas

In order to validate the use of 238U/235U as a paleoredox proxy in carbonates, we examined the incorporation and early diagenetic evolution of U isotopes in shallow Bahamian carbonate sediments. Our sample set consists of a variety of primary precipitates that represent a range of carbonate producing organisms and components that were important in the past (scleractinian corals, calcareous green and red algae, ooids, and mollusks). In addition, four short push cores were taken in different depositional environments to assess the impact of early diagenesis and pore water chemistry on the U isotopic composition of bulk carbonates. We find that U concentrations are much higher in bulk carbonate sediments (avg. 4.1 ppm) than in primary precipitates (avg. 1.5 ppm). In almost all cases, the lowest bulk sediment U concentrations were as high as or higher than the highest concentrations found in primary precipitates. This is consistent with authigenic accumulation of reduced U(IV) during early diagenesis. The extent of this process appears sensitive to pore water H2S, and thus indirectly to organic matter content. d238/235U values were very close to seawater values in all of the primary precipitates, suggesting that these carbonate components could be used to reconstruct changes in seawater U geochemistry. However, d238/235U of bulk sediments from the push cores was 0.2-0.4 per mil heavier than seawater (and primary precipitates). These results indicate that authigenic accumulation of U under open-system sulfidic pore water conditions commonly found in carbonate sediments strongly affects the bulk U concentrations and 238U/235U ratios. We also report the occurrence of dolomite in a tidal pond core which contains low 234U/238U and 238U/235U ratios and discuss the possibility that the dolomitization process may result in sediments depleted in 238U. From this initial exploration, it is clear that 238U/235U variations in ancient carbonate sediments could be driven by changes in global average seawater, by spatial and temporal variations in the local deposition environment, or subsequent diagenesis. To cope with such effects, proxies for syndepositional pore water redox conditions (e.g., organic matter content, iron speciation, and trace metal distributions) and careful consideration of possible post-deposition alteration will be required to avoid spurious interpretation of 238U/235U data from ancient carbonate sediments.

Geochemistry of interstitial waters of Lau Backarc Basin sediment samples

Interstitial water samples from Sites 834 through 839, drilled during Ocean Drilling Program Leg 135 in the backarc Lau basin (Southwestern Pacific), have been analyzed for major elements, manganese, copper, strontium, barium, vanadium, and 87Sr/86Sr isotopic composition values. The concentration-depth profiles of the major chemical components show almost straight concentration gradients at all sites, and seem to reflect slight alteration of volcanic material. However, in the lower part of the sedimentary cover, where volcanogenic material is abundant and where diagenetic minerals occur, systematic decreases in calcium, strontium, manganese, copper, and vanadium concentrations are observed. A downwelling flow of bottom seawater, which affected the diagenetic chemical signature of the interstitial water, is probably responsible for the recorded chemical features. This hypothesis is supported by strontium isotope data obtained from interstitial water samples at Site 835. It is also in accordance with data from heat flow and physical properties.

Water chemistry of lakes from the Antarctic

This paper reviews Japanese limnological studies mainly in the McMurdo and Syowa oases, with special emphasis on the nutrient distribution. Generally, the chemical composition of the major ionic components in the coastal lakes and ponds is similar to that in seawater, while that in inland Dry Valley lakes and ponds of the McMurdo Oasis is abundant in calcium, magnesium and sulfate ions. The former can be explained by the direct influences of sea salts, while the latter is mainly attributable to the accumulation of atmospheric salts. Most saline lakes are meromictic. Dissolved oxygen concentrations in the upper layers are saturated or supersaturated, but the bottom layers are anoxic and often hydrogen sulfide occurs. The concentrations of nutrients vary largely not only among the lakes but also with depth. Silicate-Si, which is generally abundant in all freshwater and saline lakes, may be due to erosions of soils and rocks. Nitrite-N concentrations in both freshwater and saline lakes are generally low. Nitrate-N concentrations in the oxic layers of the inland saline lakes in the McMurdo Oasis arc often high, but not high in the coastal saline lakes of the Syowa and Vestfold oases. The abundance of phosphate-P and ammonium-N in the bottom stagnant layers of saline lakes can be explained by the accumulation of microbially released nutrients due to the decomposition of organic substances. Nutrients are supplied mainly from meltstreams in the catchment areas, and are proved to play an important role in primary production.

Methane and microbiological processes in the Barents Sea

Biogeochemical cycle of methane in the Barents Sea was studied using isotope geochemistry to determine rates of microbial methane oxidation. It was established that microbiological processes (glucose consumption, 14CO2 assimilation, sulfate reduction, and slow methane oxidation) in oxidized surface and weakly reduced sediments are marked by only insignificant change in SO4 concentration and absence of notable increase of total alkalinity and N/NH4 downward sediment cores. Microbial methane productivity was 0.111x10**6 mol/day. Taking into account volume of the water column, microbial methane consumption therein can be as much as 1.8x10**6 mol/day.

Chemistry of interstitial waters and sediments at DSDP Leg 64 Holes

Studies of interstitial waters obtained from DSDP Leg 64 drill sites in the Gulf of California have revealed information both on early diagenetic processes in the sediments resulting from the breakdown of organic matter and on hydrothermal interactions between sediments and hot doleritic sill intrusions into the sediments. In all the sites drilled sulfate reduction occurred as a result of rapid sediment accumulation rates and of relatively high organic carbon contents; in most sites methane production occurred after sulfate depletion. Associated with this methane production are high values of alkalinity and high concentrations of dissolved ammonia, which causes ion exchange processes with the solid phases leading to intermediate maxima in Mg++, K+, Rb+, and Sr++(?). Though this phenomenon is common in Leg 64 drill sites, these concentration reversals had been noticed previously only in Site 262 (Timor Trough) and Site 440 (Japan Trench). Penetrating, hot dolerite sills have led to substantial hydrothermal alteration in sediments at sites drilled in the Guaymas Basin. Site 477 is an active hydrothermal system in which the pore-water chemistry typically shows depletions in sulfate and magnesium and large increases in lithium, potassium, rubidium, calcium, strontium, and chloride. Strontium isotope data also indicate large contributions of volcanic matter and basalt to the pore-water strontium concentrations. At Sites 478 and 481 dolerite sill intrusions have cooled to ambient temperatures but interstitial water concentrations of Li+, Rb+, Sr++ , and Cl- show the gradual decay of a hydrothermal signal that must have been similar to the interstitial water chemistry at Site 477 at the time of sill intrusion. Studies of oxygen isotopes of the interstitial waters at Site 481 indicate positive values of d18O (SMOW) as a result of high-temperature alteration reactions occurring in the sills and the surrounding sediments. A minimum in dissolved chloride at about 100-125 meters sub-bottom at Sites 478, 481, and particularly Site 479 records a possible paleosalinity signal, associated with an event that substantially lowered salinities in the inner parts of the Gulf of California during Quaternary time.

Mineral nitrogen from KCl extractions of soil from the Jena Experiment (Main Experiment up to 30cm depth, year 2002)

As an estimate of plant-available N, this data set contains measurements of inorganic nitrogen (NO3-N and NH4-N, the sum of which is termed mineral N or Nmin) determined by extraction with 1 M KCl solution of soil samples from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Five soil cores (diameter 0.01 m) were taken at a depth of 0 to 0.15 m and 0.15 to 0.3 m of the mineral soil from each of the experimental plots in September 2002. Samples of the soil cores per plot were pooled during each sampling campaign. NO3-N and NH4-N concentrations were determined by extraction of soil samples with 1 M KCl solution and were measured in the soil extract with a Continuous Flow Analyzer (CFA, Skalar, Breda, Netherlands).

Mineral nitrogen from KCl extractions of soil from the Jena Experiment (Main Experiment up to 30cm depth, year 2004)

As an estimate of plant-available N, this data set contains measurements of inorganic nitrogen (NO3-N and NH4-N, the sum of which is termed mineral N or Nmin) determined by extraction with 1 M KCl solution of soil samples from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Five soil cores (diameter 0.01 m) were taken at a depth of 0 to 0.15 m and 0.15 to 0.3 m of the mineral soil from each of the experimental plots in March and October 2004. Samples of the soil cores per plot were pooled during each sampling campaign. NO3-N and NH4-N concentrations were determined by extraction of soil samples with 1 M KCl solution and were measured in the soil extract with a Continuous Flow Analyzer (CFA, Skalar, Breda, Netherlands).

Dissolved nitrogen in soil solution of the Jena Experiment (Main Experiment, year 2004)

This data set contains measurements of dissolved nitrogen (total dissolved nitrogen: TDN, dissolved organic nitrogen: DON, dissolved ammonium: NH4+, and dissolved nitrate: NO3-) in samples of soil water collected from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In April 2002 glass suction plates with a diameter of 12 cm, 1 cm thickness and a pore size of 1-1.6 µm (UMS GmbH, Munich, Germany) were installed in depths of 10, 20, 30 and 60 cm to collect soil solution. The sampling bottles were continuously evacuated to a negative pressure between 50 and 350 mbar, such that the suction pressure was about 50 mbar above the actual soil water tension. Thus, only the soil leachate was collected. Cumulative soil solution was sampled biweekly and analyzed for nitrate (NO3-) and ammonium (NH4+) concentrations with a continuous flow analyzer (CFA, Skalar, Breda, The Netherlands). Nitrate was analyzed photometrically after reduction to NO2- and reaction with sulfanilamide and naphthylethylenediamine-dihydrochloride to an azo-dye. Our NO3- concentrations contained an unknown contribution of NO2- that is expected to be small. Simultaneously to the NO3- analysis, NH4+ was determined photometrically as 5-aminosalicylate after a modified Berthelot reaction. The detection limits of NO3- and NH4+ were 0.02 and 0.03 mg N L-1, respectively. Total dissolved N in soil solution was analyzed by oxidation with K2S2O8 followed by reduction to NO2- as described above for NO3-. Dissolved organic N (DON) concentrations in soil solution were calculated as the difference between TDN and the sum of mineral N (NO3- + NH4+). In 5% of the samples, TDN was equal to or smaller than mineral N. In these cases, DON was assumed to be zero.

Mineral nitrogen from KCl extractions of soil from the Jena Experiment (Main Experiment up to 15cm depth, year 2005)

As an estimate of plant-available N, this data set contains measurements of inorganic nitrogen (NO3-N and NH4-N, the sum of which is termed mineral N or Nmin) determined by extraction with 1 M KCl solution of soil samples from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Five soil cores (diameter 0.01 m) were taken at a depth of 0 to 0.15 m of the mineral soil from each of the experimental plots in April and September 2005. Samples of the soil cores per plot were pooled during each sampling campaign. NO3-N and NH4-N concentrations were determined by extraction of soil samples with 1 M KCl solution and were measured in the soil extract with a Continuous Flow Analyzer (CFA, Skalar, Breda, Netherlands).

Tracer release experiments in the tropical North Atlantic

Lateral diffusivity is computed from a tracer release experiment in the northeastern tropical Atlantic thermocline. The uncertainties of the estimates are inferred from a synthetic particle release using a high-resolution ocean circulation model. The main method employed to compute zonal and meridional components of lateral diffusivity is the growth of the second moment of a cloud of tracer. The application of an areal comparison method for estimating tracer-based diffusivity in the field experiments is also discussed. The best estimate of meridional eddy diffusivity in the Guinea Upwelling region at about 300 m depth is estimated to be inline image m2 s-1. The zonal component of lateral diffusivity is estimated to be inline image m2 s-1, while areal comparison method yields areal equivalent zonal diffusivity component of inline image m2 s?1. In comparison to Ky, Kx is about twice larger, resulting from the tracer patch stretching by zonal jets. Employed conceptual jet model indicates that zonal jet velocities of about inline image m s?1 are required to explain the enhancement of the zonal eddy diffusivity component. Finally, different sampling strategies are tested on synthetic tracer release experiments. They indicate that the best sampling strategy is a sparse regular sampling grid covering most of the tracer patch.

Composition of swamp waters from the lower Tom' River Basin

New data on chemical and trace component compositions of acidic and low acidic swamp waters and other types of low mineralized waters are reported in the paper. Special attention is paid to dissolved organic compounds: fulvic and humic acids, bitumen, and hydrocarbons. For the first time detailed data on organic trace components (alkanes, pentacyclic terpenoids, steranes, alkylbenzenes, naphthalenes, phenanthrenes, tetraarenes, etc.) in the swamp waters of the Western Siberia: are reported.