AquaEnv: An Aquatic Acid–Base Modelling Environment in R

AquaEnv is an integrated software package for aquatic chemical model generation focused on ocean acidification and antropogenic CO₂ uptake. However, the package is not restricted to the carbon cycle or the oceans: it calculates, converts, and visualizes information necessary to describe pH, related CO₂ air–water exchange, as well as aquatic acid–base chemistry in general for marine, estuarine or freshwater systems. Due to the fact that it includes the relevant acid–base systems, it can also be applied to pore water systems and anoxic waters. AquaEnv is implemented in the open source programming language R , which allows for a flexible and versatile application: AquaEnv ’s functionality can be used stand-alone as well as seamlessly integrated into reactive-transport models in the R modelling environment. Additionally, AquaEnv provides a routine to simulate and investigate titrations of water samples with a strong acid or base, as well as a routine that allows for a determination of total alkalinity and total carbonate values from recorded titration curves using non-linear curve-fitting.     

Effects of climate change and nutrient concentrations on carbon sources for zooplankton in a Tibetan Plateau lake over the past millennium

Journal of Paleolimnology - Autochthonous and allochthonous organic carbon (OC) are important carbon sources for zooplankton in lakes, and changes in the abundance and proportions of those sources...     

Planktonic and whole system metabolism in a nutrient-rich estuary (the Scheldt estuary)

Planktonic gross primary production (GPP), community respiration (CR), and nitrification (NIT) were measured monthly in the Scheldt estuary by the oxygen incubation method in 2003. No significant evolution of planktonic GPP was observed since the 1990s with high rates in the freshwater area (salinity 0; 97±65 mmol C m⁻² d⁻¹) decreasing seaward (22–37 mmol C m⁻² d⁻¹). A significant decrease of NIT was observed with regard to previous investigations although this process still represents up to 20% of total organic matter production in the inner estuary. Planktonic CR was highest in the inner estuary and seemed to be mainly controlled by external organic matter inputs. Planktonic net community production was negative most of the time in the estuary with values ranging from −300 to 165 mmol C m⁻² d⁻¹. Whole estuary net ecosystem production (NEP) was investigated on an annual scale using the results mentioned above and published benthic metabolic rates. A NEP of −39±8 mmol C m⁻² d⁻¹ was estimated, which confirms the strong heterotrophic status of this highly nutrified estuary. NEP rates were computed from June to December 2003 to compare with results derived from the Land-Ocean Interaction in the Coastal Zone budgeting procedure applied to dissolved inorganic phosphorus and carbon (DIP and DIC). DIP budgets failed to provide realistic estimates in the inner estuary where abiotic processes account for more than 50% of the nonconservative DIP flux. DIC budgets predicted a much lower NEP than in situ incubations (−109±31 versus −42±9 mmol C m⁻² d⁻¹) although, as each approach is associated with several critical assumptions, the source of this discrepancy remains unclear.     

Selective preservation of soil organic matter in oxidized marine sediments (Madeira Abyssal Plain)

In ocean margin sediments both marine and terrestrial organic matter (OM) are buried but the factors governing their relative preservation and degradation are not well understood. In this study, we analysed the degree of preservation of marine isoprenoidal and soil-derived branched glycerol dialkyl glycerol tetraethers (GDGTs) upon long-term oxygen exposure in OM-rich turbidites from the Madeira Abyssal Plain by analyzing GDGT concentrations across oxidation fronts. Relative to the anoxic part of the turbidites ca. 7-20% of the soil-derived branched GDGTs were preserved in the oxidized part while only 0.2-3% of the marine isoprenoid GDGT crenarchaeol was preserved. Due to these different preservation factors the Branched Isoprenoid Tetraether (BIT) index, a ratio between crenarchaeol and the major branched GDGTs that is used as a tracer for soil-derived organic matter, substantially increases from 0.02 to 0.4. Split Flow Thin Cell (SPLITT) separation of turbidite sediments showed that the enhanced preservation of soil-derived carbon was a general phenomenon across the fine particle size ranges (<38 μm). Calculations reveal that, despite their relatively similar chemical structures, degradation rates of crenarchaeol are 2-fold higher than those of soil-derived branched GDGTs, suggesting preferential soil OM preservation possibly due to matrix protection.     

Effects of Oxygen Loss on Carbon Processing and Heterotrophic Prokaryotes from an Estuarine Ecosystem: Results from Stable Isotope Probing and Cytometry Analyses

Many aquatic ecosystems are experiencing a decline in their oxygen (O₂) content and this is predicted to continue. Implications of this change on several properties of bacterioplankton (heterotrophic prokaryotes) remain however are poorly known. In this study, oxic samples (～170 μM O₂?=?controls) from an oligohaline region of the Scheldt Estuary were purged with N₂ to yield low-O₂ samples (～69 μM O₂?=?treatments); all were amended with ¹³C-glucose and incubated in dark to examine carbon incorporation and cell size of heterotrophic prokaryotes, and relationships between organic matter (OM) degradation and phosphate (P) availability in waters following O₂ loss. Stable isotope (¹³C) probing of phospholipid fatty acids (PLFA) and flow cytometry were used. In samples that have experienced O₂ loss, PLFA biomass became higher, prokaryotic cells had significantly larger size and higher nucleic acid content, but P concentrations was lower, compared to controls. P concentration and OM degradation were positively related in controls, but uncoupled in low-O₂ samples. Moreover, the dominant PLFA 16:1ω7c (likely mainly from Gram-negative bacteria) and the nucleic acid content of heterotrophic prokaryotic cells in low-O₂ samples explained (62–72 %) differences between controls and low-O₂ samples in P amounts. Shortly after incubations began, low-O₂ samples had consistently lower bacterial PLFA ¹³C-enrichments, suggesting involvement of facultatively anaerobic metabolism in carbon incorporation, and supporting the view that this metabolic pathway is widespread among pelagic bacteria in coastal nutrient-rich ecosystems. Estimates based on ¹³C-enrichment of PLFAs indicated that grazing by protozoa on some bacteria was stronger in low-O₂ samples than in controls, suggesting that the grazing pressure on some heterotrophic prokaryotes may increase at the onset of O₂ deficiency in nutrient-rich aquatic systems. These findings also suggest that physiological responses of heterotrophic prokaryotes to O₂ loss in such ecosystems include increases in cell activity, high carbon incorporation, and possibly phosphorus retention by cells that may contribute to reduce phosphate availability in waters.     

Extensive degradation and fractionation of organic matter during subsurface weathering

Organic carbon, sulphur, ¹³C_org, iron, manganese and calcium have been measured across a subsurface-weathering front in Pliocene sediments in southern Sicily. The results show an almost quantitative removal of C_org and sulphur and an increase in iron and manganese oxides over the weathering front, accompanied with a significant shift of the ¹³C_org to lower values. These data are among the first to support the rapid, extensive weathering of sedimentary organic matter and sulphur, a basic assumption made in global biogeochemical models on a Phanerozoic timescale.     

Reassessing the invasion of South African waters by the European shore-crab Carcinus maenas

The European shore-crab Carcinus maenas has been present in South Africa since 1983. Despite this species’ international reputation as a biological invader, its distribution in this region has only been considered by three outdated ‘snapshot surveys.’ The present study is the most comprehensive to date, providing an update on the species’ range and the first temporal assessment of its abundance and demographics. Along South Africa's Cape Peninsula and surrounding areas, C. maenas was absent from 12 intertidal sites surveyed, except for Sea Point, and no crabs were found during subtidal surveys along the open coastline. Subtidal harbour populations were recorded in the Cape Town harbours of Table Bay and Hout Bay (previously estimated as comprising approximately 164 200 and 6 500 individuals, respectively). Table Bay was surveyed monthly for one year, using baited traps, crab condos and postlarvae settlement collectors, to assess size distributions and reproductive seasonality of the crab. Reproductive females were recorded throughout most of the year. These results suggest that the harbour populations could be targeted by control programmes, but provide no strong evidence to support the initiation of management action during a particular season. The lack of detection of postlarval settlement, even among well-established populations, suggests this will not be a useful monitoring tool for detecting incursions.     

Carbon and nitrogen stable isotopes in suspended matter and sediments from the Schelde Estuary

The C/N and stable C and N isotope ratios (δ¹³C, δ¹⁵N) of sedimentary and suspended particulate matter were determined in the Schelde Estuary. Suspended matter was divided into 2 to 5 size fractions by centrifugation. Four major pools of organic matter were recognized: riverine, estuarine, marine and terrestrial materials. Terrestrial organic matter (δ¹³C≈−26‰, δ¹⁵N≈3.5‰, C/N≈21) is important for the sedimentary pool, but suspended matter is dominated by the marine (δ¹³C≈−18‰, δ¹⁵N≈9‰, C/N≈8), riverine (δ¹³C≈−30‰, δ¹⁵N≈9‰, C/N≈7.5) and estuarine (δ¹³C≈−29‰, δ¹⁵N≈15‰, C/N≈8) end-members. In the upper estuary, the suspended matter size fractions vary systematically in their carbon and nitrogen biogeochemistry, with the small particles having low C/N ratios, depleted δ¹³C and enriched δ¹⁵N values relative to large particles. Moreover, sedimentary and suspended matter differ significantly in terms of C/N ratios (17 vs. 8.9), δ¹³C (−26.3 vs. −28.9‰) and δ¹⁵N (+6.9 vs. 12.0‰). In the lower estuary, suspended matter fractions are similar and sedimentary and suspended organic matter differ only in terms of δ¹³C (−23.5 vs. −20.1‰). Our data indicate that autochthonous organic matter contributes significantly to the total suspended matter and that the suspended organic matter composition cannot be explained in terms of conservative mixing of riverine and terrestrial sources on the one hand and marine sources on the other hand.     

Sulfur and iron speciation in surface sediments along the northwestern margin of the Black Sea

The speciation of sedimentary sulfur (pyrite, acid volatile sulfides (AVS), S⁰, H₂S, and sulfate) was analyzed in surface sediments recovered at different water depths from the northwestern margin of the Black Sea. Additionally, dissolved and dithionite-extractable iron were quantified, and the sulfur isotope ratios in pyrite were measured. Sulfur and iron cycling in surface sediments of the northwestern part of the Black Sea is largely influenced by (1) organic matter supply to the sediment, (2) availability of reactive iron compounds and (3) oxygen concentrations in the bottom waters. Biologically active, accumulating sediments just in front of the river deltas were characterized by high AVS contents and a fast depletion of sulfate concentration with depth, most likely due to high sulfate reduction rates (SRR). The δ³⁴S values of pyrite in these sediments were relatively heavy (−8‰ to −21‰ vs. V-CDT). On the central shelf, where benthic mineralization rates are lower, re-oxidation processes may become more important and result in pyrite extremely depleted in δ³⁴S (−39‰ to −46‰ vs. V-CDT). A high variability in δ³⁴S values of pyrite in sediments from the shelf-edge (−6‰ to −46‰ vs. V-CDT) reflects characteristic fluctuations in the oxygen concentrations of bottom waters or varying sediment accumulation rates. During periods of oxic conditions or low sediment accumulation rates, re-oxidation processes became important resulting in low AVS concentrations and light δ³⁴S values. Anoxic conditions in the bottom waters overlying shelf-edge sediments or periods of high accumulation rates are reflected in enhanced AVS contents and heavier sulfur isotope values. The sulfur and iron contents and the light and uniform pyrite isotopic composition (−37‰ to −39‰ vs. V-CDT) of sediments in the permanently anoxic deep sea (1494 m water depth) reflect the formation of pyrite in the upper part of the sulfidic water column and the anoxic surface sediment. The present study demonstrates that pyrite, which is extremely depleted in ³⁴S, can be found in the Black Sea surface sediments that are positioned both above and below the chemocline, despite differences in biogeochemical and microbial controlling factors.