Microbial respiration within a floodplain aquifer of a large gravel-bed river

1. Aerobic respiration, productivity and the carbon turnover rate of microbial biofilms were determined at hyporheic and phreatic sites in the Kalispell Valley alluvial aquifer along a transect extending 3.9 km laterally from the main channel of the Flathead River, a sixth order river in Montana (U.S.A.). The effect of experimentally increasing bioavailable organic carbon (acetate) on the respiration rate of biofilms in this carbon‐poor [dissolved organic carbon (DOC) < 2 mg L^?1] aquifer was also measured. 2. Chambers containing natural substratum were placed in‐situ and allowed to colonise for 20 weeks. After 4, 12 and 20 weeks, they were taken to the laboratory where oxygen flux was measured in a computer‐controlled, flow‐through respirometry system. 3. Respiration ranged from 0.01 to 0.33 mg O₂ dm^?3 h^?1 across sites, with means ranging from 0.10 to 0.17 mg O₂ dm^?3 h^?1. Productivity estimates ranged from 0.18 to 0.32 mg C dm^?3 day^?1 (mean 0.25, SE 0.03). The total organic carbon (TOC) of the microbial biofilms ranged from 18.2 to 29.7 mg C dm^?3. Turnover rate ranged from 3.2 to 5.6 year^?1 with a mean of 4.2 year^?1. 4. At the hyporheic site very close to the river, respiration did not significantly increase when samples were supplemented with labile carbon. Respiration increased with increasing DOC addition at hyporheic sites more distant from the river, suggesting a carbon‐limitation gradient within the hyporheic zone. Microbes at the phreatic site did not respond to increasing DOC addition, suggesting that the phreatic biofilm is adapted to low carbon availability. 5. Comparing the volume of the alluvial aquifer (about 0.7 km³) to that of the river benthic sediments (to 0.25 m depth, which amounts to about 1.6 × 10^?4 km³) within the Flathead Valley, leads to the conclusion that interstitial microbial productivity is orders of magnitude greater than benthic productivity. Alluvial aquifers are often voluminous and microbial production is an enormous component of ecosystem production in rivers such as the Flathead.     

Gross nitrous oxide production drives net nitrous oxide fluxes across a salt marsh landscape

Sea level rise will change inundation regimes in salt marshes, altering redox dynamics that control nitrification – a potential source of the potent greenhouse gas, nitrous oxide (N₂O) – and denitrification, a major nitrogen (N) loss pathway in coastal ecosystems and both a source and sink of N₂O. Measurements of net N₂O fluxes alone yield little insight into the different effects of redox conditions on N₂O production and consumption. We used in situ measurements of gross N₂O fluxes across a salt marsh elevation gradient to determine how soil N₂O emissions in coastal ecosystems may respond to future sea level rise. Soil redox declined as marsh elevation decreased, with lower soil nitrate and higher ferrous iron in the low marsh compared to the mid and high marshes (P < 0.001 for both). In addition, soil oxygen concentrations were lower in the low and mid‐marshes relative to the high marsh (P < 0.001). Net N₂O fluxes differed significantly among marsh zones (P = 0.009), averaging 9.8 ± 5.4 μg N m^?2 h^?1, ?2.2 ± 0.9 μg N m^?2 h^?1, and 0.67 ± 0.57 μg N m^?2 h^?1 in the low, mid, and high marshes, respectively. Both net N₂O release and uptake were observed in the low and high marshes, but the mid‐marsh was consistently a net N₂O sink. Gross N₂O production was highest in the low marsh and lowest in the mid‐marsh (P = 0.02), whereas gross N₂O consumption did not differ among marsh zones. Thus, variability in gross N₂O production rates drove the differences in net N₂O flux among marsh zones. Our results suggest that future studies should focus on elucidating controls on the processes producing, rather than consuming, N₂O in salt marshes to improve our predictions of changes in net N₂O fluxes caused by future sea level rise.     

Enhanced root exudation stimulates soil nitrogen transformations in a subalpine coniferous forest under experimental warming

Despite the perceived importance of exudation to forest ecosystem function, few studies have attempted to examine the effects of elevated temperature and nutrition availability on the rates of root exudation and associated microbial processes. In this study, we performed an experiment in which in situ exudates were collected from Picea asperata seedlings that were transplanted in disturbed soils exposed to two levels of temperature (ambient temperature and infrared heater warming) and two nitrogen levels (unfertilized and 25 g N m^?2 a^?1). Here, we show that the trees exposed to an elevated temperature increased their exudation rates I (μg C g^?1 root biomass h^?1), II (μg C cm^?1 root length h^?1) and III (μg C cm^?2 root area h^?1) in the unfertilized plots. The altered morphological and physiological traits of the roots exposed to experimental warming could be responsible for this variation in root exudation. Moreover, these increases in root‐derived C were positively correlated with the microbial release of extracellular enzymes involved in the breakdown of organic N (R² = 0.790; P = 0.038), which was coupled with stimulated microbial activity and accelerated N transformations in the unfertilized soils. In contrast, the trees exposed to both experimental warming and N fertilization did not show increased exudation rates or soil enzyme activity, indicating that the stimulatory effects of experimental warming on root exudation depend on soil fertility. Collectively, our results provide preliminary evidence that an increase in the release of root exudates into the soil may be an important physiological adjustment by which the sustained growth responses of plants to experimental warming may be maintained via enhanced soil microbial activity and soil N transformation. Accordingly, the underlying mechanisms by which plant root‐microbe interactions influence soil organic matter decomposition and N cycling should be incorporated into climate‐carbon cycle models to determine reliable estimates of long‐term C storage in forests.     

Nitrogen Utilization and Toxin Production by Two Diatoms of the Pseudo‐nitzschia pseudodelicatissima Complex: P. cuspidata and P. fryxelliana

The toxigenic diatom Pseudo‐nitzschia cuspidata, isolated from the U.S. Pacific Northwest, was examined in unialgal batch cultures to evaluate domoic acid (DA) toxicity and growth as a function of light, N substrate, and growth phase. Experiments conducted at saturating (120 μmol photons · m^?2 · s^?1) and subsaturating (40 μmol photons · m^?2 · s^?1) photosynthetic photon flux density (PPFD), demonstrate that P. cuspidata grows significantly faster at the higher PPFD on all three N substrates tested [nitrate (NO₃^?), ammonium (NH₄⁺), and urea], but neither cellular toxicity nor exponential growth rates were strongly associated with one N source over the other at high PPFD. However, at the lower PPFD, the exponential growth rates were approximately halved, and the cells were significantly more toxic regardless of N substrate. Urea supported significantly faster growth rates, and cellular toxicity varied as a function of N substrate with NO₃^?‐supported cells being significantly more toxic than both NH₄⁺‐ and urea‐supported cells at the low PPFD. Kinetic uptake parameters were determined for another member of the P. pseudodelicatissima complex, P. fryxelliana. After growth of these cells on NO₃^? they exhibited maximum specific uptake rates (V_max) of 22.7, 29.9, 8.98 × 10^?3 · h^?1, half‐saturation constants (K_s) of 1.34, 2.14, 0.28 μg‐at N · L^?1, and affinity values (α) of 17.0, 14.7, 32.5 × 10^?3 · h^?1/(μg‐at N · L^?1) for NO₃^?, NH₄⁺ and urea, respectively. These labo‐ratory results demonstrate the capability of P. cuspidata to grow and produce DA on both oxidized and reduced N substrates during both exponential and stationary growth phases, and the uptake kinetic results for the pseudo‐cryptic species, P. fryxelliana suggest that reduced N sources from coastal runoff could be important for maintenance of these small pennate diatoms in U.S. west coast blooms, especially during times of low ambient N concentrations.     

Methanogenesis,sulfate reduction and crude oil biodegradation in hot Alaskan oilfields

Petrochemical and geological evidence suggest that petroleum in most reservoirs is anaerobically biodegraded to some extent. However, the conditions for this metabolism and the cultivation of the requisite microorganisms are rarely established. Here, we report on microbial hydrocarbon metabolism in two distinct oilfields on the North Slope of Alaska (designated Fields A and B). Signature anaerobic hydrocarbon metabolites were detected in produced water from the two oilfields offering evidence of in situ biodegradation activity. Rate measurements revealed that sulfate reduction was an important electron accepting process in Field A (6–807 µmol S l^?1 day^?1), but of lesser consequence in Field B (0.1–10 µmol S l^?1 day^?1). Correspondingly, enrichments established at 55°C with a variety of hydrocarbon mixtures showed relatively high sulfate consumption but low methane production in Field A incubations, whereas the opposite was true of the Field B enrichments. Repeated transfer of a Field B enrichment showed ongoing methane production in the presence of crude oil that correlated with ≥ 50% depletion of several component hydrocarbons. Molecular‐based microbial community analysis of the methanogenic oil‐utilizing consortium revealed five bacterial taxa affiliating with the orders Thermotogales, Synergistales, Deferribacterales (two taxa) and Thermoanaerobacterales that have known fermentative or syntrophic capability and one methanogen that is most closely affiliated with uncultured clones in the H₂‐using family Methanobacteriaceae. The findings demonstrate that oilfield‐associated microbial assemblages can metabolize crude oil under the thermophilic and anaerobic conditions prevalent in many petroleum reservoirs.     

Co-occurrence of denitrification and nitrogen fixation in a meromictic lake, Lake Cadagno (Switzerland)

The nitrogen cycling of Lake Cadagno was investigated by using a combination of biogeochemical and molecular ecological techniques. In the upper oxic freshwater zone inorganic nitrogen concentrations were low (up to ～3.4 μM nitrate at the base of the oxic zone), while in the lower anoxic zone there were high concentrations of ammonium (up to 40 μM). Between these zones, a narrow zone was characterized by no measurable inorganic nitrogen, but high microbial biomass (up to 4 × 10⁷ cells ml^?1). Incubation experiments with ¹⁵N‐nitrite revealed nitrogen loss occurring in the chemocline through denitrification (～3 nM N h^?1). At the same depth, incubations experiments with ¹⁵N₂‐ and ¹³C_DIC‐labelled bicarbonate, indicated substantial N₂ fixation (31.7–42.1 pM h^?1) and inorganic carbon assimilation (40–85 nM h^?1). Catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) and sequencing of 16S rRNA genes showed that the microbial community at the chemocline was dominated by the phototrophic green sulfur bacterium Chlorobium clathratiforme. Phylogenetic analyses of the nifH genes expressed as mRNA revealed a high diversity of N₂ fixers, with the highest expression levels right at the chemocline. The majority of N₂ fixers were related to Chlorobium tepidum/C. phaeobacteroides. By using Halogen In Situ Hybridization‐Secondary Ion Mass Spectroscopy (HISH‐SIMS), we could for the first time directly link Chlorobium to N₂ fixation in the environment. Moreover, our results show that N₂ fixation could partly compensate for the N loss and that both processes occur at the same locale at the same time as suggested for the ancient Ocean.     

Bacterivory of metazooplankton, ciliates and flagellates in a newly flooded reservoir

Bacterial consumption by metazoan zooplankton and phagotrophic protists was measured in situ during the period of thermal stratification in the epilimnion (1 m) and metalimnion (7 m) of a newly flooded reservoir (Sep reservoir, France). The mean bacterial consumption was 2.53 x 10⁶ bacterial l^-1 h^-1 at 1m and 0.97 x 10⁶ bacteria l^-1 h^-1 at 7m. The main consumers over the whole study period were the cladocerans Daphnia longispina and Ceriodaphnia quadrangula, accounting on average for 72% of the potential total predation of bacteria at 1 m and 56% at m, especially during the months of May-June and August. Heterotrophic nanoflagellates (HNF), which accounted for 12% estimated total predation of bacteria at 1 m and 13% at 7m, only exerted a limited predation, mainly by a Monas-type cell. Ciliates, dominated in terms of abundance by Pelagohalteria viridis, accounted for 4% of total predation in the epilimnion (0.00-0.42 x 10⁶ bacteria l^-1 h^-1). In a newly flooded reservoir, metazoan zooplankton appear to be the main consumers of bacteria. Predation of ciliates and HNF by zooplanktonic crustaceans could account for the low contribution of components of the microbial loop to bacterial consumption.      

In situ growth of Gallionella biofilms and partitioning of lanthanides and actinides between biological material and ferric oxyhydroxides

Gallionella ferruginea is an iron‐oxidizing chemolithotrophic micro‐organism that lives in low‐oxygen conditions (0.1–1.5 mg L^?1 saturation). It produces a stalk structure from the concave side of the cell depending on population development, pH and redox conditions. After Gallionella oxidizes ferrous iron, bacteriogenic iron oxides (BIOS) precipitate on the stalk material and over time the stalks and/or the precipitated BIOS attenuate trace metals from surrounding groundwater. Gallionella ferruginea biofilms were cultured in situ in an artificial channel (2000 × 300 × 250 mm) using groundwater sourced from a borehole 297 m below sea level in the Äspö Hard Rock Laboratory in southern Sweden. The pH of the groundwater in the channels was always between 7.4 and 7.7 with oxygen saturation below 1.5 mg L^?1 and Eh between 100 and 200 mV. Oxygen eventually declined to <0.3 mg L^?1, terminating prolific biofilm growth. Biofilms formed within 2 weeks and were sampled every 2 weeks over 3 months. Cell number, stalk length and ferric iron concentration were measured for each sample and trace metal concentration was measured by inductively coupled plasma mass spectrometry. Results from well‐developed in situ biofilms suggest that Gallionella could concentrate metals at levels up to 1 × 10³‐fold higher than found within the host rock and more than 1 × 10⁶ times the levels found in the groundwater. These new experiments were used to support the results from the well‐developed biofilms and to relate biofilm development and population characteristics to metal attenuation. After 3 months, rare earth element (REE) plots indicated that BIOS can accumulate metals at levels up to 1 × 10⁴‐fold higher than found in the groundwater and fractionate heavy rare earth elements over light rare earth elements. Generally the presence of the organic phase promotes the adsorption of all lanthanides and actinides that are not adsorbed by the inorganic phase. The iron oxides are directly correlated with stalk length (R = 0.96), indicating that rapid REE and actinide adsorption requires both iron oxides and a nucleating biological structure for the iron oxides.     

Dilution rates influence ammonia-assimilating enzyme activities and cell parameters of Selenomonas ruminantium strain D in continuous (glucose-limited) culture

Aims: The objective of this study was to examine the effect of dilution rates (Ds, varying from 0·05 to 0·42 h^?1) in glucose‐limited continuous culture on cell yield, cell composition, fermentation pattern and ammonia assimilation enzymes of Selenomonas ruminantium strain D. Methods and Results: All glucose‐limited continuous culture experiments were conducted under anaerobic conditions. Except for protein, all cell constituents including carbohydrates, RNA and DNA yielded significant cubic responses to Ds with the highest values at Ds of either 0·10 or 0·20 h^?1. At Ds higher than 0·2 h^?1, fermentation acid pattern shifted primarily from propionate and acetate to lactate production. Succinate also accumulated at the higher Ds (0·30 and 0·42 h^?1). Glucose was most efficiently utilized by S. ruminantium D at 0·20 h^?1 after which decreases in glucose and ATP yields were observed. Under energy limiting conditions, glutamine synthetase (GS) and glutamate dehydrogenase (GDH) appeared to be the major enzymes involved in nitrogen assimilation suggesting that other potential ammonia incorporating enzymes were of little importance in ammonia assimilation in S. ruminantium D. GS exhibited lower activities than GDH at all Ds, which indicates that the bacterial growth rate is not a primary regulator of their activities. Conclusions: Studied dilution rates influenced cell composition, fermentation pattern and nitrogen assimilation of S. ruminantium strain D grown in glucose‐limited continuous culture. Significance and Impact of the Study: Selenomonas ruminantium D is an ecologically and evolutionary important bacterium in ruminants and is present under most rumen dietary conditions. Characterizing the growth physiology and ammonia assimilation enzymes of S. ruminantium D during glucose limitation at Ds, which simulate the liquid turnover rates in rumen, will provide a better understanding of how this micro‐organism responds to differing growth conditions.     

In vitro and ex vivo biofilms of dermatophytes: a new panorama for the study of antifungal drugs

Abstract

This study describes an ex vivo model that creates an environment for dermatophyte biofilm growth, with features that resemble those of in vivo conditions, designing a new panorama for the study of antifungal susceptibility. Regarding planktonic susceptibility, MIC ranges were 0.125-1?µg ml^?1 for griseofulvin and 0.000097-0.25?µg ml^?1 for itraconazole and terbinafine. sMIC50 ranges were 2->512?µg ml^?1 for griseofulvin and 0.25->64?µg ml^?1 for itraconazole and terbinafine. CLSM images demonstrated a reduction in the amount of cells within the biofilm, but hyphae and conidia were still observed and biofilm biomass was maintained. SEM analysis demonstrated a retraction in the biofilm matrix, but fungal structures and water channels were preserved. These results show that ex vivo biofilms are more tolerant to antifungal drugs than in vitro biofilms, suggesting that environmental and nutritional conditions created by this ex vivo model favor biofilm growth and robustness, and hence drug tolerance.     

Improved experimental protocols to evaluate cold tolerance thresholds in Miscanthus and switchgrass rhizomes

This study investigates protocols to evaluate cold tolerance thresholds for overwintering rhizomes of perennial bioenergy grasses. Protocols examined include the temperature at which ice formation occurs, cooling rate, incubation time at the treatment temperature, and the electrolyte leakage (EL) method to assess mortality thresholds. Using these protocols, we assessed low temperature injury in two genotypes of Miscanthus and two genotypes of lowland switchgrass (Panicum virgatum). Ice formed near ?1 C in the rhizomes cooled at 1 C h^?1, but at variable temperatures at cooling rates of 3  and 5 C h^?1. Rhizome temperature followed chamber temperature at a cooling rate of 1 C h^?1, whereas at faster cooling rates, there was a lag in rhizome temperature that affected treatment exposure time. A 1 C h^?1 cooling rate is thus suitable. In rhizomes incubated for <4 h at the treatment temperature, EL values were variable, while there was no change in EL when samples were incubated 4–20 h. A continuous, steady rate of cooling at 1 C h^?1 demonstrated the Miscanthus and lowland switchgrass varieties exhibited lethal levels of electrolyte leakage below ?6 C. Continuous cooling does not allow for subzero acclimation and reflects thermal tolerances of sampled tissue in situ. To allow for maximum acclimation at subzero temperatures, a prolonged, staged‐cooling procedure was adopted. This procedure showed diploid Miscanthus rhizomes could acclimate and adjust their tolerance limit to ?12 C, while a triploid Illinois line showed little acclimation and was still killed below ?6 C.     

Subsurface Biofilm Barriers for the Containment and Remediation of Contaminated Groundwater

An engineered microbial biofilm barrier capable of reducing aquifer hydraulic conductivity while simultaneously biodegrading nitrate has been developed and tested at a field-relevant scale. The 22-month demonstration project was conducted at the MSE Technology Applications Inc. test facility in Butte, Montana, which consisted of a 130 ft wide, 180 ft long, 21 ft deep, polyvinylchloride (PVC)-lined test cell, with an initial hydraulic conductivity of 4.2 × 10^?2 cm/s. A flow field was established across the test cell by injecting water upgradient while simultaneously pumping from an effluent well located approximately 82 ft down gradient. A 30 ft wide biofilm barrier was developed along the centerline of the test cell by injecting a starved bacterial inoculum of Pseudomonas fluorescens strain CPC211a, followed by injection of a growth nutrient mixture composed of molasses, nitrate, and other additives. A 99% reduction of average hydraulic conductivity across the barrier was accomplished after three months of weekly or bi-weekly injections of growth nutrient. Reduced hydraulic conductivity was maintained by additional nutrient injections at intervals ranging from three to ten months. After the barrier was in place, a sustained concentration of 100 mg/l nitrate nitrogen, along with a 100 mg/l concentration of conservative (chloride) tracer, was added to the test cell influent over a six-month period. At the test cell effluent the concentration of chloride increased to about 80 mg/l while the effluent nitrate concentration varied between 0.0 and 6.4 mg/l.     

Porewater nutrient profiles and nutrient sediment–water exchange in a tropical mangrove waterway, Mapopwe Creek, Chwaka Bay, Zanzibar

Sediments were examined in the Mapopwe Creek, a tidally dominated mangrove waterway in the Chwaka Bay mangrove forest, Zanzibar, to assess their significance in the nutrient dynamics of the mangrove forest and the adjacent bay. Porewater concentrations of dissolved ammonium and that of soluble reactive phosphorus (SRP) were generally higher during the dry season than during the wet season. NO₃^? plus NO₂^? concentration averaged 1 µm and did not vary much between the two periods. Fluxes of ammonium ranged from ?575 to 523 µm m^?2 h^?1 and those of SRP from ?55.7 to 69.5 µm m^?2 h^?1. Measurements of NO_x did not show any consistent fluxes of this dissolved nitrogen species. Variations of flux rates between the two seasons were not significant even though there were small variations in the flux direction in both nutrients. Results imply that Mapopwe sediments are a source of NH₄⁺ but act as a sink for SRP.     

Determination of enalapril maleate and atenolol in their pharmaceutical products and in biological fluids by flow‐injection chemiluminescence

A chemiluminescent method using flow injection (FI) was investigated for rapid and sensitive determination of enalapril maleate and atenolol, which are used in the treatment of hypertension. The method is based on the sensitizing effect of these drugs on the Ce(IV)–sulfite reaction. The different experimental parameters affecting the chemiluminescence (CL) intensity were carefully studied and incorporated into the procedure. The method permitted the determination of 0.01–3.0 µg mL^?1 of enalapril maleate in bulk form with correlation coefficient r = 0.99993, lower limit of detection (LOD) 0.0025 µg mL^?1 (S/N = 2) and lower limit of quantitation (LOQ) 0.01 µg mL^?1. The linearity range of atenolol in bulk form was 0.01–2.0 µg mL^?1 (r = 0.99989) with LOD of 0.0003 µg mL^?1 (S/N = 2) and LOQ of 0.01 µg mL^?1. In biological fluids the linearity range of enalapril maleate was 0.1–2.0 µg mL^?1 in both urine and serum, and for atenolol the linearity range was 0.1–1.0 µg mL^?1 in both urine and serum. The method was also applied to the determination of the drugs in their pharmaceutical preparations. Copyright © 2009 John Wiley & Sons, Ltd.     

Considerable methane uptake by alpine grasslands despite the cold climate: in situ measurements on the central Tibetan Plateau, 2008–2013

The uptake of CH₄ by aerate soil plays a secondary role in the removal of tropospheric CH₄, but it is still highly uncertain in terms of its magnitude, spatial, and temporal variation. In an attempt to quantify the sink of the vast alpine grasslands (1 400 000 km²) of the Tibetan Plateau, we conducted in situ measurements in an alpine steppe (4730 m) and alpine meadow (4900 m) using the static chamber and gas chromatograph method. For the alpine steppe, measurements (2008–2013) suggested that there is large interannual variability in CH₄ uptake, ranging from ?48.8 to ?95.8 μg CH₄ m^?2 h^?1 (averaged of ?71.5 ± 2.5 μg CH₄ m^?2 h^?1), due to the variability in precipitation seasonality. The seasonal pattern of CH₄ uptakes in the form of stronger uptake in the early growing season and weaker uptake in the rainy season closely matched the precipitation seasonality and subsequent soil moisture variation. The relationships between alpine steppe CH₄ uptake and soil moisture/temperature are best depicted by a quadratic function and an exponential function (Q₁₀ = 1.67) respectively. Our measurements also showed that the alpine meadow soil (average of ?59.2 ± 3.7 μg CH₄ m^?2 h^?1) uptake less CH₄ than the alpine steppe and produces a similar seasonal pattern, which is negatively regulated by soil moisture. Our measurements quantified – at values far higher than those estimated by process‐based models – that both the alpine steppe and alpine meadow are considerable CH₄ sinks, despite the cold weather of this high‐altitude area. The consecutive measurements gathered in this study also highlight that precipitation seasonality tends to drive the interannual variation in CH₄ uptake, indicating that future study should be done to better characterize how CH₄ cycling might feedback to the more extreme climate.     

Exploitation and mortality rates of European hake (Merluccius merluccius) in the Aegean Sea (Izmir Bay,Turkey)

Experimental trawl surveys in Izmir Bay (Aegean Sea) were taken seasonally between 2007 and 2009. A total of 1353 specimens were sampled ranging from 5.9 cm (1.4 g) to 44.4 cm (670 g). The main size group of Merluccius merluccius was between 14 and 25 cm total length (TL). In total, the mean catch per unit effort (CPUE) for hake by number and weight was 101.4 ± 18.4 ind h^?1 and 10.7 ± 1.5 kg h^?1, respectively. Highest mean CPUE by number and biomass was determined as 257.1 ± 15.1 ind h^?1 and 15.1 ± 4.9 kg h^?1 in summer. Mortality (M, F, Z) ratios of hake were 0.58 year^?1, 1.66 year^?1 and 2.24 year^?1, respectively. Because of the many smaller specimens caught in this study, this seems to indicate that there may be heavy fishing pressures on the hake population; the high exploitation rate (E = 0.74) appears to confirm this conclusion.     

Biomarkers at the microscopic range: ToF-SIMS molecular imaging of Archaea-derived lipids in a microbial mat

Time‐of‐Flight Secondary Ion Mass Spectrometry (ToF‐SIMS) with a bismuth cluster primary ion source was used for analysing microbial lipid biomarkers in 10‐µm‐thick microscopic cryosections of methanotrophic microbial mats from the Black Sea. Without further sample preparation, archaeal isopranyl glycerol di‐ and tetraether core lipids, together with their intact diglycoside (gentiobiosyl‐) derivatives, were simultaneously identified by exact mass determination. Utilizing the imaging capability of ToF‐SIMS, the spatial distributions of these biomarkers were mapped at a lateral resolution of < 5 µm in 500 × 500 µm² areas on the mat sections. Using cluster projectiles in the burst alignment mode, it was possible to reach a lateral resolution of 1 µm on an area of 233 × 233 µm, thus approaching the typical size of microbial cells. The mappings showed different ‘provenances’ within the sections that are distinguished by individual lipid fingerprints, namely (A) the diethers archaeol and hydroxyarchaeol co‐occurring with glycerol dialkyl glycerol tetraethers (GDGT), (B) hydroxyarchaeol and dihydroxyarchaeol, and (C) GDGT and gentiobiosyl‐GDGT. Because ToF‐SIMS is a virtually nondestructive technique affecting only the outermost layers of the sample surface (typically 10–100 nm), it was possible to further examine the studied areas using conventional microscopy, and associate the individual lipid patterns with specific morphological traits. This showed that provenance (B) was frequently associated with irregular, methane‐derived CaCO₃ crystallites, whereas provenance (C) revealed a population of fluorescent, filamentous microorganisms showing the morphology of known methanotrophic ANME‐1 archaea. The direct coupling of imaging mass spectrometry with microscopic techniques reveals interesting perspectives for the in‐situ study of lipids in geobiology, microbial ecology, and organic geochemistry. After further developing protocols for handling different kinds of environmental samples, ToF‐SIMS could be used as a tool to attack many challenging problems in these fields, such as the attribution of biological source(s) to particular biomarkers in question, or the high‐resolution tracking of biogeochemical processes in modern and ancient natural environments.     

Assessment of Nitrification Potential in Ground Water Using Short Term, Single-Well Injection Experiments

Nitrification was measured within a sand and gravel aquifer on Cape Cod, MA, using a series of single-well injection tests. The aquifer contained a wastewater-derived contaminant plume, the core of which was anoxic and contained ammonium. The study was conducted near the downgradient end of the ammonium zone, which was characterized by inversely trending vertical gradients of oxygen (270 to 0 μM) and ammonium (19 to 625 μM) and appeared to be a potentially active zone for nitrification. The tests were conducted by injecting a tracer solution (ambient ground water + added constituents) into selected locations within the gradients using multilevel samplers. After injection, the tracers moved by natural ground water flow and were sampled with time from the injection port. Rates of nitrification were determined from changes in nitrate and nitrite concentration relative to bromide. Initial tests were conducted with ¹⁵N-enriched ammonium; subsequent tests examined the effect of adding ammonium, nitrite, or oxygen above background concentrations and of adding difluoromethane, a nitrification inhibitor. In situ net nitrate production exceeded net nitrite production by 3- to 6- fold and production rates of both decreased in the presence of difluoromethane. Nitrification rates were 0.02–0.28 μmol (L aquifer)⁻¹ h⁻¹ with in situ oxygen concentrations and up to 0.81 μmol (L aquifer)⁻¹ h⁻¹ with non-limiting substrate concentrations. Geochemical considerations indicate that the rates derived from single-well injection tests yielded overestimates of in situ rates, possibly because the injections promoted small-scale mixing within a transport-limited reaction zone. Nonetheless, these tests were useful for characterizing ground water nitrification in situ and for comparing potential rates of activity when the tracer cloud included non-limiting ammonium and oxygen concentrations.     

The effect of benthic sediments on dissolved nutrient concentrations and fluxes

The Ria Formosa is a meso-tidal coastal lagoon experiencing enhanced nutrient concentrations. Assessment of sediment–seawater interaction is essential if nutrient dynamics and the risk of eutrophication are to be fully understood. Pore water concentrations of dissolved inorganic and organic phosphorus, ammonium, nitrate and nitrite were determined in cores from six sites. Changes in nutrients concentrations were measured in intertidal pools on sand and mud between tides. Dissolved inorganic phosphorus (DIP) concentrations (~200 μmol l⁻¹) and effluxes (123 ± 14 μmol m⁻² h⁻¹) were greater from sand than mud (37 ± 10 μmol m⁻² h⁻¹), possibly due to the binding of P with the <63 μm fraction. NH₄⁺ effluxes were high outside the Anc?o Basin (821 ± 106 μmol m⁻² h⁻¹) and were associated with Enteromorpha sp. mats. The greatest NO₃⁻ efflux was from sediments near a salt marsh (170 ± 67 μmol m⁻² h⁻¹). These sediment fluxes of P were not sufficient to account for elevated P concentrations seen by other workers on the ebb tide from the Anc?o Basin. Intertidal pools were sinks for Dissolved Inorganic Nitrogen (DIN) and DIP over the 6 h exposure period. Thus, tidepools may be an important route of nutrients into sediments that enhances the effects of sediments on seawater nutrient concentrations.     

Quantum requirements for growth and fatty acid biosynthesis in the marine diatom Phaeodactylum tricornutum (Bacillariophyceae) in nitrogen replete and limited conditions

We determined the quantum requirements for growth (1/?_μ) and fatty acid (FA) biosynthesis (1/?_FA) in the marine diatom, Phaeodactylum tricornutum, grown in nutrient replete conditions with nitrate or ammonium as nitrogen sources, and under nitrogen limitation, achieved by transferring cells into nitrogen free medium or by inhibiting nitrate assimilation with tungstate. A treatment in which tungstate was supplemented to cells grown with ammonium was also included. In nutrient replete conditions, cells grew exponentially and possessed virtually identical 1/?_μ of 40–44 mol photons · mol C^?1. In parallel, 1/?_FA varied between 380 and 409 mol photons · mol C^?1 in the presence of nitrate, but declined to 348 mol photons · mol C^?1 with ammonium and to 250 mol photons · mol C^?1 with ammonium plus tungstate, indicating an increase in the efficiency of FA biosynthesis relative to cells grown on nitrate of 8% and 35%, respectively. While the molecular mechanism for this effect remains poorly understood, the results unambiguously reveal that cells grown on ammonium are able to direct more reductant to lipids. This analysis suggests that when cells are grown with a reduced nitrogen source, fatty acid biosynthesis can effectively become a sink for excess absorbed light, compensating for the absence of energetically demanding nitrate assimilation reactions. Our data further suggest that optimal lipid production efficiency is achieved when cells are in exponential growth, when nitrate assimilation is inhibited, and ammonium is the sole nitrogen source.