bluuebunny/crossref_metadata_2025 huggingface dataset:
Carbonate chemistry in the coastal zone responds more strongly to eutrophication than ocean acidification
Authors: Borgesa Alberto V. , Gypensb Nathalie
Published: January 2011

The accumulation of anthropogenic CO2 in the ocean has altered carbonate chemistry in surface waters since preindustrial times and is expected to continue to do so in the coming centuries. Changes in carbonate chemistry can modify the rates and fates of marine primary production and calcification. These modifications can in turn lead to feedback on increasing atmospheric CO2. We show, using a numerical model, that in highly productive nearshore coastal marine environments, the effect of eutrophication on carbon cycling can counter the effect of ocean acidification on the carbonate chemistry of surface waters. Also, changes in river nutrient delivery due to management regulation policies can lead to stronger changes in carbonate chemistry than ocean acidification. Whether antagonistic or synergistic, the response of carbonate chemistry to changes of nutrient delivery to the coastal zone (increase or decrease, respectively) is stronger than ocean acidification.
In situ measurements of turbulence in fish shoals
Authors: Lorkea Andreas , Probsta W. Nikolaus
Published: January 2011

Turbulence was measured in situ within shoals of juvenile perch Perca fluviatilis with a self‐contained autonomous microstructure profiler near an artificial reef in Lake Constance, Germany. Depth‐averaged dissipation rates of turbulent kinetic energy (TKE) correlated with the density of shoaling fish, providing evidence for fish‐induced turbulence in a large and stratified lake. The observed range and the depth‐averaged values of TKE dissipation rates associated with fish‐generated turbulence were comparable with magnitudes of turbulence typically caused by internal waves or wind forcing. Enhanced turbulence within fish shoals could only be observed during periods of low background turbulence and high fish abundance. The observed rates of dissipation of TKE are about two orders of magnitude smaller than production rates of TKE estimated from empirical models on the basis of observed fish size and swimming speed.
Molecular evidence for anaerobic ammonium‐oxidizing (anammox) bacteria in continental shelf and slope sediments off northwest Africa
Authors: Jaeschke Andrea , Abbas Ben , Zabel Matthias , Hopmans Ellen C. , Schouten Stefan , Sinninghe Damstéa Jaap S.
Published: January 2011

The presence and abundance of anaerobic ammonium‐oxidizing (anammox) bacteria was investigated in continental shelf and slope sediments (300‐3000 m water depth) off northwest Africa in a combined approach applying quantitative polymerase chain reaction (q‐PCR) analysis of anammox‐specific 16S rRNA genes and anammox‐specific ladderane biomarker lipids. We used the presence of an intact ladderane monoether lipid with a phosphocholine (PC) headgroup as a direct indicator for living anammox bacteria and compared it with the abundance of ladderane core lipids derived from both living and dead bacterial biomass. All investigated sediments contained ladderane lipids, both intact and core lipids, in agreement with the presence of anammoxspecific 16S rRNA gene copies, indicating that anammox occurs at all sites. Concentrations of ladderane core lipids in core top sediments varied between 0.3 and 97 ng g−1 sediment, with the highest concentrations detected at the sites located on the shelf at shallower water depths between 300 and 500 m. In contrast, the C20 [3]‐ ladderane monoether‐PC lipid was most abundant in a core top sediment from 1500 m water depth. Both anammox‐specific 16S rRNA gene copy numbers and the concentration of the C20 [3]‐ladderane monoether‐PC lipid increased downcore in sediments located at greater water depths, showing highest concentrations of 1.2 × 108 copies g−1 sediment and 30 pg g−1 sediment, respectively, at the deepest station of 3000 m water depth. This suggests that the relative abundance of anammox bacteria is higher in sediments at intermediate to deep water depths where carbon mineralization rates are lower but where anammox is probably more important than denitrification.
Resilience of pore‐water chemistry and calcification in photosynthetic zones of calcifying sediments
Authors: Schoon Raphaela , Bissett Andrew , Beer Dirk de
Published: January 2011

Photosynthetically driven calcification was investigated in diatom‐dominated carbonate sediments from Bait Reef, Australia. Laboratory measurements conducted over complete diel cycles, using O2, pH, CO32‐, and Ca2+ microsensors, confirmed that photosynthesis and respiration drive calcification and calcium release via their respective effects on the local pH. However, the dark situation does not simply mirror the light situation. Profiles showed that calcification and calcium release are not necessarily tightly coupled to the light cycle and that mass transfer phenomena need to be considered in diel chemical dynamics. The magnitude and timing of pH and CO2{ 3 concentration changes did not simply follow the light cycle. The pH in the upper 3 mm of the sediment changed more rapidly upon illumination than upon darkening. Consequently, photosynthetically induced calcification began shortly (within 1 h) after illumination, but the pH remained elevated and calcification continued for ~7 h after darkening. Thus, calcification in marine phototrophic sediments is not limited to light periods, but may continue for extended periods after darkening. This decoupling of light, photosynthesis, and calcification has profound consequences for estimates of daily calcification rates, which have previously been made from measurements assuming close to steady states and 12 : 12 h light : dark calcification and decalcification. In Bait Reef sediments, such an assumption underestimates daily calcification rates by two‐ to threefold.
Nitrogen source preference of Aspergillus sydowii, an infective agent associated with aspergillosis of sea fan corals
Authors: Rivest Emily B. , Baker David M. , Rypien Krystal L. , Harvella C. Drew
Published: January 2011

We attempt to identify the mechanism by which nitrogen enrichment increases the prevalence of aspergillosis, a disease caused by the terrestrial fungus Aspergillus sydowii, which infects sea fan corals (Gorgonia ventalina) throughout the Caribbean, by looking at the metabolic capabilities of the pathogen to (1) determine whether A. sydowii can catabolize sea fan‐derived nitrogen, (2) ascertain fungal preference for different nitrogen sources, and (3) determine whether fungi isolated from diseased sea fans preferentially assimilate sea fan‐derived nitrogen. Stable nitrogen isotope experiments demonstrated that A. sydowii is capable of assimilating and prefers sea fan‐ derived nitrogen (72% of available nitrogen) to nitrate and more readily assimilates nitrogen from coral tissue than gorgonin skeleton. Variation in the proportion of sea fan‐derived nitrogen assimilated by different fungal isolates was significant, with those from diseased sea fans showing greater nitrogen assimilation of sea fan tissue.
Isotope enrichment in mangrove forests separates microphytobenthos and detritus as carbon sources for animals
Authors: Oakes Joanne M. , Connolly Rod M. , Revill Andrew T.
Published: January 2011

Microphytobenthos (MPB) and mangrove detritus were labeled with a carbon isotope (13C) in separate experiments to quantify their contributions to the nutrition of major faunal components within a mangrove forest. Within 7 d of MPB labeling, crabs (Parasesarma erythrodactyla and Australoplax tridentata) and foraminifera (Ammonia beccarii and Trochammina inflata) were enriched. A. tridentata became more enriched (e.g., hepatopancreas, 522‰) than P. erythrodactyla (110‰), and A. beccarii (245‰) became more enriched than T. inflata (12‰). Addition of labeled mangrove detritus (‐11.5‰ final enrichment vs. ‐28.8‰ for controls) to sediment resulted in enrichment of P. erythrodactyla (hepatopancreas, ‐21.2‰ vs. ‐26.6‰ for controls), A. tridentata (hepatopancreas, ‐24.2‰ vs. ‐27.1‰) and A. beccarii (‐21.0‰ vs. ‐25.1‰) within 7 d. Compartment modeling showed that MPB contributed 93% of the nutrition for A. tridentata and 33% of the nutrition for P. erythrodactyla and that MPB provided more nutrition to A. beccarii (14%) than to T. inflata (minimal). There was a complementary estimated contribution of mangrove detritus to the diets of P. erythrodactyla (80%), A. beccarii (97%), and A. tridentata (minimal), although these estimates should be viewed with caution, due to low initial enrichment and the apparent short temporal persistence of 13C‐labeled detritus added to sediments. T. inflata was barely enriched in either experiment and may rely on a carbon source not considered. The combination of isotope labeling and compartment modeling is relatively new to ecology and shows potential for revealing differences in the patterns of use of algae and macrophyte detritus by consumers.
Two‐step dialogue between the cladoceran Bosmina and invertebrate predators: Induction and natural selection
Authors: Kerfoot W. Charles , McNaught A. Scott
Published: January 2011

Aquatic prey species respond to predators with fast (developmental) and slow (selective) feedbacks. Natural selection is assumed to fashion details of induction and to modify baseline morphology, but only rarely do we catch the slower (multi‐generation) process in action. Laboratory experiments with Bosmina detected predatormediated induction and estimated spine heritability (h2 5 0.2‐0.5). Third Sister Lake, Michigan, U.S.A., Bosmina exhibited induction to resident (Mesocyclops) and to two nonresident, neighborhood predators (Epischura and Leptodora). However, the magnitude of induction in Third Sister Lake Bosmina to nonresident predators (Epischura, Leptodora) was muted, when compared with induction and final spine lengths in Epischura‐Leptodora lakes. Inadvertent escape of Leptodora into Third Sister Lake in 1987 created a long‐term (multiyear), whole‐lake experiment, where resident Bosmina populations fell under intense size selection. During the interval, Leptodora suppressed a late‐season smaller, short‐featured species (B. freyii), favored seasonal expansion of an overwintering long‐featured species (B. liederi), and selected for longer features in the latter species. Before local extinction, defensive spines of B. liederi achieved lengths comparable to populations that co‐occur with Epischura and Leptodora.
Nitrogen and phosphorus inputs control phytoplankton growth in eutrophic Lake Taihu, China
Authors: Xu Hai , Paerl Hans W. , Qin Boqiang , Zhu Guangwei , Gaoa Guang
Published: January 2011

Lake Taihu (Taihu) is the third largest freshwater lake in China and an important drinking water, fishing, and tourism resource for Jiangsu Province. Recent toxic cyanobacterial blooms caused by excessive human nutrient loading have focused attention on arresting blooms and restoring the lake to acceptable water quality conditions by reducing nutrient inputs. Field sampling and in situ nutrient enrichment bioassays were conducted to determine seasonal patterns of nutrient limitation and nutrient thresholds for phytoplankton growth. The TN: TP and TDN:TDP mass ratios in the ambient water showed high seasonal variation and changed from 33‐80 : 1 and 52‐212 : 1, respectively, in winter and spring, and both declined to below 20 : 1 in summer. In spring and winter, total phytoplankton biomass and growth rates increased significantly with additions of P, with no primary effects from N, suggesting P limitation of phytoplankton growth. During the summer and fall bloom periods, however, N additions alone revealed a significant positive effect on phytoplankton growth, and P additions only stimulated phytoplankton growth once N had been added, suggesting that N was the primary limiting nutrient, with P being a secondarily limiting nutrient. When P enrichment was ≤ 0.20 mg P L−1 and N enrichment ≤0.80 mg N L−1, growth of the toxin‐producing, dominant bloom‐forming cyanobacteria Microcystis spp. was not nutrient limited. This study suggests that availability of N during the summer is a key growth‐limiting factor for the proliferation and maintenance of toxic Microcystis spp. blooms. Therefore, although P load reduction is important, N load reduction is essential for controlling the magnitude and duration of algal booms in Taihu.
General empirical models for estimating nutrient load limits for Florida's estuaries and inland waters
Authors: Steward Joel S. , Lowe Edgar F.
Published: January 2011

We developed empirical models that can predict maximum allowable, nutrient loading rates or load limits (LM) for maintenance of mesotrophy in Florida’s fresh and estuarine waters. Water residence time (tw) explains most of the variation in LM previously set by the U.S. Environmental Protection Agency and Florida’s environmental agencies for total phosphorus (TP) and for total nitrogen (TN). We found that a single model for TP and for TN fit data from both estuarine and freshwater systems. Further, we show that the models are consistent with or analogous to the critical loading model of the Organization of Economic Cooperation and Development (OECD 1982): Lc = [TP or TN]c x z/Τw(1 + Τw0.5). The LM ‐ Τw model for TP is sufficiently similar to the OECD model as to indicate that either model could provide a reasonable fit to mesotrophy in both temperate and subtropical systems. The models can facilitate the development of total maximum daily loads for estuaries and inland waters of Florida and may have broader regional utility. They may also aid the development of nutrient concentration criteria.
Production of chromophoric dissolved organic matter by marine phytoplankton
Authors: Castillo Cristina Romera , Sarmento Hugo , Álvarez-Salgado Xosé Antón , Gasol Josep M. , Marraséa Celia
Published: January 2011

Incubation experiments with axenic cultures of four common phytoplankton species of the genera Chaetoceros, Skeletonema, Prorocentrum, and Micromonas were performed to test for the production of fluorescent dissolved organic matter (FDOM) by marine phytoplankton. Our results prove that the four species exuded both fluorescent protein‐like and marine humic‐like materials in variable amounts, with more production by the diatoms Chaetoceros sp. and Skeletonema costatum and less by Prorocentrum minimum. Whereas the exudation of protein‐like substances by healthy phytoplankton cells has been recognized, the in situ production of marine humic‐like substances is still a matter of debate. Using axenic cultures, we demonstrate unequivocally that phytoplankton can directly contribute to the autochthonous production of colored humic‐like substances in the ocean. Extrapolation of these findings to the field indicates that about 20% of the marine humic‐like substances produced in the highly productive coastal upwelling system of the Ria de Vigo could originate from growing phytoplankton. Therefore, the exudation of FDOM by marine phytoplankton should be considered in future studies of the dynamics of colored DOM in marine systems.
Anthropogenic eutrophication shapes the past and present taxonomic composition of hybridizing Daphnia in unproductive lakes
Authors: Rellstab Christian , Keller Barbara , Girardclos Stèphanie , Anselmetti Flavio S. , Spaak Piet
Published: January 2011

It has been proposed that anthropogenic eutrophication of lakes facilitated the establishment of populations of the cladoceran Daphnia galeata into the originally oligotrophic lakes north of the European Alps in the 1960s. This hypothesis lacks the support of studies on unproductive lakes, in which the past eutrophication is assumed to have never been on the level necessary for D. galeata to reach high abundances and to establish permanently. In order to investigate if such species shifts also happened in unproductive systems, we studied the past and present taxonomic composition of three ultra‐oligotrophic Swiss lakes that were only marginally affected by eutrophication using molecular methods on diapausing eggs sampled from sediment cores. D. galeata temporarily established in unproductive lakes, but its colonization success seemed to depend on the general trophic state of the lake and the magnitude of eutrophication. In two of the studied lakes, D. galeata could establish a significant population size, whereas it was not successful in the most unproductive lake with the weakest eutrophication. Even in unproductive lakes, eutrophication led to partly irreversible species changes, providing evidence that this anthropogenic disturbance is responsible for species shifts in many pre‐alpine lakes in Central Europe.
Seasonal variability of the inorganic carbon system in the Amundsen Gulf region of the southeastern Beaufort Sea
Authors: Shadwick E. H. , Thomas H. , Chierici M. , Else B. , Fransson A. , Michel C. , Miller L. A. , Mucci A. , Niemi A. , Papakyriakou T. N. , Tremblay J.-É.
Published: January 2011

During a year‐round occupation of Amundsen Gulf in the Canadian Arctic Archipelago dissolved inorganic and organic carbon (DIC, DOC), total alkalinity (TA), partial pressure of CO2 (pCO2) and related parameters were measured over a full annual cycle. A two‐box model was used to identify and assess physical, biological, and chemical processes responsible for the seasonal variability of DIC, DOC, TA, and pCO2. Surface waters were undersaturated with respect to atmospheric CO2 throughout the year and constituted a net sink of 1.2 mol C m−2 yr−1, with ice coverage and ice formation limiting the CO2 uptake during winter. CO2 uptake was largely driven by under ice and open‐water biological activity, with high subsequent export of organic matter to the deeper water column. Annual net community production (NCP) was 2.1 mol C m−2 yr−1. Approximately one‐half of the overall NCP during the productive season (4.1 mol C m−2 from Apr through Aug) was generated by under‐ice algae and amounted to 1.9 mol C m−2 over this period. The surface layer was autotrophic, while the overall heterotrophy of the system was fueled by either sedimentary or lateral inputs of organic matter.
Phosphate and adenosine‐5'‐triphosphate uptake by cyanobacteria and heterotrophic bacteria in the Sargasso Sea
Authors: Michelou Vanessa K. , Lomas Michael W. , Kirchman David L.
Published: January 2011

We used flow cytometry sorting to quantify assimilation of phosphate and adenosine‐59‐triphosphate (ATP) by heterotrophic bacteria and the cyanobacteria Prochlorococcus and Synechococcus during the fall of 2007 and 2008 and the spring of 2009 in the western Sargasso Sea. Phosphate and ATP uptake rates per cell were 50‐fold and 80‐fold higher, respectively, for Synechococcus than for the other two microbial groups, whereas there was no significant difference between ATP and phosphate uptake per cell by Prochlorococcus and heterotrophic bacteria. Both cyanobacterial groups had higher rates of phosphate uptake per surface area than did the heterotrophic bacteria; Synechococcus had the highest rates per cellular phosphorus (P)‐quota for ATP uptake, and Prochlorococcus usually had lower rates. Heterotrophic bacteria had the lowest uptake rates of ATP and phosphate per cellular P quota. In contrast, total uptake of phosphate and ATP per liter of seawater was dominated by heterotrophic bacteria, while uptake by Prochlorococcus and Synechococcus was less than 10% of the total, as a result of their low abundance (15% and 1.5% of total prokaryotes, respectively). Uptake rates of phosphate and ATP for heterotrophic bacteria and Prochlorococcus were less tightly coupled than for Synechococcus, and phosphate appeared to be favored over ATP for all three groups. Uptake rates of both compounds by Synechococcus were much higher than by the other microbial groups. Cyanobacteria are successful competitors for phosphate and ATP in the Sargasso Sea.
Degradation of particulate organic matter in the equatorial Pacific Ocean: Biotic or abiotic?
Authors: Rontani J.-F. , Zabeti N. , Wakeham S. G.
Published: January 2011

The behavior of organic matter (OM) in suspended and sinking particles in the equatorial Pacific Ocean was monitored by measuring lipid degradation products that are specific for biodegradation, photooxidation, and autoxidation. Photodegradation and autoxidation were significant for lipids associated with both suspended and sinking particles. Abiotically degraded terrestrial material strongly contributed to suspended particles and to sinking material in the deep ocean, probably as the result of incorporation of terrestrial particles into sinking aggregates. Analyses of degradation products of 24‐methylcholesta‐5,22‐dien‐3β‐ol, 24‐ethylcholest‐5‐en‐3β‐ol, and cholest‐5‐en‐3β‐ol gave diagnostic information concerning the differential behavior of phytoplanktonic, terrestrial, and zooplanktonic OM, respectively. Planktonic lipids were more susceptible to biodegradation than terrestrial lipids and biodegradation was more intense in sinking particulate organic matter (POM) than suspended POM, which we attribute to efficient transfer of singlet oxygen from suspended and senescent phytoplankton cells to associated bacteria and subsequent inhibition of heterotrophic degradation. There is a direct link between the photooxidation state of lipids of senescent phytoplankton cells in suspended particles and the apparent resistance of lipids toward biotic degradation. Terrigenous vascular plant OM, which is strongly autoxidized on land or in the atmosphere as it is transported to the remote ocean, is only weakly biodegraded during sedimentation in this open ocean setting. A significant increase in alkenone‐based UK′37 values (+0.07 equivalent to an inferred temperature change of +2°C) was observed in sinking particles with depth and the detection of epoxyalkenones further confirming the potential detrimental effect of aerobic bacterial degradation processes on the UK′37 paleotemperature proxy.
Does the Pareto distribution adequately describe the size‐distribution of lakes?
Authors: Seekell David A. , Pace Michael L.
Published: January 2011

When it comes to evaluating lakes at regional and global scales, a key need is accurate estimates of the abundance and size‐distribution of lakes, which are usually described with the Pareto distribution. We demonstrate the considerable uncertainty that truncation in the lower tail of the Pareto distribution introduces into lake abundance estimates and the selection of the lake size‐distribution. Truncation in the lower tail eliminates lakes below a certain size and is generally performed because small lakes are not accurately represented on maps. When simulated data are truncated to mimic available lake size data, non‐Pareto distributions are visually and statistically indistinguishable from the Pareto distribution. The Pareto distribution may be one of many possible forms that mimic the global lake size‐distribution in the upper tail, but the fit of the Pareto to the lower tail is uncertain, largely because the abundance of small lakes is uncertain. Some other potential size‐distributions, such as the lognormal distribution, predict abundances of small lakes to be orders of magnitude lower than do the Pareto distribution predictions. Highly resolved regional lake size data for the Adirondack Mountains of New York and the Northern Highland Lake District of Wisconsin do not conform to the Pareto distribution. Lake sizes on Mars also do not conform to the Pareto. Uncertainty in the lake size‐distribution seriously limits understanding of the significance of lakes as repositories of organic carbon as well as the calculation of global greenhouse gas emissions from these systems.
Photoacclimation of the seagrass Halophila stipulacea to the dim irradiance at its 48‐meter depth limit
Authors: Sharon Yoni , Levitan Orly , Spungin Dina , Berman-Frank Ilana , Beer Sven
Published: January 2011

The seagrass Halophila stipulacea grows in the northern Red Sea from the intertidal to depths of ~ 50 m. Along that gradient, there is a > 1 order of magnitude difference in irradiance and the spectrum narrows from that of full sunlight to dim blue‐green light. Based on these differences, we set out to estimate the molar ratios and potential contributions of photosystem II (PSII) and photosystem I (PSI) to light absorption, and photosynthetic electron transport rates (ETR), in plants growing at 1‐m and 48‐m depths. The amount of PsaC (a proxy for PSI) was three times higher in the deep‐growing plants. On the other hand, the amount of PsbA (a proxy for PSII) did not differ significantly between the two depths. Thus, the PSII : (PSII + PSI) ratio (FII) was 0.62 in the shallow and 0.41 in the deep‐growing plants. Similar results were obtained by 77K emission fluorescence. Because ETR is linearly dependent on FII, it follows that the ETR vs. irradiance curves differed significantly if calculated based on the commonly used FII value of 0.5 or the FII values we found. As a result, the photosynthetic parameters ETRmax and α also differed when using the different FII values. Correct(ed) FII values should, therefore, be used in the calculation of photosynthetic ETRs. The ability of H. stipulacea to alter its amount of PSI relative to PSII according to the ambient irradiance and spectrum may be one reason why this organism can grow down to its exceptional depth limit in clear tropical waters.
Mechanisms for copepod resting egg accumulation in seagrass sediments
Authors: Scheef Lindsay P. , Marcus Nancy H.
Published: January 2011

We identify several mechanisms by which seagrass presence can enhance the retention and benthic abundance of copepod eggs on a shallow reef in Florida: (1) benthic macrofauna are more abundant in seagrass patches than in bare sediment and bioturbation by these animals may contribute to egg retention through burial; (2) the physical presence of the seagrass canopy inhibits the resuspension of fine particles and thereby promotes egg accumulation; (3) the persistent low oxygen conditions at the sediment surface sustained in seagrass patches during warm summer months promote egg retention by inhibiting the hatch of newly settled eggs. Understanding how these factors contribute to copepod egg accumulation in the seagrass beds of other areas could give valuable insights into how seagrass presence may influence local copepod populations.
Avoidance, movement, and mortality: The interactions between a protistan grazer and Heterosigma akashiwo, a harmful algal bloom species
Authors: Harvey Elizabeth L. , Menden-Deuer Susanne
Published: January 2011

A reduction in predator‐induced grazing pressure may be a mechanism that facilitates the formation and persistence of harmful algal blooms. Here, the hypothesis was tested that the heterotrophic ciliate Favella ehrenbergii would use avoidance behaviors to reduce encounters with the toxic bloom‐forming alga, Heterosigma akashiwo. Using video and image‐analysis, population distributions and three‐dimensional movements of F. ehrenbergii and H. akashiwo were quantified in triplicate, hourly for 11 h, at nine horizons in a 1‐liter experimental column. The salinity structure in the column was manipulated to include a halocline, resulting in layer formation by H. akashiwo. The ciliate's vertical distributions were restricted to high‐salinity waters below the halocline, while H. akashiwo was broadly halo‐tolerant and could occupy the whole water column. When observed together, F. ehrenbergii did not avoid layers of H. akashiwo. In the presence of H. akashiwo, F. ehrenbergii mortality rates were higher than in either no prey or beneficial prey controls. Swimming behaviors of F. ehrenbergii were erratic, in response to H. akashiwo, compared to aggregative movements in response to beneficial prey, indicating either a behavioral response or the effect of H. akashiwo toxicity on the ciliate. The inability of F. ehrenbergii to avoid H. akashiwo enhanced predator mortality and may contribute to the survival of the harmful algal bloom species, ultimately promoting the formation of H. akashiwo harmful algal blooms.
Active pockmarks in a large lake (Lake Constance, Germany): Effects on methane distribution and turnover in the sediment
Authors: Bussmann Ingeborg , Schlömer Stefan , Schlüter Michael , Wessels Martin
Published: January 2011

In the eastern part of Lake Constance, the second largest prealpine lake in Europe, about 500 pockmarks (morphological depressions on the lake floor) were recently discovered. The diameters of these pockmarks are as large as 16 m, and about 24% of them continuously release methane in the form of visible bubbles. The isotopic composition of the escaping gas indicated that the methane was of biogenic origin and was predominantly produced by the CO2‐reduction pathway. In shallow‐water pockmarks (9 m and 12 m), pore‐water analysis revealed increased methane concentrations of > 1100 µmol L−1 in the sediment. Diffusive methane fluxes and oxidation rates within these shallow pockmarks were much higher than in sediments outside pockmarks. An estimated methane ebullition into the water column of about 40 L h−1 per pockmark showed that methane ebullition is by far the dominant pathway of methane release from these shallow pockmarks. Meiofauna abundance and organic carbon contents of the sediment were also higher in the shallow pockmarks, but there were no differences in macrofauna. In a deep pockmark (80 m), even though bubble release was observed, the sediment inside the pockmark had almost the same methane concentrations and isotopic compositions as a site outside of the pockmark. At both sites, the shallow and deep pockmark act mainly as sedimentation traps, the emanating gas has only minor influence on the methane inventory of the sediments and, therefore, gas bubbles enter the water column essentially unaffected.
Direct measurements of root growth and productivity in the seagrasses Posidonia australis and P. sinuosa
Authors: Hovey Renae K. , Cambridge Marion L. , Kendrick Gary A.
Published: January 2011

The effects of nutrients and planting season on root growth were investigated in transplants of the seagrasses Posidonia australis and P. sinuosa. Difficulties with sampling and estimating root growth of these submerged plants were overcome by growing transplants, with all roots removed initially, in pots containing a standardized sand medium. Nitrogen (N), phosphorus (P), and nitrogen and phosphorus combined (N + P) were added to pots. Root elongation and productivity were measured after harvesting at 1 month, 4 months, and 6 months in consecutive experiments beginning in autumn and spring. Roots formed within a month, growing into extensive root systems. Posidonia australis root growth was three‐fold less over winter (10 mm d−1 per plant) than summer (33 mm d21 per plant), with some plants producing up to 9 m of roots in 6 months. Posidonia sinuosa root‐growth rates were significantly lower than those of P. australis and did not vary between winter and summer (6 mm d−1 per plant). Root productivity was lower with N and N + P addition for P. sinuosa and with N addition for P. australis in summer. In contrast, P addition had little effect on root growth, reducing only primary root growth in P. australis. Addition of nutrients did not result in the expected increases in fine roots in the zone around the nutrient source. This technique for measuring root growth demonstrated the potential of these Posidonia transplants to produce extensive root systems within months of planting, in contrast to the much slower growth of roots in mature seagrass meadows.
Metabolic rates and carbon budget of early developmental stages of the marine cyclopoid copepod Oithona davisae
Authors: Almeda Rodrigo , Alcaraz Miquel , Calbet Albert , Saiz Enric
Published: January 2011

The genus Oithona has been considered the most abundant and ubiquitous copepod in the world's oceans. However, despite its importance, the metabolism of its developmental stages (nauplii and copepodites), crucial to explain their evolutionary success, is almost unknown. We determined respiration rates, ammonium and phosphate excretion rates, and the net growth efficiencies of early developmental stages of Oithona davisae as related to stage, body weight, temperature, and food availability. Respiration and excretion rates increased with increasing body weight and were positively related to temperature and food. Specific respiration rates of nauplii and copepodites varied from 0.11 to 0.55 d−1 depending on stage, body weight, temperature, and food availability. Metabolic C:N ratios were higher than 14, indicating lipid‐oriented metabolism. Assimilation efficiencies and net growth efficiencies ranged from 65% to 86% and from 23% to 32%, respectively, depending on body weight, stage, and temperature. Assimilation efficiencies and net growth efficiencies estimated using the respiration rates of nauplii with food were 1.7 times higher and 0.6 times lower, respectively, than those calculated using respiration rates of nauplii without food. Therefore, the use of respiration rates measured in filtered seawater led to substantial bias on the estimations of zooplankton carbon budget. O. davisae developmental stages exhibited similar assimilation and growth efficiencies but lower carbon‐specific respiratory losses than calanoid copepods. Hence, the low metabolic costs of Oithona compared with calanoids may be one reason for their success in marine ecosystems.
Trophic role and carbon budget of metazoan microplankton in northwest Mediterranean coastal waters
Authors: Almeda Rodrigo , Calbet Albert , Alcaraz Miquel , Saiz Enric , Trepat Isabel , Arin Laura , Movilla Juancho , Saló Violeta
Published: January 2011

We determined the feeding rates, trophic effect, and growth efficiencies of natural assemblages of metazoan microplankton from a coastal site in the northwest (NW) Mediterranean over a seasonal cycle in laboratory incubations. Micrometazoans, i.e., multicellular heterotrophic plankters between 20 and 200 µm, were mainly constituted by invertebrate larval stages. Copepod nauplii and copepodites dominated the community, except in April, when polychaete larvae dominated. We analyzed the grazing pressure of micrometazoans on chlorophyll a (Chl a; total and > 10 µm), nanoflagellates, phototrophic nanoflagellates, dinoflagellates, diatoms, and ciliates. Micrometazoans grazed on all the prey groups, with carbon‐specific ingestion rates ranging from 0.31 to 1.24 d−1. The gross growth efficiencies for the entire metazoan microplankton community, calculated as the slope of the linear regression relating specific growth rates vs. specific ingestion rates, varied between 0.27 and 0.39. The respiratory carbon losses of micrometazoans depended on temperature and ranged from 0.16 to 0.36 d−1, with a Q10 = 2. The average net growth efficiency, 0.41, was independent of temperature and food availability. Overall micrometazoans have higher specific growth rates than, but similar food conversion efficiencies to, mesozooplankton. The grazing effect on the standing stock of the different prey was < 1% d−1 for Chl a (total and > 10 µm) and < 2.5% d−1 for the other studied prey, which seems insufficient to exert relevant control on phytoplankton and protozoan dynamics. The inclusion of micrometazoans did not change appreciably our current view of the role of metazooplankton in marine trophic webs of NW Mediterranean coastal waters.
Nonlinear electrostatic ion-acoustic "oscilliton" waves driven by charge non-neutrality effects
Authors: Ma J. Z. G. , Hirose A. , -Maurice J.-P. St. , Liu W.
Published: January 2011

Abstract. Nonlinear "oscilliton" structures features a low-frequency (LF) solitary envelope, the amplitude of which is modulated violently by superimposed high-frequency (HF) oscillations. We have studied the charge non-neutrality effects on the excitation of electrostatic ion-acoustic (IA) oscillitons. A two-fluid, warm plasma model is employed, and a set of nonlinear self-similar equations is solved in a cylindrical geometry. Under charge-neutrality conditions, three conventional IA structures (namely, sinusoidal, sawtooth, and spicky/bipolar) are obtained. By contrast, under charge non-neutrality conditions, oscilliton structures are excited, where the LF envelope is in the sound-wave (SW) mode, while the HF ingredients include the IA mode and the ion-Langmiur (IL) mode. The amplitudes of the SW wave are violently modulated by the IA oscillations, whereas the upward sides of the IA amplitudes are modulated by the IL oscillations of smaller amplitudes, and the downward sides are modulated by hybrid IA/IL oscillations. The nonlinear oscillitons are found to be dependent not only upon the input parameters (e.g., the Mach number, the Debye length, and the initial temperature of particles), but on initial conditions as well.
A Molecular Dynamic Analysis of Gelatin as an Amorphous Material: Prediction of Mechanical Properties of Gelatin Systems
Authors: Zaupa Alessandro , Neffe Axel T. , Pierce Benjamin F. , Lendlein Andreas , Hofmann Dieter
Published: January 2011

Biomaterials are used in regenerative medicine for induced autoregeneration and tissue engineering. This is often challenging, however, due to difficulties in tailoring and controlling the respective material properties. Since functionalization is expected to offer better control, in this study gelatin chains were modified with physically interacting groups based on tyrosine with the aim of causing the formation of physical crosslinks. This method permits application-specific properties like swelling and better tailoring of mechanical properties. The design of the crosslink strategy was supported by molecular dynamic (MD) simulations of amorphous bulk models for gelatin and functionalized gelatins at different water contents (0.8 and 25 wt.-%). The results permitted predictions to be formulated about the expected crosslink density and its influence on equilibrium swelling behavior and on elastic material properties. The models of pure gelatin were used to validate the strategy by comparison between simulated and experimental data such as density, backbone conformation angle distribution, and X-ray scattering spectra. A key result of the simulations was the prediction that increasing the number of aromatic functions attached to the gelatin chain leads to an increase in the number of physical netpoints observed in the simulated bulk packing models. By comparison with the Flory-Rehner model, this suggested reduced equilibrium swelling of the functionalized materials in water, a prediction that was subsequently confirmed by our experimental work. The reduction and control of the equilibrium degree of swelling in water is a key criterion for the applicability of functionalized gelatins when used, for example, as matrices for induced autoregeneration of tissues.
Conditional Depletion of Nuclear Proteins by the Anchor Away System
Authors: Fan Xiaochun , Geisberg Joseph V. , Wong Koon Ho , Jin Yi
Published: January 2011

Nuclear proteins play key roles in the regulation of many important cellular processes. In Saccharomyces cerevisiae, many genes encoding nuclear proteins are essential. This unit describes a method termed Anchor Away that can be used to conditionally and rapidly deplete nuclear proteins of interest. It involves conditional export of the protein of interest out of the nucleus and its subsequent sequestration in the cytoplasm. This method can be used to simultaneously deplete multiple proteins from the nucleus. Curr. Protoc. Mol. Biol. 93:13.10B.1‐13.10B.8. © 2011 by John Wiley & Sons, Inc.
Quantification of Gene Transcripts with Deep Sequencing Analysis of Gene Expression (DSAGE) Using 1 to 2 µg Total RNA
Authors: C. Christodoulou Danos , Gorham Joshua M. , Kawana Masataka , DePalma Steven R. , Herman Daniel S. , Wakimoto Hiroko
Published: January 2011

Deep sequencing analysis of gene expression (DSAGE) measures global gene transcript levels from only 1 to 2 µg total RNA by massively parallel sequencing of cDNA tags. This unit describes the construction of 21‐bp cDNA tag libraries appropriate for massively parallel sequencing and analysis of the resulting sequence data. The adapter oligonucleotides used are optimized for sequencing with current Illumina massively parallel sequencers, and a step‐by‐step implementation of the analysis protocol is described. The expression profiles obtained are highly reproducible, enabling sensitive detection of differences between experimental conditions as well as assessment of the relative transcript abundance of different genes. Curr. Protoc. Mol. Biol. 93:25B.9.1‐25B.9.16. © 2011 by John Wiley & Sons, Inc.
Parallel High‐Throughput Automated Assays to Measure Cell Growth and Beta‐Galactosidase Reporter Gene Expression in the Yeast Saccharomyces cerevisiae
Authors: Napper Andrew D. , Motlekar Nuzhat , de Almeida Rogerio Alves , Pavitt Graham D.
Published: January 2011

Parallel high‐throughput automated assays are described for the measurement of cell growth and β‐galactosidase reporter gene expression from a single culture of the yeast S. cerevisiae. The dual assay measures the effect of test compounds on expression of a specific gene of interest linked to the β‐galactosidase reporter gene, and simultaneously tests for compound toxicity and other effects on cell growth. Examples of assay development and validation results are used to illustrate how this protocol may be used to screen two yeast cell lines in parallel. Yeast cells are grown overnight in V‐bottom polypropylene 384‐well plates, after which portions of the cell suspension are transferred to clear and to white flat‐bottom 384‐well plates for measurement of cell growth and reporter gene expression, respectively. Cell growth is determined by measurement of absorbance at 595 nm, and β‐galactosidase expression is quantified by Beta‐Glo, a commercially available luminescent β‐galactosidase substrate. Curr. Protoc. Chem. Biol. 3:1‐14 © 2011 by John Wiley & Sons, Inc.
The neuropsychological correlates of cognitive insight in healthy participants
Authors: Orfei Maria Donata , Caltagirone Carlo , Cacciari Claudia , Assogna Francesca , Spalletta Gianfranco
Published: January 2011

Cognitive insight is the ability to monitor and correct one's own erroneous convictions. The Beck Cognitive Insight Scale (BCIS) assesses two sub‐dimensions of cognitive insight: self‐reflectiveness (SR), which is the attitude of questioning one's own judgments; and self‐certainty (SC), which is the unwillingness to modify and correct one's own convictions. There is little information about cognitive insight in healthy participants (HP). Here we investigated the socio‐demographic and neuropsychological correlates of cognitive insight in 50 HP who were administered the BCIS and a comprehensive neuropsychological battery. The global BCIS R‐C index correlated positively with age and WCST perseverative errors. SR correlated positively with age. These data support the hypothesis that a less self‐reflective and more self‐confident style is cognitively functional in HP. Thus, what has been found malfunctioning in mental illnesses is adaptive in HP. Future studies should consider a wider range of factors that might affect this complex construct. Copyright © 2011 John Wiley & Sons, Ltd.
Use of B‐type natriuretic peptide as a screening tool for left ventricular diastolic dysfunction in rheumatoid arthritis patients without clinical cardiovascular disease
Authors: Crowson Cynthia S. , Myasoedova Elena , Davis John M. , Roger Veronique L. , Karon Barry L. , Borgeson Daniel , Rodeheffer Richard J. , Therneau Terry M. , Gabriel Sherine E.
Published: January 2011

Objective

Patients with rheumatoid arthritis (RA) are at an increased risk for heart failure and left ventricular diastolic dysfunction (LVDD). B‐type natriuretic peptide (BNP) may be useful to screen for LVDD in the general population. We compared the effectiveness of BNP as a screening tool for LVDD in RA and non‐RA subjects without cardiovascular disease (CVD).

Methods

Study subjects were recruited from population‐based samples with and without RA, excluding subjects with CVD. LVDD was assessed by 2‐dimensional and Doppler echocardiography and categorized as none, mild, moderate/severe, or indeterminate. Linear regression and proportional odds models evaluated the association between LVDD and BNP, adjusting for age, sex, and body mass index.

Results

Among 231 RA and 1,730 non‐RA subjects without CVD, BNP was significantly higher in subjects with moderate/severe LVDD compared to those with no or mild LVDD (P = 0.02 for RA and P < 0.001 for non‐RA subjects). More RA subjects had elevated BNP than non‐RA subjects (16% versus 9%; P < 0.001). Positive predictive value (25% in RA and 18% in non‐RA subjects) and sensitivity (40% in RA and 26% in non‐RA subjects) were similarly low in both cohorts, but specificity was significantly lower in RA than in non‐RA subjects (89% versus 94%; P = 0.02).

Conclusion

While RA subjects were more likely to have elevated BNP, few RA patients with elevated BNP actually have LVDD. Also, normal BNP levels are less likely to rule out LVDD in RA than in non‐RA subjects. Therefore, BNP may be less effective for screening in RA subjects compared to the general population.
Cardiovascular and disease‐related predictors of depression in systemic lupus erythematosus
Authors: Julian Laura J. , Tonner Chris , Yelin Ed , Yazdany Jinoos , Trupin Laura , Criswell Lindsey A. , Katz Patricia P.
Published: January 2011

Objective

Depression and cardiovascular disease are common and debilitating comorbidities associated with systemic lupus erythematosus (SLE). In this study, history of cardiovascular events, cardiovascular risk factors, and SLE disease‐related factors were evaluated as longitudinal predictors of depression in a large cohort of patients with SLE.

Methods

Data were derived from 663 adult participants in the 2004–2008 Lupus Outcomes Study, who were followed for up to 5 annual interviews. Multivariate logistic regression analyses using generalized estimating equations were used to determine predictors of the development of increased depressive symptom severity over a 12‐month period (Center for Epidemiologic Studies Depression Scale [CES‐D] score of 23 or greater), yielding 2,224 paired observations. Predictors included sociodemographics, traditional cardiovascular risk factors (reported presence of heart disease, history of stroke or myocardial infarction, hypertension, hypercholesterolemia, diabetes mellitus, obesity, smoking status, and family history), and SLE‐specific risk factors (glucocorticoid use, renal involvement, disease duration, and disease activity).

Results

The annual incidence of depression was 12% in this cohort. Multivariate predictors of new‐onset depression included younger age (ages 20–39 years: odds ratio [OR] 2.3, 95% confidence interval [95% CI] 1.3–3.9; ages 40–59 years: OR 1.8, 95% CI 1.1–2.7), Hispanic/Latino ethnicity (OR 1.8, 95% CI 1.2–2.8), having some college education (OR 1.8, 95% CI 1.1–3.0), baseline CES‐D score (OR per point 1.1, 95% CI 1.1–1.2), presence of diabetes mellitus (OR 1.8, 95% CI 1.1–2.8), and baseline SLE disease activity (OR 1.2, 95% CI 1.1–1.4).

Conclusion

These results suggest that, in addition to known sociodemographic factors, the presence of diabetes mellitus and SLE disease activity may play a role in the development of depression in SLE.