Evolution of shallow benthic communities during the Late Paleocene–earliest Eocene transition in the Northern Tethys (SW Slovenia)

A paleoecological and sedimentological study was carried out on shallow-water carbonates of the Kras Plateau (SW Slovenia) with the goal of reconstructing paleoenvironmental conditions and evolution of foraminiferal communities on the northwestern Adriatic Carbonate Platform (AdCP) during the Late Paleocene–earliest Eocene. Three facies have been recognized and summarized in a carbonate ramp model. Within these facies, six foraminiferal assemblages, representing different ramp sub-environments, have been defined: during the Late Paleocene sedimentation took place in a protected innermost ramp with (1) smaller miliolids- and (2) small benthic foraminifera-dominated assemblages thriving on partly vegetated, soft substrates. In the Uppermost Paleocene, sedimentation primarily occurred along a mid ramp. The upper mid-ramp was sporadically influenced by storms/currents and occupied by (3) Assilina-dominated assemblage occurring on a soft sandy substrate. The deeper mid-ramp was characterized by (4) ‘bioconstructors’- and (5) orthophragminids-dominated assemblages, colonizing biotopes with substrates of different nature. During the earliest Eocene, deposition occurred in an inner-ramp setting with (6) alveolinids-nummulitids assemblage thriving on muddy and sandy substrate, partly covered or close to seagrass beds. The Late Paleocene–earliest Eocene environmental conditions, coupled with the long-term evolution of larger benthic foraminifera (LBF), seem to have favored this low-light dependent group as common sediment contributors. By comparing the evolution of the shallow-water biota from the Adriatic area with data from the Pyrenees and Egypt, a general latitudinal trend can be recognized. However, on a smaller geographical scale, local conditions are likely to have played a pivotal role in promoting the evolution of biota characterized by suites of unique features.     

Effects of benthic filamentous algae on the sediment–water interface in an acidic mining lake

Natural alkalinity generation by microbial sulphate reduction in acidic lakes is usually inhibited by the low pH and a low primary production which results in a lack of suitable organic carbon sources. In some acidic mining lakes mass developments of filamentous benthic algae occur. The effects of this periphyton layer on the biogeochemistry of the sediment–water interface were investigated by in situ microsensor measurements and laboratory incubations in Mining Lake Grünewalder Lauch (Germany). Microsensor measurements showed that the oxic–anoxic boundary was located in the periphyton layer and was moving up and down depending on light triggered photosynthesis. The sediment itself was permanently anoxic. The diurnal redox shift and the maintenance of neutral conditions in the periphyton layer lead to an effective precipitation of iron and phosphorus. Under the periphyton layer very high sulphate reduction rates up to 265 nmol cm⁻³ d⁻¹ were measured in the sediment. These are the highest rates reported for mining lakes so far. The microbial activity was high enough to keep the pH in the surface sediment neutral and contributed to natural alkalinity production. Handling editor: L. Naselli-Flores     

Changes in the species composition of benthic macroalgal communities of the upper subtidal zone on a coral reef in Sanya Bay (Hainan Island, China) during 2009–2012

Investigations of macroalgae were carried out on a coral reef at the Luhuitou Peninsula in Sanya Bay (Hainan Island, China) in the upper subtidal zone at a depth of 0.5 to 4 m during the dry season (in April 2009 and 2012). In total, 130 species, varieties, and forms of marine macroalgae were found: 71 (54%) Rhodophyta, 33 (25%) Chlorophyta, and 26 (21%) Phaeophyceae. In terms of the number of species and the floristic composition of algae in the communities, the reef benthic flora in the subtidal zone of Sanya Bay, which is polluted by municipal waste waters and aquaculture wastes, was close to the flora of Indo-Pacific coral reefs situated in areas with low pollution. In 2009 and 2012, the algal turf communities differed both in the algal species diversity and in the composition of dominant species. These differences might be due to an annual periodicity of changes in vegetation: algal turf patches are detached from the hard substrate and a new algal community is formed at this location.     

Biomass and primary production of Cladophora glomerata (L.) Kütz. in the Neva Estuary

The dynamics of the biomass, primary production, and P/B ratio of floating and attached forms of green filamentous alga Cladophora glomerata (L.) Kütz. was studied for the shallow water littoral area of the Neva Estuary in 2003–2006. The biomass of the floating algae constituted up to 70% of the total biomass, and the primary production reached up to 90% of the total for the depths of 0–1 m from the middle of July to the end of August.     

Seasonal dynamics of benthic macroinvertebrate communities in the Lower Ardèche River (France)

Seasonal sampling at six locations on the Lower Ardèche River was effected irregularly during 1982, 1983 and 1984. The seasonal structure of the taxa-sample matrix, much more important than sample location, is demonstrated using graphical interpretation.The Mediterranean aspect of the lower reaches of the Ardèche River is pointed out through its community structure which includes species often collected in other typical Mediterranean streams, e.g. Oligoneuriella rhenana, Ephoron virgo, Ecdyonurus dispar, E. insignis, Choroterpes picteti.Water temperature and day length were the determinant influences on seasonal variations in population structure of benthic macroinvertebrates. Three periods were distinguished: water (November to April), spring (May, June and beginning July) and summer (end of July to October). Spring and autumnal spates marked the limits of the summer and winter periods. Hence, annual fluctuations of this seasonal typology may occur in response to the hydrological regime.     

Atomistic basis for the on–off signaling mechanism in SAM-II riboswitch

Many bacterial genes are controlled by metabolite sensing motifs known as riboswitches, normally located in the 5′ un-translated region of their mRNAs. Small molecular metabolites bind to the aptamer domain of riboswitches with amazing specificity, modulating gene regulation in a feedback loop as a result of induced conformational changes in the expression platform. Here, we report the results of molecular dynamics simulation studies of the S-adenosylmethionine (SAM)-II riboswitch that is involved in regulating translation in sulfur metabolic pathways in bacteria. We show that the ensemble of conformations of the unbound form of the SAM-II riboswitch is a loose pseudoknot structure that periodically visits conformations similar to the bound form, and the pseudoknot structure is only fully formed upon binding the metabolite, SAM. The rate of forming contacts in the unbound form that are similar to that in the bound form is fast. Ligand binding to SAM-II alters the curvature and base-pairing of the expression platform that could affect the interaction of the latter with the ribosome.     

Assessment of the influence of the patient’s inflammatory state on the accuracy of a haptoglobin selected reaction monitoring assay

Background

The use of targeted LC-MS/MS methods for protein quantitation in clinical laboratories implies a careful evaluation of potential sources of analytical interference. In this study, we investigated whether inflammation, which is associated with both the release of proteolytic enzymes and increased expression of acute phase protease inhibitors, is affecting the accuracy of a haptoglobin selected reaction monitoring (SRM) assay.

Results

A SRM assay was developed and used to quantify haptoglobin in 57 human serum samples. The SRM assay had CVs (n = 6) of 12.9% at 698 mg/L and 11.8% at 1690 mg/L. Results of the SRM assay were compared to those of a commercial immunonephelometric test. Passing-Bablok regression gave a proportional bias of 0.92 (95% CI: 0.82 to 1.04) and a constant bias of 75.40 (95% CI: −71.09 to 251.04), indicating that SRM and immunonephelometric assays provided comparable results. We then investigated whether the accuracy of the SRM assay was influenced by the patient’s inflammatory state by assessing the relationship between the serum CRP concentration and the bias between the two methods. No correlation was found between the SRM/immunoassay bias and the CRP concentration (Pearson correlation coefficient r = 0.0898).

Conclusions

These data indicate that neither the release of proteolytic enzymes nor the increased level of protease inhibitors occurring during inflammation processes have a significant impact on the haptoglobin SRM assay accuracy. Such studies provide important information about potential sources of analytical interferences in protein SRM assays.

Electronic supplementary material

The online version of this article (doi:10.1186/1559-0275-11-38) contains supplementary material, which is available to authorized users.     

Plant and animal communities in brackish supra-littoral pools (‘dobben’) in the northern part of the Netherlands

Fifty brackish supra-littoral pools bordering the Waddenzee were studied. The structure of plant communities (Potamogeton pectinatus L., Ranunculus baudotii Godr. and Zannichellia pedunculata Rchb.) is discussed in relation to water level fluctuations, chlorinity and water transparency. Chlorinity tolerances of the macrophytes (7 species) are discussed. The macrofauna was studied semi-quantitatively. The aquatic Coleoptera had the greatest diversity (24 species). A distinct relationship between the number of Coleoptera species and the percentage of macrophyte coverage was found. The distribution patterns of the most frequent species with respect to chlorinity categories are shown in histograms. The number of aquatic Heteroptera species is also discussed in relation to chlorinity and vegetation coverage. Less important macrofaunal groups (the Crustacea, Mollusca and Odonata) occurred in low species numbers.     

Variation in the methods leads to variation in the interpretation of biodiversity–ecosystem multifunctionality relationships

生物多样性常常和生态系统多功能性(生态系统同时提供多个生态系统功能的能力)正相关。然而,生物多样性与生态系统多功能性的关系是否依赖于生态系统功能的数目有诸多争议。其中,生物多样性对生态系统多功能性的影响或许不随生态系统功能数目的变化而变化,或者随生态系统功能数目的增多而增强。我们期望通过研究不同生态系统多功能性指数的统计原理来解决这些争议。 我们使用了模型模拟和一系列来自不同空间尺度(从局域到全球)和不同生物群系(温带和高寒草地、森林和干旱地)的经验数据。我们回顾了量化生态系统多功能性的三种方法,包括平均值法、加和法和阈值法。我们发现随着生态系统功能数目的增加,生物多样性与生态系统多功能性的关系要么不变,要么增强。这些结果可由平均和加和的多功能性指数的统计原理来解释。具体来讲,当利用生态系统功能的平均值计算多功能性指数时,由于多样性对多功能性的效应等于多样性对单个生态系统功能效应的平均值,所以不会随生态系统功能数目的变化而变化。同样的道理,当利用单个生态系统的加和值计算多功能性指数时,多样性的效应会随着生态系统功能数目的增加而增强。我们提出了一个改进的多功能性指数,将平均或加和多功能性指数转化为标准化的多功能性指数, 以便于对不同研究的结果进行比较。此外,我们提出了基于变量数值范围的标准化方法来解决阈值法的数学假象问题(多样性效应随生态系统功能数目的增加而增强)。我们的研究结果表明,量化多功能性指数的方法不同,结果也不同。因此,有必要加深对不同方法数理基础的理解。而标准化的多功能性指数为比较不同研究中的生物多样性与生态系统多功能性的关系提供了有效的方法。     

Removal of livestock alters native plant and invasive mammal communities in a dry grassland–shrubland ecosystem

The impacts of domesticated herbivores on ecosystems that did not evolve with mammalian grazing can profoundly influence community composition and trophic interactions. Also, such impacts can occur over long time frames by altering successional vegetation trajectories. Removal of domesticated herbivores to protect native biota can therefore lead to unexpected consequences at multiple trophic levels for native and non-native species. In the eastern South Island of New Zealand large areas of seral grassland–shrubland have had livestock (sheep and cattle) removed following changes in land tenure. The long-term (>10 years) outcomes for these communities are complex and difficult to predict: land may return to a native-dominated woody plant community or be invaded by exotic plants and mammals. We quantified direct and indirect effects of livestock removal on this ecosystem by comparing plant and invasive mammal communities at sites where grazing by livestock ceased c.10–35 years ago (conservation sites) with paired sites where pastoralism has continued to the present (pastoral sites). There was higher total native plant richness and reduced richness of exotic plants on conservation sites compared with pastoral sites. Further, there were differences in the use of conservation and pastoral sites by invasive mammals: rabbits and hedgehogs favoured sites grazed by livestock whereas house mice, brushtail possums and hares favoured conservation sites. Changes in the relative abundance of invasive mammal species after removal of domesticated livestock may compromise positive outcomes for conservation in successional plant communities with no evolutionary history of mammalian grazing.     

Effects of the hummock–depression microhabitat on plant communities of alpine marshy meadows in the Yellow River Source Zone,China

黄河源区丘-洼微生境对高寒沼泽草甸植物群落的影响 黄河源区高寒沼泽草甸中有许多不均匀的小丘和洼地,形成了独特的微生境,深刻影响着植物特性和土壤养分含量。通过研究高寒湿地冻融丘和洼地空间异质性对植物群落和土壤性质的影响,可以深入了解微地形水文条件对丘-洼微生境空间波动的影响。本研究在黄河源区高寒沼泽湿地的冻融丘 (淹水和无淹水)和洼地(蓄水和无蓄水)共设置36个样地(1 m × 1 m),采集了45个植物样和225个土壤样, 并采用比较法评价高寒沼泽湿地是否存在“肥岛效应”。研究结果显示,冻融丘的存在增加了微生境的 空间异质性,促进了藏嵩草群落的物种多样性和土壤肥力。淹水和无淹水的冻融丘生境下的植物高度、 盖度、地上生物量、物种丰富度和多样性均显著高于湿地外围的高寒草甸。与高寒草甸相比,高寒沼泽 湿地丘-洼复合体为莎草科植物的生长提供了有利的微生境。另外,湿地丘-洼微生境与周围高寒草甸 在0–50 cm土层之间的比较表明,土壤有机碳和全氮距离地表越近含量越高。在深层次土壤中,丘洼微生 境与高寒草甸土壤养分之间的差距变小。因此,湿地丘-洼微生境形成了一个富饶的“肥沃岛”格局。这些研究结果有助于加深对高寒沼泽草甸生态系统恢复的认识。     

Plant community composition and structural characteristics of an invaded forest in the Galápagos

Non-native species have invaded habitats worldwide, greatly impacting the structure and function of native communities and ecosystems. To better understand mechanisms of invasion impacts and how to restore highly impacted and transformed ecosystems, studies are needed that evaluate invader effects on both biotic communities and structural characteristics. On Santa Cruz Island in Galápagos we compared biotic (plant species richness, diversity, and community composition) and structural (canopy openness, forest height, and leaf litter) characteristics of a relic forest dominated by an endemic and highly threatened tree and a forest dominated by an invasive tree. The forests are located within the historical distribution of the endemic tree, which now occupies only 1% of its original extent. We found that the invaded forest had 42% lower native plant species richness and 17% less plant diversity than the endemic tree dominated forest. Additionally, with the invader there was 36% greater non-native plant species richness, 37% higher non-native plant diversity, and highly dissimilar plant composition when compared to the endemic-dominated forest. Additionally, the invaded forest had a more open and taller tree canopy and greater leaf litter cover than native forest. The presence of the invasive tree and the associated forest structural changes were the primary factors in models that best explained higher non-native diversity in the invaded forest. Our correlational results suggest that an invasive tree has significantly altered plant assemblage and forest structural characteristics in this unique ecosystem. Experiments that remove the invader and evaluate native plant community responses are needed to identify thresholds for practical restoration of this threatened and biologically unique native forest.     

Impacts of grazing on the alkalinized–salinized meadow steppe ecosystem in the Songnen Plain,China – A simulation study

A process-based model was built to describe the ecological processes of an alkalinized–salinized meadow steppe ecosystem, including the hydrological and alkalization–salinization processes in the soil, as well as the succession and growth dynamics of the grassland communities. A numerical integration model and a water and salt balance model were integrated into a physically-based model, describing the dynamics of soil moisture, salt concentration, exchangeable sodium percentage (ESP) and pH. Meteorological variables and soil characteristics were the main environmental factors used to estimate the growth dynamics of three herbaceous communities that were dominated by Aneurolepidium chinense, Chloris virgata, and Suaeda glauca, respectively. Model validation showed good agreement between the simulated results and the observed data. Simulation studies were conducted to evaluate the potential changes in hydrological and alkalization–salinization processes, succession and growth dynamics from 1991 to 1998, under five grazing intensities, namely 0%, 25%, 50%, 75% and 90% above-ground biomass removal (AGBR). The simulations show that soil moisture decreased markedly under the 50%, 75% and 90% AGBR, but increased slightly under the 25% AGBR. The de-alkalization and de-salinization processes would be predominant under the 0% AGBR, and the processes became a little slower under the 25% AGBR. In contrast, the 50%, 75% and 90% AGBR accelerated the degradation of soil properties. The grassland was dominated by A. chinense under the 0% AGBR, and by A. chinense and C. virgata under the 25% AGBR. C. virgata could grow on slightly alkalinized–salinized soil and became a dominant species after three years of 50% AGBR. The soil degraded quickly and only S. glauca could grow on the severe alkalinized–salinized soil if the grassland received 75% or 90% AGBR. The grassland grew well under the 0% AGBR, and the biomass stayed at moderate level under 25% AGBR. The 50%, 75% and 90% AGBR decreased the grassland growth greatly. After accumulating the grazed biomass for each year, the 25% AGBR would provide the highest production, and the grassland production would decrease sharply with the increasing of grazing intensities. The simulation results indicate that 25% AGBR is significant for preserving the soil from degradation, and maintaining high grassland production.     

Control of the redox state of the nicotinamide–adenine dinucleotide couple in rat liver cytoplasm

1. A study has been made of the ability of rat liver in vivo to maintain equilibrium in the combined glyceraldehyde 3-phosphate dehydrogenase, 3-phosphoglycerate kinase and lactate dehydrogenase reactions, i.e. in the system: [Formula: see text] Attempts were made to upset equilibrium. The [lactate]/[pyruvate] ratio was rapidly changed by injection of ethanol or crotyl alcohol, and the value of [ATP]/[ADP][HPO(4) (2-)] was rapidly changed by injection of ethionine or carbonyl cyanide p-trifluoromethoxy-phenylhydrazone. 2. The concentrations of the metabolites occurring in the above equation were measured in freeze-clamped liver. 3. Although the injected agents caused large changes in the concentrations of the individual components, near-equilibrium in the system was maintained, as indicated by the fact that the value of [ATP]/[ADP][HPO(4) (2-)], referred to as the phosphorylation state of the adenine nucleotides, measured directly agreed with the value calculated for equilibrium conditions from the above equation. 4. The results are discussed and taken to confirm that the order of magnitude of the value of the redox state of the cytoplasmic NAD couple in rat liver is controlled by the phosphorylation state of the adenine nucleotide system.     

Influence of the electron density on the characteristics of terahertz waves generated under laser–cluster interaction

A theory of generation of terahertz radiation under laser–cluster interaction, developed earlier for an overdense cluster plasma [A. A. Frolov, Plasma Phys. Rep. 42. 637 (2016)], is generalized for the case of arbitrary electron density. The spectral composition of radiation is shown to substantially depend on the density of free electrons in the cluster. For an underdense cluster plasma, there is a sharp peak in the terahertz spectrum at the frequency of the quadrupole mode of a plasma sphere. As the electron density increases to supercritical values, this spectral line vanishes and a broad maximum at the frequency comparable with the reciprocal of the laser pulse duration appears in the spectrum. The dependence of the total energy of terahertz radiation on the density of free electrons is analyzed. The radiation yield is shown to increase significantly under resonance conditions, when the laser frequency is close to the eigenfrequency of the dipole or quadrupole mode of a plasma sphere.     

Assessment of ecosystem health during the past 40 years for Lake Taihu in the Yangtze River Delta,China

An assessment of the ecosystem health of Lake Taihu in eastern China from 1960 to 2005 was conducted using separate and aggregated chemical and biological indicators. The chemical oxygen demand, the total nitrogen, total inorganic nitrogen and total phosphorus concentrations, and the molar ratio of TN to TP (N/P) have all significantly increased (P < 0.05) since 1980. The trophic state index increased from 35.0 in 1960 to >60.0 in 1990, confirming that Lake Taihu changed from being oligotrophic to being eutrophic. These changes in water quality have led to corresponding changes in species composition and in the densities and biomasses of many aquatic species. Algal blooms have occurred frequently since the late 1980s, leading to the dominance of small zooplankton and benthic invertebrates. About 41 fish, 65 zooplankton and 16 macrophyte species were estimated to have disappeared from the lake since the late 1980s. Buffer capacity increased for phytoplankton and zooplankton but decreased for zoobenthos. These results suggest that the Lake Taihu ecosystem was in better health in 1960, and has deteriorated since 1980.