The shredding activity of gammarids facilitates the processing of organic matter by the subterranean amphipod Niphargus rhenorhodanensis

1. The functional feeding group approach has been widely used to describe the community structure of benthic invertebrates in relation to organic matter resources. Based on this functional framework, positive interactions between feeding groups (especially shredders and collector‐gatherers) were postulated in the River Continuum Concept. However, relationships with organic matter have been poorly documented for invertebrates living in the hyporheic zone. 2. We hypothesised that the common subterranean amphipod Niphargus rhenorhodanensis would feed on fine particulate organic matter (FPOM), which is more abundant than coarse particulate organic matter (CPOM) in hyporheic habitats, and should be favoured by the occurrence of shredders that produce FPOM from CPOM. 3. We used laboratory experiments to quantify leaf litter processing by N. rhenorhodanensis and a common shredder, the surface amphipod Gammarus roeselii. We estimated rates of feeding and assimilation (using nitrogen stable isotopes) of the two species separately and together to reveal any potential shredder–collector facilitation between them. 4. Measured leaf litter mass loss showed that N. rhenorhodanensis did not act as a shredder, unlike G. roeselii. Organic matter dynamics and ¹⁵N/¹⁴N ratios in tissues of niphargids indicated that N. rhenorhodanensis was a collector‐gatherer feeding preferentially on FPOM. We also found a positive influence of the gammarid shredders on the assimilation rate of N. rhenorhodanensis, which fed on FPOM produced by the shredders, supporting the hypothesis of a positive interaction between surface shredders and hyporheic collector‐gatherers.     

Gradients of life-history variation: an intercontinental comparison of fishes

Multivariate analysis identified atwo-dimensional continuum of life-historyvariation among 301 fish species from Europe,North America, South America and the Atlanticand Pacific coasts of North America. The firstaxis was associated with larger body size,higher fecundity, delayed maturation, fewerreproductive events, and shorter breedingseason on one end and small size, lowfecundity, early maturity, multiplereproductive events per year, and prolongedbreeding season on the other. The second axiscontrasted fishes having larger eggs and moreparental care against fishes with the oppositesuite of traits.Phylogenetic affiliations of species wereapparent in the general patterns of ordinationof species within orders, indicatingevolutionary divergences in life-historypatterns. In fact, partitioning the variance oflife-history traits showed that taxonomic orderand latitude were the most important factorsand geographic region and habitat the least.Despite phylogenetic constraints, basiclife-history patterns showed consistencybetween distantly geographical regions,latitudinal ranges and basic adult habitats,indicating convergences in life-historypatterns. Although the basic life-historypatterns seemed repeatable among distantlyrelated taxa, geographical and latitudinalaffiliations were apparent. Species from SouthAmerica are skewed toward the opportunisticendpoint, whereas North American marine speciesare skewed toward the periodic endpoint of thetrilateral continuum model. Most of the fishspecies from South American data set came fromfluctuating environments, so an opportunisticstrategy of early maturation and continuousspawning permits efficient recolonization ofhabitats over small spatial scales. Incontrast, most species in the North Americanand European data sets came from seasonalhabitats that are nonetheless more hydrologicalstable, so a periodic strategy of delayingmaturation to attain large clutches enhancesadult survivorship during suboptimalenvironmental conditions and recruitment whenearly life stages encounter suitableenvironmental conditions. Similarly,latitudinal affiliations were also observed:opportunistic strategists more common intropical latitudes and periodic strategistsmore common in temperate and Arctic latitudes.     

Binding of amphipathic α-helical antimicrobial peptides to lipid membranes: Lessons from temporins B and L

Temporins constitute a family of amphipathic α-helical antimicrobial peptides (AMP) and contain some of the shortest cytotoxic peptides, comprised of only 10-14 residues. General characteristics of temporins parallel those of other AMP, both in terms of structural features and biophysical properties relating to their interactions with membrane lipids, with selective lipid-binding properties believed to underlie the discrimination between target vs host cells. Lipid-binding properties also contribute to the cytotoxicity AMP, causing permeabilization of their target cell membranes. The latter functional property of AMP involves highly interdependent acidic phospholipid-induced conformational changes, aggregation, and formation of toxic oligomers in the membrane. These oligomers are subsequently converted to amyloid-type fibers, as demonstrated for e.g. temporins B and L in our laboratory, and more recently for dermaseptins by Auvynet et al. Amyloid state represents the generic minimum in the folding/aggregation free energy landscape, and for AMP its formation most likely serves to detoxify the peptides, in keeping with the current consensus on mature amyloid being inert and non-toxic. The above scenario is supported by sequence analyses of temporins as well as other amphipathic α-helical AMP belonging to diverse families. Accordingly, sequence comparison identifies ‘conformational switches’, domains with equal probabilities for adopting random coil, α-helical and β-sheet structures. These regions were further predicted also to aggregate and assemble into amyloid β-sheets. Taken together, the lipid-binding properties and structural characterization lend support to the notion that the mechanism of membrane permeabilization by temporins B and L and perhaps of most AMP could be very similar, if not identical, to that of the paradigm amyloid forming cytotoxic peptides, responsible for degenerative cell loss in e.g. prion, Alzheimer's and Parkinson's disease, and type 2 diabetes.     

Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle

Bacteriorhodopsin is the smallest autonomous light-driven proton pump. Proposals as to how it achieves the directionality of its trans-membrane proton transport fall into two categories: accessibility-switch models in which proton transfer pathways in different parts of the molecule are opened and closed during the photocycle, and affinity-switch models, which focus on changes in proton affinity of groups along the transport chain during the photocycle. Using newly available structural data, and adapting current methods of protein protonation-state prediction to the non-equilibrium case, we have calculated the relative free energies of protonation microstates of groups on the transport chain during key conformational states of the photocycle. Proton flow is modeled using accessibility limitations that do not change during the photocycle. The results show that changes in affinity (microstate energy) calculable from the structural models are sufficient to drive unidirectional proton transport without invoking an accessibility switch. Modeling studies for the N state relative to late M suggest that small structural re-arrangements in the cytoplasmic side may be enough to produce the crucial affinity change of Asp96 during N that allows it to participate in the reprotonation of the Schiff base from the cytoplasmic side. Methodologically, the work represents a conceptual advance compared to the usual calculations of pK(a) using macroscopic electrostatic models. We operate with collective states of protonation involving all key groups, rather than the individual-group pK(a) values traditionally used. When combined with state-to-state transition rules based on accessibility considerations, a model for non-equilibrium proton flow is obtained. Such methods should also be applicable to other active proton-transport systems.     

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides

pK(a) calculations based on the Poisson-Boltzmann equation have been widely used to study proteins and, more recently, DNA. However, much less attention has been paid to the calculation of pK(a) shifts in RNA. There is accumulating evidence that protonated nucleotides can stabilize RNA structure and participate in enzyme catalysis within ribozymes. Here, we calculate the pK(a) shifts of nucleotides in RNA structures using numerical solutions to the Poisson-Boltzmann equation. We find that significant shifts are predicted for several nucleotides in two catalytic RNAs, the hairpin ribozyme and the hepatitis delta virus ribozyme, and that the shifts are likely to be related to their functions. We explore how different structural environments shift the pK(a)s of nucleotides from their solution values. RNA structures appear to use two basic strategies to shift pK(a)s: (a) the formation of compact structural motifs with structurally-conserved, electrostatic interactions; and (b) the arrangement of the phosphodiester backbone to focus negative electrostatic potential in specific regions.     

黔西北次生林优势树种叶片-凋落物-土壤连续体有机质碳稳定同位素特征

稳定性碳同位素自然丰度(δ13C)能够揭示生态系统长时间尺度的有机碳动态变化,阐明生态系统功能的变化特征。以黔西北次生林14个优势树种为研究对象,测定叶片、凋落物以及根区土壤有机碳含量和δ13C值,分析不同层次碳含量和δ13C丰度之间的相关性。结果表明:14个优势树种叶片碳含量为404.67—487.14 g/kg,总体为针叶树种较高、常绿灌木较低;δ13C值为-31.2‰—-27.1‰,随生活型的变化规律不明显。凋落物碳含量为414.62—561.31 g/kg,与叶片碳含量的变化规律较为一致;δ13C值为-31.5‰—-27.3‰,随树种生活型的变化特征也不明显。根区土壤碳含量为10.02—91.59 g/kg,δ13C值为-26.8‰—-22.5‰,碳含量以光皮桦、银白杨等落叶乔木较高。叶片、凋落物和根区土壤3个层次的碳含量与δ13C丰度之间均呈不显著相关,不同层次的δ13C丰度之间和碳含量之间均为正相关。研究结果有助于反映森林生态系统碳循环过程的关键信息,为森林植被恢复提供理论依据。     

Changes in nitrogen cycling and retention processes in soils under spruce forests along a nitrogen enrichment gradient in Germany

A network of long-term monitoring sites on nitrogen (N) input and output of forests across Germany showed that a number of Germany's forests are subject to or are experiencing N saturation and that spruce (Picea abies) stands have high risk. Our study was aimed at (1) quantifying the changes in gross rates of microbial N cycling and retention processes in forest soils along an N enrichment gradient and (2) relating the changes in soil N dynamics to N losses. We selected spruce sites representing an N enrichment gradient (indicated by leaching : throughfall N ratios) ranging from 0.04–0.13 (low N),≤0.26 (intermediate N enrichment) to≥0.42 (highly N enriched). To our knowledge, our study is the first to report on mechanistic changes in gross rates of soil N cycling and abiotic NO₃⁻ retention under ambient N enrichment gradient. Gross N mineralization, NH₄⁺ immobilization, gross nitrification, and NO₃⁻ immobilization rates increased up to intermediate N enrichment level and somewhat decreased at highly N-enriched condition. The turnover rates of NH₄⁺ and microbial N pools increased while the turnover rates of the NO₃⁻ pool decreased across the N enrichment gradient. Abiotic immobilization of NH₄⁺ did not differ across sites and was lower than that of NO₃⁻. Abiotic NO₃⁻ immobilization decreased across the N enrichment gradient. Microbial assimilation and turnover appeared to contribute largely to the retention of NH₄⁺. The increasing NO₃⁻ deposition and decreasing turnover rates of the NO₃⁻ pool, combined with decreasing abiotic NO₃⁻ retention, possibly contributed to increasing NO₃⁻ leaching and gaseous emissions across the N enrichment gradient. The empirical relationships of changes in microbial N cycling across the N enrichment gradient may be integrated in models used to predict responses of forest ecosystems (e.g. spruce) to increasing N deposition.