Camera trap data suggest uneven predation risk across vegetation types in a mixed farmland landscape

Ground‐nesting farmland birds such as the grey partridge (Perdix perdix) have been rapidly declining due to a combination of habitat loss, food shortage, and predation. Predator activity is the least understood factor, especially its modulation by landscape composition and complexity. An important question is whether agri‐environment schemes such as flower strips are potentially useful for reducing predation risk, for example, from red fox (Vulpes vulpes). We employed 120 camera traps for two summers in an agricultural landscape in Central Germany to record predator activity (i.e., the number of predator captures) as a proxy for predation risk and used generalized linear mixed models (GLMMs) to investigate how the surrounding landscape affects predator activity in different vegetation types (flower strips, hedges, field margins, winter cereal, and rapeseed fields). Additionally, we used 48 cameras to study the distribution of predator captures within flower strips. Vegetation type was the most important factor determining the number of predator captures and capture rates in flower strips were lower than in hedges or field margins. Red fox capture rates were the highest of all predators in every vegetation type, confirming their importance as a predator for ground‐nesting birds. The number of fox captures increased with woodland area and decreased with structural richness and distance to settlements. In flower strips, capture rates in the center were approximately 9 times lower than at the edge. We conclude that the optimal landscape for ground‐nesting farmland birds seems to be open farmland with broad extensive vegetation elements and a high structural richness. Broad flower blocks provide valuable, comparatively safe nesting habitats, and the predation risk can further be minimized by placing them away from woods and settlements. Our results suggest that adequate landscape management may reduce predation pressure.     

Plant roots fuel tropical soil animal communities

Belowground life relies on plant litter, while its linkage to living roots had long been understudied, and remains unknown in the tropics. Here, we analysed the response of 30 soil animal groups to root trenching and litter removal in rainforest and plantations in Sumatra, and found that roots are similarly important to soil fauna as litter. Trenching effects were stronger in soil than in litter, with an overall decrease in animal abundance in rainforest by 42% and in plantations by 30%. Litter removal little affected animals in soil, but decreased the total abundance by 60% in rainforest and rubber plantations but not in oil palm plantations. Litter and root effects on animal group abundances were explained by body size or vertical distribution. Our study quantifies principle carbon pathways in soil food webs under tropical land use, providing the basis for mechanistic modelling and ecosystem-friendly management of tropical soils.     

Rainforest conversion to plantations fundamentally alters energy fluxes and functions in canopy arthropod food webs

Tropical rainforests around the world are rapidly being converted into cash crop agricultural systems. The associated massive losses of plant and animal species lead to changes in arthropod food webs and the energy fluxes therein. These changes are poorly understood, in particular in the extremely biodiverse canopies of tropical ecosystems. Using canopy fogging followed by stable isotope and energy flux analyses, we show that land-use conversion from rainforest to rubber and oil palm plantations not only causes a drastic reduction in energy fluxes of up to 75%, but also shifts fluxes among trophic groups. While rainforest featured high levels of both herbivory and algae-microbivory, and a balanced ratio of herbivory to predation, relative fluxes were shifted towards predation in rubber and towards herbivory in oil palm plantations, indicating profound shifts in ecosystem functioning. Our results highlight that the ongoing loss of animal biodiversity and biomass in tropical canopies degrades animal-driven functions and restructures canopy food webs.     

Decomposition of 14C-labeled cellulose substrates in litter and soil from a beechwood on limestone

The decomposition of three different ¹⁴C-labeled cellulose substrates (plant holocellulose, plant cellulose prepared from ¹⁴C-labeled beech wood (Fagus sylvatica) and bacterial cellulose produced by Acetobacter xylinum) in samples from the litter and mineral soil layer of a beechwood on limestone was studied. In a long-term (154 day) experiment, mineralization of cellulose materials, production of ¹⁴C-labeled water-soluble compounds, and incorporation of ¹⁴C in microbial biomass was in the order Acetobacter cellulose > holocellulose > plant cellulose in both litter and soil. In general, mineralization of cellulose, production of ¹⁴C-labeled water-soluble compounds, and incorporation of ¹⁴C in microbial biomass were more pronounced, but microbial biomass ¹⁴C declined more rapidly in litter than in soil. In short-term (14 day) incubations, mineralization of cellulose substrates generally corresponded with cellulase and xylanase activities in litter and soil. Pre-incubation with trace amounts of unlabeled holocellulose significantly increased the decomposition of ¹⁴C-labeled cellulose substrates and increased cellulase activity later in the experiment but did not affect xylanase activity. The sum of ¹⁴CO₂ production, ¹⁴C in microbial biomass, and ¹⁴C in water-soluble compounds is considered to be a sensitive parameter by which to measure cellulolytic activity in soil and litter samples in short-term incubations. Shorter periods than 14 days are preferable in assays using Acetobacter cellulose, because the decomposition of this substrate is more variable than that of holocellulose and plant cellulose.Offprint requests to: S. Scheu.     

Affibody protein capture microarrays: synthesis and evaluation of random and directed immobilization of affibody molecules

Affibody molecules, 58-amino acid three-helix bundle proteins directed to different targets by combinatorial engineering of staphylococcal protein A, were used as capture ligands on protein microarrays. An evaluation of slide types and immobilization strategies was performed to find suitable conditions for microarray production. Two affibody molecules, Z(Taq) and Z(IgA), binding Taq DNA polymerase and human IgA, respectively, were synthesized by solid phase peptide synthesis using an orthogonal protection scheme, allowing incorporation of selective immobilization handles. The resulting affibody variants were used for random surface immobilization (through amino groups) or oriented surface immobilization (through cysteine or biotin coupled to the side chain of Lys58). Evaluation of the immobilization techniques was carried out using both a real-time surface plasmon resonance biosensor system and a microarray system using fluorescent detection of Cy3-labeled target protein. The results from the biosensor analyses showed that directed immobilization strategies significantly improved the specific binding activity of affibody molecules. However, in the microarray system, random immobilization onto carboxymethyl dextran slides and oriented immobilization onto thiol dextran slides resulted in equally good signal intensities, whereas biotin-mediated immobilization onto streptavidin-coated slides produced slides with lower signal intensities and higher background staining. For the best slides, the limit of detection was 3 pM for IgA and 30 pM for Taq DNA polymerase.     

Carbon availability controls the growth of detritivores (Lumbricidae) and their effect on nitrogen mineralization

Activity of soil decomposer microorganisms is generally limited by carbon availability, but factors controlling saprophagous soil animals remain largely unknown. In contrast to microorganisms, animals are unable to exploit mineral nutrient pools. Therefore, it has been suggested that soil animals, and earthworms in particular, are limited by the availability of nitrogen. In contrast to this view, a strong increase in density and biomass of endogeic earthworms in response to labile organic carbon addition has been documented in field experiments. The hypothesis that the growth of endogeic earthworms is primarily limited by carbon availability was tested in a laboratory experiment lasting for 10 weeks. In addition, it was investigated whether the effects of earthworms on microbial activity and nutrient mineralization depend on the availability of carbon resources. We manipulated food availability to the endogeic earthworm species Octolasion tyrtaeum by using two soils with different organic matter content, providing access to different amounts of soil, and adding labile organic carbon (glucose) enriched in ¹³C.Glucose addition strongly increased the growth of O. tyrtaeum. From 8 to 17% of the total C in earthworm tissue was assimilated from the glucose added. Soil microbial biomass was not strongly affected by the addition of glucose, though basal respiration was significantly increased and up to 50% of the carbon added as glucose was incorporated into soil organic matter. The impact of earthworms on the mineralization and leaching of nitrogen depended on C availability. As expected, in C-limited soil, the presence of earthworms strongly increased nitrogen leaching. However, when C availability was increased by the addition of glucose, this pattern was reversed, i.e. the presence of O. tyrtaeum decreased nitrogen leaching and its availability to soil microflora. We conclude that irrespective of the total carbon content of soils, O. tyrtaeum was primarily limited by carbon, and that increased carbon availability allowed earthworms to be more effective in mobilizing N. The presence of earthworms increases C limitation of soil microorganisms, due to increased availability of N and P in earthworm casts or a direct depletion of easily available carbon resources by earthworms.     

Fluorescence resonance energy transfer-based detection of analytes using antiidiotypic affinity protein pairs

A new method for specific detection of proteins based on fluorescence resonance energy transfer (FRET) using affinity proteins (affibodies) derived from combinatorial engineering of Staphylococcal protein A has been developed. Antiidiotypic affibody pairs were used in a homogeneous competitive binding assay, where the idiotypic, target-specific affibody was labeled with fluorescein and the antiidiotypic affibody was labeled with tetramethylrhodamine. Intermolecular FRET between the two fluorescent probes was observed in the antiidiotypic affibody complex, but upon addition of target protein the antiidiotypic affibody was displaced, which was monitored by a shift in the relative emission of the donor and acceptor fluorophores. The feasibility of the system was demonstrated by the detection of IgA and Taq DNA polymerase with high specificity, using two different antiidiotypic affibody pairs. Detection of Taq DNA polymerase in 25% human plasma was successfully carried out, demonstrating that the method can be used for analysis of proteins in samples of complex composition.     

In vitro measurement of enzymatic markers as a tool to detect mouse cardiomyocytes injury

Primary cultures of cardiomyocytes represent a useful model for analyzing cardiac cell biology as well as pathogenesis of several cardiovascular disorders. Our aim was to standardize protocols for determining the damage of cardiac cells cultured in vitro by measuring the creatine kinase and its cardiac isotype and lactate dehydrogenase activities in the supernatants of mice cardiomyocytes submitted to different protocols of cell lysis. Our data showed that due to its higher specificity, the cardiac isotype creatine kinase was the most sensitive as compared to the others studied enzymatic markers, and can be used to monitor and evaluate cardiac damage in in vitro assays.     

Testing the validity of functional response models using molecular gut content analysis for prey choice in soil predators

Analysis of predator–prey interactions is a core concept of animal ecology, explaining structure and dynamics of animal food webs. Measuring the functional response, i.e. the intake rate of a consumer as a function of prey density, is a powerful method to predict the strength of trophic links and assess motives of prey choice, particularly in arthropod communities. However, due to their reductionist set‐up, functional responses, which are based on laboratory feeding experiments, may not display field conditions, possibly leading to skewed results. Here, we tested the validity of functional responses of centipede predators and their prey by comparing them with empirical gut content data from field‐collected predators. Our predator–prey system included lithobiid and geophilomorph centipedes, abundant and widespread predators of forest soils and their soil‐dwelling prey. First, we calculated the body size‐dependent functional responses of centipedes using a published functional response model in which we included natural prey abundances and animal body masses. This allowed us to calculate relative proportions of specific prey taxa in the centipede diet. In a second step, we screened field‐collected centipedes for DNA of eight abundant soil‐living prey taxa and estimated their body size‐dependent proportion of feeding events. We subsequently compared empirical data for each of the eight prey taxa, on proportional feeding events with functional response‐derived data on prey proportions expected in the gut, showing that both approaches significantly correlate in five out of eight predator–prey links for lithobiid centipedes but only in one case for geophilomorph centipedes. Our findings suggest that purely allometric functional response models, which are based on predator–prey body size ratios are too simple to explain predator–prey interactions in a complex system such as soil. We therefore stress that specific prey traits, such as defence mechanisms, must be considered for accurate predictions.