Julia Seeber

Chapter Three – Empirically Characterising Trophic Networks: What Emerging DNA-Based Methods, Stable Isotope and Fatty Acid Analyses Can Offer

Abstract Food webs in agricultural systems are complex and trophic linkages are difficult to track using conventional methodologies. Here, we review three alternative approaches that allow empirical assessment of feeding interactions: DNA-based techniques, and stable isotope and fatty acid analyses. DNA-based methods, namely multiplex PCR and next-generation sequencing, allow identification of food types and host–parasitoid linkages, resulting in taxonomically highly resolved feeding networks. Stable isotopes and fatty acids reflect the assimilation of broader categories of resources, as metabolised into the consumers’ tissue, together with the associated energy and nutrient fluxes in the food web. We discuss the strengths of the approaches but also highlight their limitations, providing practical advice on which technique is best suited to answer specific questions in examining food web interactions in agroecosystems. Future refinements of these techniques, especially when used in combination, could herald a new era in agricultural food web ecology, enabling management and environmental impact to be placed in the mechanistic context of trophic networks.

Application of denaturing gradient gel electrophoresis for analysing the gut microflora of Lumbricus rubellus Hoffmeister under different feeding conditions

The earthworm, Lumbricus rubellus, plays an essential role in soil ecosystems as it affects organic matter decomposition and nutrient cycling. By ingesting a mixture of organic and mineral material, a variety of bacteria and fungi are carried to the intestinal tract of the earthworm. To get a better understanding of the interactions between L. rubellus and the microorganisms ingested, this study tried to reveal if the diet affects the composition of the gut microflora of L. rubellus or if its intestinal tract hosts an indigenous, species-specific microbiota. A feeding experiment with L. rubellus was set up; individuals were collected in the field, transferred to a climate chamber and fed with food sources of different quality (dwarf shrub litter, grass litter or horse dung) for six weeks. DNA was extracted from the guts of the earthworms, as well as from the food sources and the surrounding soil, and further analysed by a molecular fingerprinting method, PCR-DGGE (Polymerase Chain Reaction -- Denaturing Gradient Gel Electrophoresis). We were able to demonstrate that the gut microbiota was strongly influenced by the food source ingested and was considerably different to that of the surrounding soil. Sequencing of dominant bands of the bacterial DGGE fingerprints revealed a strong occurrence of y-Proteobacteria in all gut samples, independent of the food source. A specific microflora in the intestinal tract of L. rubellus, robust against diet changes, could not be found.

Bacterial community composition of the gut microbiota of Cylindroiulus fulviceps (diplopoda) as revealed by molecular fingerprinting and cloning

Bacterial clone libraries of the gut microbiota of nurtured and starved Cylindroiulus fulviceps specimens displayed the predominance of the phyla Bacteroidetes (55 and 37 %, respectively) and Proteobacteria (40 and 35 %, respectively) and a high similarity to bacteria previously detected in the intestinal tract of termites and beetles, which are known to harbor symbiotic bacteria essential for digestive activity. Bacterial isolates were dominated by Proteobacteria (74 %), followed by members of the phyla Actinobacteria, Firmicutes and Bacteroidetes. PCR-DGGE fingerprints of the gut samples showed that intestinal bacteria were affected by starvation, although the change was not significant.

Palatability of selected alpine plant litters for the decomposer Lumbricus rubellus (Lumbricidae).

On alpine pastureland the decline in large-bodied earthworm numbers and biomass after abandonment of management might be the result of a shift from highly palatable grass litter to poorly digestible leaf litter of dwarf shrubs. To test this hypothesis, we analysed nitrogen, phosphorous and total phenolic contents of fresh and aged litter of eight commonly occuring alpine plant species and compared consumption rates of these food sources in a controlled feeding experiment with Lumbricus rubellus (Lumbricidae). Furthermore, we analysed the microbial community structure of aged litter materials to check for a relationship between the microbial characteristics of the different plant litter types and the food choice of earthworms. Plant litters differed significantly in their chemical composition, earthworms, however, showed no preference for any litter species, but generally rejected fresh litter material. Microbial community structures of the litter types were significantly different, but we could find no evidence for selective feeding of L. rubellus. We conclude that L. rubellus is a widespread, adaptable ubiquist, which is able to feed on a variety of food sources differing in quality and palatability, as long as they have been exposed to wheathering.

Genomic Resources Notes Accepted 1 June 2015 - 31 July 2015

This article documents the public availability of (i) microbiomes in diet and gut of larvae from the dipteran Dilophus febrilis using massive parallel sequencing, (ii) SNP and SSR discovery and characterization in the transcriptome of the Atlantic mackerel (Scomber scombrus, L) and (iii) assembled transcriptome for an endangered, endemic Iberian cyprinid fish (Squalius pyrenaicus).

Effects of Alpine land-use changes: Soil macrofauna community revisited

Abstract Although soil invertebrates play a decisive role in maintaining ecosystem functioning, little is known about their structural composition in Alpine soils and how their abundances are affected by the currently ongoing land‐use changes. In this study, we re‐assessed the soil macrofauna community structure of managed and abandoned Alpine pastureland, which has already been evaluated 14 years earlier. Our results confirm clear shifts in the community composition after abandonment, in that (1) Chilopoda and Diplopoda were recorded almost exclusively on the abandoned sites, (2) Coleoptera larvae and Diptera larvae were more abundant on the abandoned than on the managed sites, whereas (3) Lumbricidae dominated on the managed sites. By revisiting managed and abandoned sites, we infer community patterns caused by abandonment such as changes in the epigeic earthworm community structure, and we discuss seasonal and sampling effects. Our case study improves the still limited understanding of spatio‐temporal biodiversity patterns of Alpine soil communities.

Life-history traits and physiological limits of the alpine fly Drosophila nigrosparsa (Diptera: Drosophilidae): A comparative study

Abstract Interspecific variation in life‐history traits and physiological limits can be linked to the environmental conditions species experience, including climatic conditions. As alpine environments are particularly vulnerable under climate change, we focus on the montane‐alpine fly Drosophila nigrosparsa. Here, we characterized some of its life‐history traits and physiological limits and compared these with those of other drosophilids, namely Drosophila hydei, Drosophila melanogaster, and Drosophila obscura. We assayed oviposition rate, longevity, productivity, development time, larval competitiveness, starvation resistance, and heat and cold tolerance. Compared with the other species assayed, D. nigrosparsa is less fecund, relatively long‐living, starvation susceptible, cold adapted, and surprisingly well heat adapted. These life‐history characteristics provide insights into invertebrate adaptations to alpine conditions which may evolve under ongoing climate change.

Decline of rare and specialist species across multiple taxonomic groups after grassland intensification and abandonment

Traditionally managed mountain grasslands are declining as a result of abandonment or intensification of management. Based on a common chronosequence approach we investigated species compositions of 16 taxonomic groups on traditionally managed dry pastures, fertilized and irrigated hay meadows, and abandoned grasslands (larch forests). We included faunal above- and below-ground biodiversity as well as species traits (mainly rarity and habitat specificity) in our analyses. The larch forests showed the highest species number (345 species), with slightly less species in pastures (290 species) and much less in hay meadows (163 species). The proportion of rare species was highest in the pastures and lowest in hay meadows. Similar patterns were found for specialist species, i.e. species with a high habitat specificity. After abandonment, larch forests harbor a higher number of pasture species than hay meadows. These overall trends were mainly supported by spiders and vascular plants. Lichens, bryophytes and carabid beetles showed partly contrasting trends. These findings stress the importance to include a wide range of taxonomic groups in conservation studies. All in all, both abandonment and intensification had similar negative impacts on biodiversity in our study, underlining the high conservation value of Inner-Alpine dry pastures.