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Oaks ( Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags ( ESTs) have been characterized in ectomycorrhizal ( EM) symbioses., We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone ( DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum., Using the Mimicking Intelligent Read Assembly ( MIRA) and Trinity assembler, the OakContig DF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated., In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees. [ABSTRACT FROM AUTHOR]

Subsurface microorganisms are crucial for contaminant degradation and maintenance of groundwater quality. This study investigates the microbial biomass and community composition [by phospholipid fatty acids (PLFAs)], as well as physical and chemical soil characteristics at woodland flooding sites of an artificial groundwater recharge system used for drinking water production. Vertical soil profiles to c. 4 m at two watered and one nonwatered site were analyzed. The microbial biomass was equal in watered and nonwatered sites, and considerable fractions (25–42%) were located in 40–340 cm depth. The microbial community structure differed significantly between watered and nonwatered sites, predominantly below 100 cm depth. Proportions of the bacterial PLFAs 16:1ω5, 16:1ω7, cy17:0 and 18:1ω9t, and the long-chained PLFAs 22:1ω9 and 24:1ω9 were more prominent at the watered sites, whereas branched, saturated PLFAs (iso/anteiso) dominated at the nonwatered site. PLFA community indices indicated stress response ( trans/ cis ratio), higher nutrient availability (unsaturation index) and changes in membrane fluidity (iso/anteiso ratio) due to flooding. In conclusion, water recharge processes led to nutrient input and altered environmental conditions, which resulted in a highly active and adapted microbial community residing in the vadose zone that effectively degraded organic compounds. [ABSTRACT FROM AUTHOR]

Low amounts of root infestation by plant parasitic nematodes are suggested to increase nutrient supply and in turn enhance microbial activity and net mineralization rate in the rhizosphere. These effects are generally related to “leakage” of plant-derived metabolites from damaged roots. Besides leakage, the present study examines other nematode–host interactions such as alterations in root exudation and morphology, which were almost not considered yet. This includes undamaged root parts in order to assess systemic plant response. The root-knot nematode Meloidogyne incognita (Kofoid and White 1919; Chitwood 1949) and barley ( Hordeum vulgare L. cv. Europa) was used as model system. Host plants were grown in mini-rhizotrons inoculated with 0, 2,000, 4,000 or 8,000 M. incognita for 4 weeks. Root morphology, rhizodeposition (sugars, carboxylates, amino acids), and rhizosphere microbial communities (PLFAs) were assessed. In treatments with 4,000 nematodes, shoot biomass, total N and P content increased by the end of the experiment. Generally, an enhanced release of plant metabolites (sugars, carboxylates, amino acids) from the apical root zone occurred 1 week after inoculation with 4,000 and 8,000 M. incognita, indicating root leakage. Low levels of root herbivory stimulated root hair elongation in both infected and uninfected roots. These systemic changes in root morphology likely contributed to the increased sugar exudation in uninfected roots in all nematode treatments at 3 weeks after inoculation. Root-knots formed a separate microhabitat within the root-system. They were characterised by decreased rhizodeposition and increased fungal to bacterial ratio in the adhering rhizosphere soil. The present study provides the first evidence that, apart from leakage, nematode root herbivory at background levels induces local and systemic effects on root morphology and exudation, which in turn may affect plant performance. [ABSTRACT FROM AUTHOR]

Trophic interactions in cryptic belowground systems are difficult to assess, either experimentally or by direct observation. We used lipid analysis to determine feeding strategies in Collembola raised on various bacterial, fungal, plant, or nematode diets. Dietary fatty acids (FAs) were conserved and transferred through the trophic cascade into the neutral lipids of consumers. The presence of vaccenic type FAs (ω7 family) was indicative of a bacterial diet in general. More specifically, methyl-branched (iso, anteiso) and cyclic forms of FAs were markers for consumption of gram-positive and gram-negative bacteria, respectively. Fungal-feeding Collembola comprised a higher proportion of linoleic acid, whereas the profile of plant feeders showed an increased amount of oleic acid. The FA 20:1 ω9 was only present in Collembola with nematodes as prey. Based on the assigned marker FAs, field populations of Collembola in three deciduous forest stands were ascribed to feeding guilds (i.e., fungivores, bacterivores, herbivores, predators). In conclusion, FA biomarkers provide a high-resolution method to define feeding strategies of decomposer invertebrates and to determine their diets in situ. Lipid analysis has considerable potential as a new tool in soil food web studies. [ABSTRACT FROM AUTHOR]

This study analyses trophic interactions between soil fungi, micro- and mesofauna in microcosm experiments. The trophic shift of 15N and fatty acids (FAs) was investigated in different food chains, which comprised either two (fungi and grazers) or three (fungi, nematodes and Collembola) levels. Contrary to the widely accepted assumption of 15N enrichment in trophic cascades the experiments revealed enrichment, depletion or no change in 15N of consumers compared to their diet. Factors responsible for this pattern were suggested to be: (1) the main metabolic pathway used for N excretion in ammonotelic nematodes to be similar or depleted in the heavier isotope, and uricotelic Collembola mostly enriched in the heavier isotope; (2) a higher shift in 15N with a high-protein diet (e.g. for predators); (3) compensation due to low-quality food altering the fractionation of 15N. Analysis of the lipid composition showed phospholipids to be generally unaffected and neutral lipids closely related to the FA pattern of the food source. Dietary routing of FAs into neutral lipids occurred, as evidenced by corresponding frequencies of FAs in host and consumer profiles. Additionally, several FAs were only detected in the grazer when present in the food source. Oleic acid showed a shift over three trophic levels, from fungi to nematodes to Collembola. The assimilation of dietary FAs resulted in a more diverse neutral lipid profile, i.e. animals higher in the food chain contained more individual FAs compared to animals lower in the food chain. The results indicate that monoenoic C18 and monoenoic C20 FAs have the potential to act as tools for the bioindication of feeding strategies in belowground systems. We suggest that primary consumers will have no or only trace amounts of monoenoic C20 acids in their neutral lipid profile, whereas consumers feeding on a eukaryote diet will show a considerably higher frequency. [ABSTRACT FROM AUTHOR]

Nutrient availability is a major constraint on plant production and carbon storage in arctic ecosystems but knowledge on the decomposer food web interactions and their effect on nutrient cycling is scarce. We manipulated the soil food web at two contrasting subarctic sites, a low altitude heath and a high altitude fell-field. The influx of nutrients and energy in the soil was increased by addition of fertiliser nitrogen, phosphorus and potassium and of labile carbon (sugar). In addition, two bactericides (penicillin and streptomycin) and a fungicide (benomyl) were applied to manipulate the bacterial and fungal component of the soil. Experiments were carried out in a factorial design with repeated additions over four growing seasons. The present study investigated the nematode fauna and the effects of the manipulations on the abundance of nematode species. Fertilisation resulted in an increase of general opportunists, especially Aphelenchoides. Application of carbon or bactericides had only minor impact on the nematode community. In contrast, the fungicide was very toxic to non-target organisms and greatly reduced the abundance of most nematode species, although Acrobeloides buetschlii showed tolerance and greatly increased in number. At both sites, Eudorylaimus was most affected by the treatments. Generally the manipulations performed resulted in a significant increase in stress tolerant or competitive dominant nematode species. [ABSTRACT FROM AUTHOR]