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Soil faunal communities are often phylogenetically diverse and the accurate assessment of the taxonomic structure of these communities is both time-consuming and requires a high level of taxonomic expertise. Here we describe a DNA sequence-based methodology for characterizing soil micro- and mesofaunal communities that is similar to the molecular approaches commonly used to survey soil microbial diversity. The technique involves the direct extraction of faunal DNA from soil, PCR amplification of the extracted DNA with metazoan-specific primers, followed by the construction of clone libraries and direct sequencing of individual PCR products. We used this technique to characterize micro- and mesofaunal community composition from six individual soils representing two land-use types. The technique captured the more abundant faunal groups in the soils (nematodes, Collembola, Acari, tardigrades, enchytraeids) and provided sufficient taxonomic resolution to describe the overall structure of the communities. We compared the results obtained using this molecular approach to results obtained using a traditional, microscopy-based approach and found that the results were broadly similar. However, since biases are inherent in both methods it remains unclear which method provides a more accurate assessment of soil faunal community composition. Although this molecular approach has some distinct disadvantages over the more widely-used direct extraction methods, one advantage is that the taxo- nomic identification it can provide will be more accurate and consistent across research groups, facili- tating effective comparisons of mesofaunal surveys.

Soil is both a chemically and biologically complex environment of great ecological importance. It is the primary store of terrestrial carbon (C) and is one of the most actively cycling pools of carbon (Schlesinger 1997; Manzoni and Porporato 2009). Additionally, it is a reservoir for plant nutrients, which fuel primary production (Epstein and Bloom 2005). Yet, not all soils are equal regarding their chemical and physical properties. For example, the underlying parent material of a soil can greatly impact its properties (e.g., pH, clay type, and soil texture). Additionally, soil mineralogy inuences cation exchange capacity, which is an important determinant of traits such as soil fertility (Evangelou and Phillips 2005).

Endophytic fungi are ubiquitous in nature and can play important roles in regulating plant–herbivore interactions. While some aboveground obligate symbionts are considered defensive mutualists of host plants, the importance of root endophytes in plant defense, especially against root-feeding insects, remains unclear. This study aimed to investigate the effects of root fungal endophytes on plant resistance against belowground herbivores and the recovery of host plants from damage. We grew the common grass Festuca arundinacea (tall fescue) semi-aeroponically in the laboratory and inoculated roots with one of five fungal endophytes isolated from field-collected tall fescue or meadow soil. Endophyte-inoculated and uninoculated control plants were subjected to feeding by larvae of the generalist root herbivore Rhizotrogus majalis (European chafer). Herbivory intensity was quantified after eight days, and regrowth of roots and shoots following root herbivory and mechanical shoot damage was measured thereafter for each treatment. Fungal identifications by DNA sequence analysis were conducted after completion of the herbivory experiments and revealed that the five endophytes included the decomposer fungi Trametes versicolor and Mortierella alpina, the entomopathogenic fungi Isaria fumosorosea and Beauveria bassiana, and a potential plant pathogen/entomopathogen Fusarium cf. equiseti. The effects of these root endophytes on plant defense against root-feeding insects were species-specific. While four endophytes had few effects on plant resistance, endophytic B. bassiana significantly reduced herbivore damage to roots. In comparison, plant tolerance to damage was impaired after colonization by all endophyte species except T. versicolor and M. alpina. The contrasting effects of endophytes on plant resistance and plant tolerance suggest that research solely evaluating plant resistance is likely to overestimate the benefits conferred by endophytes without accounting for potential negative effects on plant tolerance. We propose a conceptual framework to include both plant resistance and tolerance as two dimensions of a defensive strategy and show that plant associations with different root endophytes may shift the relative importance of resistance and tolerance for plant defense.

There is growing evidence that terrestrial ecosystems are exporting more dissolved organic carbon (DOC) to aquatic ecosystems than they did just a few decades ago. This “browning” phenomenon will alter the chemistry, physics, and biology of inland water bodies in complex and difficult-to-predict ways. Experiments provide an opportunity to elucidate how browning will affect the stability and functioning of aquatic ecosystems. However, it is challenging to obtain sources of DOC that can be used for manipulations at ecologically relevant scales. In this study, we evaluated a commercially available source of humic substances (“Super Hume”) as an analog for natural sources of terrestrial DOC. Based on chemical characterizations, comparative surveys, and whole-ecosystem manipulations, we found that the physical and chemical properties of Super Hume are similar to those of natural DOC in aquatic and terrestrial ecosystems. For example, Super Hume attenuated solar radiation in ways that will not only influence the physiology of aquatic taxa but also the metabolism of entire ecosystems. Based on its chemical properties (high lignin content, high quinone content, and low C:N and C:P ratios), Super Hume is a fairly recalcitrant, low-quality resource for aquatic consumers. Nevertheless, we demonstrate that Super Hume can subsidize aquatic food webs through 1) the uptake of dissolved organic constituents by microorganisms, and 2) the consumption of particulate fractions by larger organisms (i.e., Daphnia). After discussing some of the caveats of Super Hume, we conclude that commercial sources of humic substances can be used to help address pressing ecological questions concerning the increased export of terrestrial DOC to aquatic ecosystems.

A common finding in multiple CO(2) enrichment experiments in forests is the lack of soil carbon (C) accumulation owing to microbial priming of 'old' soil organic matter (SOM). However, soil C losses may also result from the accelerated turnover of 'young' microbial tissues that are rich in nitrogen (N) relative to bulk SOM. We measured root-induced changes in soil C dynamics in a pine forest exposed to elevated CO(2) and N enrichment by combining stable isotope analyses, molecular characterisations of SOM and microbial assays. We find strong evidence that the accelerated turnover of root-derived C under elevated CO(2) is sufficient in magnitude to offset increased belowground inputs. In addition, the C losses were associated with accelerated N cycling, suggesting that trees exposed to elevated CO(2) not only enhance N availability by stimulating microbial decomposition of SOM via priming but also increase the rate at which N cycles through microbial pools.