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Soil food web structure and function is primarily determined by the major basal resources, which are living plant tissue, root exudates and dead organic matter. A field experiment was performed to disentangle the interlinkage of the root-and detritus-based soil food chains. An arable site was cropped either with maize, amended with maize shoot litter or remained bare soil, representing food webs depending on roots, aboveground litter and soil organic matter as predominant resource, respectively. The soil micro-food web, i.e. microorganisms and nematodes, was investigated in two successive years along a depth transect. The community composition of nematodes was used as model to determine the changes in the rhizosphere, detritusphere and bulk soil food web. In the first growing season the impact of treatments on the soil micro-food web was minor. In the second year plant-feeding nematodes increased under maize, whereas after harvest the Channel Index assigned promotion of the detritivore food chain, reflecting decomposition of root residues. The amendment with litter did not foster microorganisms, instead biomass of Gram-positive and Gram-negative bacteria as well as that of fungi declined in the rooted zone. Likely higher grazing pressure by nematodes reduced microbial standing crop as bacterial and fungal feeders increased. However, populations at higher trophic levels were not promoted, indicating limited flux of litter resources along the food chain. After two years of bare soil microbial biomass and nematode density remained stable, pointing to soil organic matter-based resources that allow bridging periods with deprivation. Nematode communities were dominated by opportunistic taxa that are competitive at moderate resource supply. In sum, removal of plants from the system had less severe effects than expected, suggesting considerable food web resilience to the disruption of both the root and detrital carbon channel, pointing to a legacy of organic matter resources in arable soils.

Subsurface microorganisms are essential constituents of the soil purification processes associated with groundwater quality. In particular, soil enzyme activity determines the biodegradation of organic compounds passing through the soil profile. Transects from surface soil to a depth of 3.5 m were investigated for microbial and chemical soil characteristics at two groundwater recharge sites and one control site. The functional diversity of the microbial community was analyzed via the activity of eight enzymes. Acid phosphomonoesterase was dominant across sites and depths, followed by L-leucine aminopeptidase and beta-glucosidase. Structural [e.g. phospholipid fatty acid (PLFA) pattern] and functional microbial diversities were linked to each other at the nonwatered site, whereas amendment with nutrients (DOC, NO(3)(-)) by flooding uncoupled this relationship. Microbial biomass did not differ between sites, whereas microbial respiration was the highest at the watered sites. Hence, excess nutrients available due to artificial groundwater recharge could not compensate for the limitation by others (e.g. phosphorus as assigned by acid phosphomonoesterase activity). Instead, at a similar microbial biomass, waste respiration via overflow metabolism occurred. In summary, ample supply of carbon by flooding led to a separation of decomposition and microbial growth, which may play an important role in regulating purification processes during groundwater recharge.

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 16:1omega5, 16:1omega7, cy17:0 and 18:1omega9t, and the long-chained PLFAs 22:1omega9 and 24:1omega9 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.

Top–down control by nematodes over soil microorganisms – considered to be stronger over bacteria than over fungi – may dampen microbial responses to global changes in tundra. To test whether large grazers alter the responses of belowground trophic networks to global changes, we employed factorial warming and nitrogen fertilization treatments in adjacent sites with different reindeer grazing intensities for the past 50 years. Lightly grazed tundra is dominated by dwarf shrubs and a more fungal‐based microbial community, while in heavily grazed tundra the high reindeer densities during autumn migration have induced a shift into graminoids and a more bacterial‐based microbial community. We analysed the soil micro‐food web (i.e. the nematode density, trophic structure and species composition) as well as fungal, bacterial and total phospholipid fatty acids (PLFAs) after four growing seasons of warming and fertilization both before and during reindeer migration. We predicted that bacterivore densities are higher and fungivore densities lower under heavy than light grazing (i.e. nematode populations before migration reflect grazing effects via the base of the food web), whereas reindeer migration induces a negative impact on nematode densities under heavy grazing (disturbance by trampling is the driving factor). We further predicted that nematodes negate treatment effects on microbial biomass to a stronger extent in the bacterial‐based heavily grazed tundra than in the fungal‐based lightly grazed tundra. Fungivore densities were higher under light than under heavy grazing, but nematodes did not respond to trampling. Warming increased fungivores and the fungal PLFAs irrespective of grazing and timing but, under heavy grazing, it increased bacterivores while the bacterial PLFAs remained steady. Fertilization increased carnivores and influenced nematode species composition, diversity and maturity interactively with warming. Our data suggest that large grazers affect tundra soil nematodes via bottom–up effects through microbial community composition and biomass, which in turn may alter the strength of their top–down control over soil bacteria under climate warming. [ABSTRACT FROM AUTHOR]

Interactions between bacteria and nematode grazers are an important component of soil food webs yet, due to the cryptic habitat, they are almost exclusively investigated in artificial agar substrate. Transport, food choice and foraging experiments were performed in a modular microcosm system with the nematode Acrobeloides buetschlii and bacterial diets (Escherichia coll, Pseudomonas putida and Bacillus subtilis) in gamma-irradiated soil. Bacterial biomass was assessed by soil phospholipid fatty acids (PLFAs). Continuous random foraging of nematodes was affected by soil type. Food choice experiments revealed diet switch and time lag preference responses, suggesting that nematode population fluctuations are driven by multiple factors such as bacterial attractants, defence strategies or food quality. Application of PLFA markers revealed a strong nematode predation pressure, as biomass in P. putida declined by 50%, whereas no transport of bacteria through soil was indicated. Overall, semi-natural experimental systems are an essential prerequisite to gain a realistic picture in microbial-microfaunal interactions. [ABSTRACT FROM AUTHOR]

The complexity of soil food webs and the cryptic habitat hamper the analyses of pools, fluxes and turnover rates of carbon (C) in organisms and the insight into their interactions. Stable isotope analysis has been increasingly used to disentangle soil food web structure, yet it has not been applied to quantitatively characterize C dynamics at the level of the entire soil food web., The present study employed 13CO2 pulse labelling to investigate the incorporation of maize root-derived C into major soil compartments and food web players in an arable field for 25 days. Bulk tissue and compound-specific (lipids) C isotope ratios were used to quantify pool sizes and 13C incorporation in bacteria and fungi as primary decomposers, nematodes as key drivers of the microfood web and decomposers and predators among the meso- and macrofauna., About 20% of the C assimilated by maize was transferred to below-ground pools. 13C was predominantly incorporated into rhizosphere micro-organisms rather than in those of the bulk soil. 13C in phospholipid fatty acid biomarkers revealed that root-derived C was incorporated into the soil food web mainly via saprotrophic fungi rather than via bacteria. Only small amounts of 13C were transferred to higher trophic levels, predominantly into fungal-feeding nematodes and macrofauna decomposers., Most importantly, C pool size and 13C incorporation did not match closely. Although the fungal C stock was less than half that of bacteria, C transfers from fungi into higher trophic levels of the fungal energy pathway, that is fungal-feeding nematodes and meso- and macrofauna decomposers, by far exceed that of bacterial C. This challenges previous views on the dominance of bacteria in root C dynamics and suggests saprotrophic fungi to function as major agents channelling recent photoassimilates into the soil food web. [ABSTRACT FROM AUTHOR]

Soil animals live in complex and heterogeneous habitats including litter of various types but also microhabitats such as mosses, fungal mats and grass patches. Soil food webs have been separated into a slow fungal and a fast bacterial energy channel. Bacterial-feeding nematodes are an important component of the bacterial energy channel by consuming bacteria and forming prey for higher trophic levels such as soil microarthropods. Investigating the role of nematodes as prey for higher trophic level consumers has been hampered by methodological problems related to their small body size and lack in skeletal structures which can be traced in the gut of consumers. Recent studies using molecular gut content analyses suggest that nematodes form major prey of soil microarthropods including those previously assumed to live as detritivores. Using molecular markers we traced nematode prey in fourteen abundant soil microarthropod taxa of Mesostigmata and Oribatida (both Acari) from three different microhabitats (litter, grass and moss). Consumption of nematodes varied between mite species indicating that trophic niche variation contributes to the high diversity of microarthropods in deciduous forests. Further, consumption of nematodes by Mesostigmata (but not Oribatida) differed between microhabitats indicating that trophic niches vary with habitat characteristics. Overall, the results suggest that free-living bacterial-feeding nematodes form important prey for soil microarthropods including those previously assumed to live as detritivores. [ABSTRACT FROM AUTHOR]

Abstract: Positive relationships between biodiversity and ecosystem functioning are reported in many studies. The underlying mechanisms are, however, only little understood, likely due to the focus on the aboveground system and neglecting species-specific traits. We used different clusters of tree species composition to investigate how tree species diversity and tree species identity affect belowground nematode communities. Since soil nematodes comprise different trophic groups and are strongly linked to the microbial community, results can provide insight on how soil food webs are structured. In addition, data on leaf litter and fine root biomass were included to account for different effects of aboveground and belowground resources. Clusters of three trees of one, two and three species were identified within a temperate deciduous forest. Target tree species were European beech (Fagus sylvatica), common ash (Fraxinus excelsior) and lime (Tilia cordata, T. platyphyllos) differing in physiology, leaf litter quality and type of mycorrhiza. Tree species identity strongly affected nematode trophic structure, whereas tree species diversity had no impact. Ash beneficially affected bacterial-feeding nematodes, whereas fungal feeders were suppressed, likely caused by ash litter increasing soil pH. Fostering of the bacterial food chain by ash additionally could be related to rhizodeposition gaining importance after disappearance of high quality ash litter in spring, highlighting seasonal shifts in root and leaf litter-derived resources. The negative effect of ash on fungal-feeding nematodes is suggested to be due to the lack of ectomycorrhizal fungi as ash roots only form arbuscular mycorrhiza. In contrast, beech benefited fungal feeders and detrimentally affected bacterial feeders due to more acidic soil conditions that increase the competitive strength of fungi. Lime tended to negatively impact total nematode density but positively influenced plant-feeding nematodes. Generally, beech and ash strongly but opposingly influenced the trophic structure of nematode communities suggesting that changes in tree species identity result in major shifts in the channeling of energy through decomposer food webs. The results indicate that the structure of soil food webs varies markedly with tree species and point to the importance of basal resources, i.e., leaf litter and rhizodeposits. This suggests bottom-up forces mediated by individual tree species to control major decomposition pathways rather than tree diversity. [Copyright &y& Elsevier]

Soil organisms constitute multitrophic food webs, which are important determinants for nutrient and carbon flow through terrestrial systems. However, these complex interactions are not well understood, particular in the most cryptic compartment – the link between microorganisms and microfauna. The present study investigates binary trophic links between microbial prey and nematodes in a controlled semi-natural soil environment. A microcosm system with circulating airflow was filled with γ-irradiated arable soil (Luvisol), inoculated with 13C labelled microbial diet and nematode grazers, and incubated for 72 h. Signatures of 13C and CO 2 evolved from microcosms, soil phospholipid fatty acids and nematode densities were determined. Except for the model nematode Caenorhabditis elegans, all organisms joint in the 12 different investigated binary links represent dominant taxa at the arable field site. Studied were the fungal grazers Aphelenchoides saprophilus and Aphelenchus sp. in combination with the fungi Chaetomium globosum, Aspergillus terreus or Cryptococcus terreus as well as the bacterial grazers C. elegans and Acrobeloides buetschlii in combination with the bacteria Pseudomonas putida , Kitasatospora sp. or Sphingomonas trueperi. The results assigned trophic and non-trophic interactions and considerable variation between binary links. The biomass decline of S. trueperi in presence of C. elegans as well as the increased release of 13C in links of C. globosum and A. terreus with Aphelenchus sp. and S. trueperi with A. buetschlii assign nematode grazing and thus a classical predator-prey system. Such direct trophic interactions can induce distinct C fluxes within a binary link as assigned by the increased density (i.e. biomass) of C. elegans when feeding on S. trueperi. In contrast, the numbers of Aphelenchus sp. declined when feeding on A. terreus , and thus reduced C flow to the next trophic level. Grazing can also foster C allocation in microbial biomass via compensatory growth, as indicated e.g. for the link of Aphelenchus sp. with the fungi C. globosum and A. terreus. While these diverse responses to grazing were to be expected, the use of CO 2 and 13C measurements further revealed that non-trophic interactions shape C flux in a binary link, particularly in the bacterial channel. Besides the fungal link of C. terreus with Aphelenchus sp., non-trophic interactions were obvious for the bacterial links Kitasatospora sp. with C. elegans or A. buetschlii, and P. putida with A. buetschlii. The presence of nematodes caused a reduction in respiration (evolved CO 2), thus a decline in microbial activity. The formation of chemical and/or morphological defense is likely a reason for that reduced prey activity. For further studies the inclusion of such non-trophic interactions is necessary to achieve realistic models for C flow through soil food webs. • Microbial traits cause variation in palatability for nematode grazers. • Predator-prey interactions of nematodes within a functional guild differ. • Impact of non-trophic interactions on C flux depends on the specific binary link. [ABSTRACT FROM AUTHOR]

Abstract: Fatty acid (FA) analysis is a promising tool to study trophic relationships in soil food webs. We determined FA biomarkers to trace bacterial food sources (Bacillus megaterium, Pseudomonas putida, Enterobacter aerogenes) of Collembola (Heteromurus nitidus, Protaphorura fimata, Folsomia candida). In addition, δ15N, δ13C, C/N ratio, body weight and NLFA/PLFA ratio (neutral lipid/phospholipid fatty acids) of Collembola were assessed. These measures indicated that P. putida ranked first, B. megaterium second and E. aerogenes third in food quality. FAs specific for bacteria were found in the NLFAs of the Collembola reflecting the respective bacterial diet. Biomarker FAs for gram-positive bacteria were methyl branched i14:0, i15:0, a15:0 and i17:0. Consumption of gram-negative bacteria was reflected by the cyclic form cy17:0 (E. aerogenes, P. putida) and by 16:1ω5 (P. putida). [Copyright &y& Elsevier]

• Anthropogenic forest use and management may affect ecological communities. • Aquatic communities in water-filled tree holes were used as a model system. • Forest management showed strong, often negative and indirect effects on insects. • Nematode and bacterial communities were less affected. • Forest management impacts are complex but should be considered explicitly. Ecological communities in forests have been shown to be strongly affected by forest management but a detailed understanding of how different components of management affect insect communities directly and indirectly via environmental variables, how management influences functional trait diversity and composition, and whether these results can be transferred to other functional groups besides insects (e.g. bacteria or nematodes) is still missing. To address these questions we used water-filled tree holes, which provide habitats for insect larvae and other aquatic organisms in forests, as a model system. We mapped all water-filled tree holes in 75 forest plots (1 ha) under different management intensity in three regions of Germany. We measured structural and climatic conditions at different spatial scales, sampled insect communities in 123 tree holes and bacterial and nematode communities in a subset of these. We found that forest management in terms of harvesting intensity and the proportion of non-natural tree species (species not part of the natural vegetation at the sites) negatively affected tree-hole abundance. An increased proportion of non-natural tree species had a positive direct effect on insect richness and functional diversity in the tree holes. However, a structural equation model showed that increasing management intensity had negative indirect effects on insect abundance and richness, operating via environmental variables at stand and tree-hole scale. Functional diversity and trait composition of insect communities similarly responded to changes in management-related variables. In contrast to insects, bacterial and nematode richness were not directly impacted by forest management but by other environmental variables. Our results suggest that forest management may strongly alter insect communities of tree holes, while nematodes and bacteria seem less affected. Most effects in our study were indirect and negative, indicating that management has often complex consequences for forest communities that should be taken into account in forest management schemes. [ABSTRACT FROM AUTHOR]