We here review the ecological role of essential nutritional biomolecules [fatty acids (FA), amino acids (AA), sterols, vitamins] in aquatic and terrestrial food webs, encompassing the forces behind their environmental distribution. Across ecosystems, mutualistic relationships frequently ensure exchanges of vitamins between producer and demander, especially between B₁₂ and other B vitamins as well as the AA methionine. In contrast, FA, sterols and most AA are transferred up the food chain via classical predator-prey interactions, and therefore have good biomarker potential for trophic interactions. As biomass-flow depends on the absolute amounts of potential limiting resources, considering solely the relative share in the respective biochemical group may under- or overestimate the availability to consumers. Moreover, if not accounted for, “hidden” trophic channels, such as gut symbionts as well as metabolic conversion of precursor molecules, can hamper food web analyses. Fundamental differences exist between aquatic and terrestrial ecosystems: Vitamin B₁₂ produced by ammonium oxidizing Archaea is essential to many aquatic algae, whereas terrestrial plants escaped this dependency by using B₁₂ independent enzymes. Long-chain ω3 polyunsaturated FA (LC-ω3PUFA) in aquatic systems mainly originate from planktonic algae, while in terrestrial systems, belowground invertebrates can well be a source, also supporting aboveground biota. Interlinks from terrestrial to aquatic ecosystems are of a biochemically totally different nature than vice versa. While biomass rich in proteins and LC-ω3PUFA is transferred to land, e.g., by trophic relationships, the link from terrestrial to aquatic ecosystems provides recalcitrant plant carbon, mainly devoid of essential nutrients, fuelling detrital food chains. Recent global changes influence food webs via altered input and transfer of essential biomolecules, but separating the effects of nutrients, CO₂, and warming is not trivial. Current evolutionary concepts (e.g., Black Queen, relaxed selection) considering the costs of metabolic production partly explain food web dynamics, especially for vitamins, whereas adaptations to potential oxidative stress seem to be more important for LC-PUFA. Overall, the provision with essential biomolecules is precious for both heterotrophs and auxotrophs. These nutritional valuable molecules often are kept unaltered in consumer metabolism, including their stable isotope composition, offering a great advantage for their use as trophic markers.

Pedunculate oak (Quercus robur L.), an important forest tree in temperate ecosystems, displays an endogenous rhythmic growth pattern, characterized by alternating shoot and root growth flushes paralleled by oscillations in carbon allocation to below- and aboveground tissues. However, these common plant traits so far have largely been neglected as a determining factor for the outcome of plant biotic interactions. This study investigates the response of oak to migratory root-parasitic nematodes in relation to rhythmic growth, and how this plant-nematode interaction is modulated by an ectomycorrhizal symbiont. Oaks roots were inoculated with the nematode Pratylenchus penetrans solely and in combination with the fungus Piloderma croceum, and the systemic impact on oak plants was assessed by RNA transcriptomic profiles in leaves. The response of oaks to the plant-parasitic nematode was strongest during shoot flush, with a 16-fold increase in the number of differentially expressed genes as compared to root flush. Multi-layered defence mechanisms were induced at shoot flush, comprising upregulation of reactive oxygen species formation, hormone signalling (e.g. jasmonic acid synthesis), and proteins involved in the shikimate pathway. In contrast during root flush production of glycerolipids involved in signalling cascades was repressed, suggesting that P. penetrans actively suppressed host defence. With the presence of the mycorrhizal symbiont, the gene expression pattern was vice versa with a distinctly stronger effect of P. penetrans at root flush, including attenuated defence, cell and carbon metabolism, likely a response to the enhanced carbon sink strength in roots induced by the presence of both, nematode and fungus. Meanwhile at shoot flush, when nutrients are retained in aboveground tissue, oak defence reactions, such as altered photosynthesis and sugar pathways, diminished. The results highlight that gene response patterns of plants to biotic interactions, both negative (i.e. plant-parasitic nematodes) and beneficial (i.e. mycorrhiza), are largely modulated by endogenous rhythmic growth, and that such plant traits should be considered as an important driver of these relationships in future studies.

Soil food webs are important drivers for key ecological functions in terrestrial systems such as carbon and nutrient cycling. However, soil food web models generally lack quantitative data, mainly due to the shortage in high-throughput methods to describe energy flows. In marine environments, multivariate optimization models (Quantitative Fatty Acid Signature Analysis) and Bayesian approaches (source-tracking algorithm) were established to predict the proportion of predator diets using lipids as tracers. A premise for the application of such models to soil systems is to acquire the fatty acid pattern of a broad range of resources and to reveal potential overlap in their signatures. We present a comprehensive comparison of lipid pattern across widespread taxa of plants (leaves and roots, n = 48), algae (n = 59), fungi (n = 60), and bacteria (n = 62) as basal food web resources. Lipid profiles from microorganisms and algae were assessed from laboratory cultures, whereas plant tissue was derived from an arable field. A lipid library was constructed and multivariate data analyses (hierarchical clustering, nMDS) was used to assess the extent of separation in lipid pattern by species or resource type. The performance of the lipid library was tested by leave-one-prey-out (LOPO) analysis, giving the distinctiveness of the resource (prey) groups. Fungi and plant leaves were correctly assigned based on their lipid pattern with more than 98%, while plant roots and bacteria achieved 88 and 85%, respectively. However, algae were only correctly classified by 60%, pointing to a bias in the herbivore food chain. Fatty acids most important for separation of algae and plant leaves were of the omega 3 type, i.e. 16:3ω3 and 18:3ω3. In plant roots 18:1ω9 was most important, whereas bacteria were distinguished predominantly by methyl-branched fatty acids. Overall, the lipid pattern of major soil food web resources are sufficiently differentiated to allow for qualitative (biomarker) analyses as well as quantitative modelling, yet with precaution in the case of algae.

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.

Numerous lab and field studies have reported the potential of soil predatory mites for the biological control of plant-parasitic nematodes and arthropods pests. Most of these studies have utilized biocontrol agents in augmentative releases, essentially controlling the pest with the released predators. While this may be a valid approach, we hypothesize that conservation of soil mite predators with available, suitable, and accessible free-living nematodes as prey, will provide better agricultural ecosystem performance and long-range sustainability. In this manuscript, we review the relevant studies on soil predatory mite–nematode interactions and highlight their potential for conservation biological control of soil-borne pests. Additionally, we emphasize the importance of implementing environmentally sound soil management practices for the sustainability and conservation of functional soil food webs.