Many studies of the microbial ecology of agricultural ecosystems focus on surface soils, whereas the impacts of management practice and season on soil microbial community composition and function ...below the plough zone are largely neglected. Deep soils have a high potential to store carbon; therefore any management driven stimulation or repression of microorganisms in subsoil could impact biogeochemical cycling in agricultural sites. The aim of this study was to understand whether soil management affects microbial communities in the topsoil (0–10 cm), rooted zone beneath the plough layer (40–50 cm), and the unrooted zone (60–70 cm). In a field experiment with different crops wheat (Triticum aestivum L.) and maize (Zea mays L.) and agricultural management strategies (litter amendment) we analysed microbial biomass as phospholipid fatty acids (PLFAs) and enzyme activities involved in the C-cycle (β-glucosidase, N-acetyl-β-d-glucosaminidase, β-xylosidase, phenol- and peroxidase) across a depth transect over a period of two years. Wheat cultivation resulted in higher bacterial and fungal biomass as well as higher enzyme activities at most sampling dates in comparison to maize cultivated plots, and this effect was visible to 50 cm depth. Litter application increased bacterial and fungal biomass as well as hydrolytic enzyme activities but effects were apparent only in the topsoil. In winter high microbial biomass and enzyme activities were measured in all soil layers, possibly due to increased mobilization and translocation of organic matter into deeper soil. Hydrolytic enzyme activities decreased with depth, whereas oxidative enzyme activities showed no decrease or even an increase with depth. This could have been due to differing sorption mechanisms of hydrolytic and oxidative enzymes. Specific enzyme activities (enzyme activity per microbial biomass) were higher in the deeper layers and possible reasons are discussed.
► Crop type affects bacteria, fungi and enzyme activities down to a depth of 50 cm. ► Maize litter affects PLFAs and hydrolytic enzyme activities only in the topsoil. ► In winter, high substrate availability raises bacteria, fungi and enzyme activities. ► Varying sorption of enzyme classes result in a different depth distribution. ► Specific enzyme activities are higher in subsoil in comparison to topsoil.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
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.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Essential Biomolecules in Food Webs Ruess, Liliane; Müller-Navarra, Dörthe C.
Frontiers in ecology and evolution,
07/2019, Volume:
7
Journal Article
Peer reviewed
Open access
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.
To understand consumer dietary requirements and resource use across ecosystems, researchers have employed a variety of methods, including bulk stable isotope and fatty acid composition analyses. ...Compound-specific stable isotope analysis (CSIA) of fatty acids combines both of these tools into an even more powerful method with the capacity to broaden our understanding of food web ecology and nutritional dynamics. Here, we provide an overview of the potential that CSIA studies hold and their constraints. We first review the use of fatty acid CSIA in ecology at the natural abundance level as well as enriched physiological tracers, and highlight the unique insights that CSIA of fatty acids can provide. Next, we evaluate methodological best practices when generating and interpreting CSIA data. We then introduce three cutting-edge methods: hydrogen CSIA of fatty acids, and fatty acid isotopomer and isotopologue analyses, which are not yet widely used in ecological studies, but hold the potential to address some of the limitations of current techniques. Finally, we address future priorities in the field of CSIA including: generating more data across a wider range of taxa; lowering costs and increasing laboratory availability; working across disciplinary and methodological boundaries; and combining approaches to answer macroevolutionary questions. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
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.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Collembola are abundant and ubiquitous soil decomposers, being particularly active in the rhizosphere of plants where they are assumed to be attracted by high microbial activity and biomass. While ...feeding on root associated microorganisms or organic matter they may also ingest plant roots, e.g. particularly root hairs and fine roots. Employing stable isotope analysis we investigated Collembola (
Protaphorura fimata Gisin) feeding preferences and types of ingested resources. We offered Collembola two resources with distinct isotope signatures: a C4 plant (
Zea mays L.) planted in soil mixed with
15N labelled litter of
Lolium perenne L. (C3 plant). We hypothesised that Collembola obtain their nutrients (C and N) from different resources, with their carbon being mainly derived from resources that are closely associated to the plant root, e.g. root exudates, causing enrichment in
13C in Collembola tissue, while the incorporated nitrogen originating from litter resources. In contrast to our hypothesis, stable isotope analysis suggests that in absence of plant roots Collembola derived both the incorporated C and N predominantly from litter whereas in presence of plant roots they switched diet and obtained both C and N almost exclusively from plant roots.
The results indicate that Collembola in the rhizosphere of plants, being assumed to be mainly decomposers, in fact predominately live on plant resources, presumably fine roots or root hairs, i.e. are herbivorous rather than detritivorous or fungivorous. These findings have major implications on the view how plants respond to decomposers in the rhizosphere.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Recent stable isotope analyses indicate that a number of putative detritivorous soil microarthropods is not typical detritivores but rather live as predators or scavengers. Using molecular gut ...content analyses the present study investigates if nematodes indeed form part of the diet of oribatid mites. First, in a no-choice laboratory feeding experiment two nematode species (
Phasmarhabditis hermaphrodita and
Steinernema feltiae) were offered to eight species of oribatid mites and one gamasid mite. Second, after feeding for 4 and 48
h on each nematode species the detection time of prey DNA in the oribatid mite species
Steganacarus magnus was investigated. Third, in a field experiment nematode prey (
P. hermaphrodita and
S. feltiae) in the diet of microarthropods was investigated distinguishing between scavenging and predation. In the no-choice laboratory experiment not only the gamasid mite but also several of the studied oribatid mite species consumed nematodes. After feeding on nematodes for 4
h prey DNA was detectable in
S. magnus for only 4
h, but after feeding for 48
h prey DNA was detectable for 128
h, indicating that the duration of feeding on prey is an important determinant for prey DNA detection. The field experiment confirmed that oribatid mite species including
Liacarus subterraneus,
Platynothrus peltifer and
S. magnus intensively prey on nematodes. Interestingly, DNA of dead
P. hermaphrodita was detectable to a similar degree as that of living individuals indicating that scavenging is of significant importance in decomposer food webs. Results of our study indicate that predation and scavenging on nematodes by “detritivorous” microarthropods in soil food webs need to be reconsidered.
► Oribatid mites prey on nematodes and prey DNA is identified in their gut. ► Oribatid species vary in the extent to which they consume nematodes. ► Molecular gut content analyses were used to distinguish between predation and scavenging in the field.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
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.
► Tree species identity is more important than diversity in structuring soil food webs. ► Beech fostered the fungal energy channel and ash the bacterial energy channel. ► Root and litter-derived resources differently affect soil food webs.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Microplastics (MP) are pervasive in the environment. There is ample evidence of negative MP effects on biota in aquatic ecosystems, though little is known about MP effects in terrestrial ecosystems. ...Given numerous entry routes into soils, soil organisms are likely to be exposed to MP. We compared potential toxicological effects of MP from (i) low-density polyethylene (LDPE) (mean diameter ± standard deviation: 57 ± 40 µm) or (ii) a blend of biodegradable polymers polylactide (PLA) and poly(butylene adipate-co-terephthalate) (PBAT) (40 ± 31 µm) on the reproduction and body length of the soil-dwelling bacterivorous nematode Caenorhabditis elegans. Feed suspensions without (control) or with MP (treatments) at concentrations of 1, 10, and 100 mg MP L -1 were prepared and nematodes were exposed to those suspensions on NGM agar plates until completion of their reproductive phase (~ 6 days). Using Nile red-stained PLA/PBAT MP particles and fluorescence microscopy, we demonstrated the ingestion of MP by C. elegans into pharynges and intestines. Under MP exposure, nematodes had fewer offspring (up to 22.9%) compared to nematodes in the control group. This decline was independent on the plastic type. We detected a tendency towards greater decreases in offspring at higher concentrations. Despite hints of negative effects on nematode body length under MP exposure, we could not derive a consistent pattern. We conclude that in MP-contaminated soils, the reproduction of nematodes, central actors in the soil food web, can be affected, with potentially negative implications for key soil functions, e.g., the regulation of soil biogeochemical cycles.
Endogenous rhythmic growth (ERG) is displayed by many tropical and some major temperate tree species and characterized by alternating root and shoot flushes (RF and SF). These flushes occur parallel ...to changes in biomass partitioning and in allocation of recently assimilated carbon and nitrogen. To address how biotic interactions interplay with ERG, we cross-compared the RF/SF shifts in oak microcuttings in the presence of pathogens, consumers and a mycorrhiza helper bacterium, without and with an ectomycorrhizal fungus (EMF), and present a synthesis of the observations. The typical increase in carbon allocation to sink leaves during SF did not occur in the presence of root or leaf pathogens, and the increase in nitrogen allocation to lateral roots during RF did not occur with the pathogens. The RF/SF shifts in resource allocation were mostly restored upon additional interaction with the EMF. Its presence led to increased resource allocation to principal roots during RF, also when the oaks were inoculated additionally with other interactors. The interactors affected the alternating, rhythmic growth and resource allocation shifts between shoots and roots. The restoring role of the EMF on RF/SF changes in parallel to the corresponding enhanced carbon and nitrogen allocation to sink tissues suggests that the EMF is supporting plants in maintaining the ERG.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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