Compound-specific isotope analysis of amino acids as a new tool to uncover trophic chains in soil food webs

Food webs in soil differ fundamentally from those aboveground; they are based on inputs from both living plants via root exudates, and from detritus, which is a complex mixture of fungi, bacteria, and dead plant remains. Trophic relationships are difficult to disentangle due to the cryptic lifestyle of soil animals and inevitable microbial contributions to their diet. Compound‐specific isotope analysis of amino acids (AAs) is increasingly used to explore complex food webs. The combined use of AA δ^(13)C and δ^(15)N values is a promising new approach to disentangle trophic relationships since it provides independent but complementary information on basal resources, as well as the trophic position of consumers. We conducted a controlled feeding study in which we reconstructed trophic chains from main basal resources (bacteria, fungi, plants) to primary consumers (springtails, oribatid mites) and predators (gamasid mites, spiders). We analyzed dual compound‐specific isotope AA values of both resources and consumers. By applying an approach termed “stable isotope (^(13)C) fingerprinting” we identified basal resources, and concomitantly calculated trophic positions using ^(15)N values of trophic and source AAs in consumers. In the ^(13)C fingerprinting analysis, consumers in general grouped close to their basal resources. However, higher than usual offsets in AA δ^(13)C between diet and consumers suggest either gut microbial supplementation or the utilization of specific resource fractions. Identification of trophic position crucially depends on correct estimates of the trophic discrimination factor (TDF_(Glu‐Phe)), which was close to the commonly applied value of 7.6‰ in primary consumers feeding on microbial resources, but considerably lower in arachnid predators (~2.4‰), presumably due to higher diet quality, excretion of guanine, and fluid feeding. While our feeding study demonstrates that dual compound‐specific AA analyses hold great promise in delineating trophic linkages among soil‐dwelling consumers and their resources, it also highlights that a “one‐size‐fits‐all” approach to TDF_(Glu‐Phe) does not apply to soil food webs

Rainforest transformation reallocates energy from green to brown food webs.

Terrestrial animal biodiversity is increasingly being lost because of land-use change1,2. However, functional and energetic consequences aboveground and belowground and across trophic levels in megadiverse tropical ecosystems remain largely unknown. To fill this gap, we assessed changes in energy fluxes across 'green' aboveground (canopy arthropods and birds) and 'brown' belowground (soil arthropods and earthworms) animal food webs in tropical rainforests and plantations in Sumatra, Indonesia. Our results showed that most of the energy in rainforests is channelled to the belowground animal food web. Oil palm and rubber plantations had similar or, in the case of rubber agroforest, higher total animal energy fluxes compared to rainforest but the key energetic nodes were distinctly different: in rainforest more than 90% of the total animal energy flux was channelled by arthropods in soil and canopy, whereas in plantations more than 50% of the energy was allocated to annelids (earthworms). Land-use change led to a consistent decline in multitrophic energy flux aboveground, whereas belowground food webs responded with reduced energy flux to higher trophic levels, down to -90%, and with shifts from slow (fungal) to fast (bacterial) energy channels and from faeces production towards consumption of soil organic matter. This coincides with previously reported soil carbon stock depletion3. Here we show that well-documented animal biodiversity declines with tropical land-use change4-6 are associated with vast energetic and functional restructuring in food webs across aboveground and belowground ecosystem compartments

Global fine-resolution data on springtail abundance and community structure

Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.</p

Globally invariant metabolism but density-diversity mismatch in springtails.

Soil life supports the functioning and biodiversity of terrestrial ecosystems. Springtails (Collembola) are among the most abundant soil arthropods regulating soil fertility and flow of energy through above- and belowground food webs. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset representing 2470 sites, we estimate the total soil springtail biomass at 27.5 megatons carbon, which is threefold higher than wild terrestrial vertebrates, and record peak densities up to 2 million individuals per square meter in the tundra. Despite a 20-fold biomass difference between the tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the changes in temperature with latitude. Neither springtail density nor community metabolism is predicted by local species richness, which is high in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation and resource limitation in soil communities. Contrasting relationships of biomass, diversity and activity of springtail communities with temperature suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting soil functioning

Global change in above-belowground multitrophic grassland communities

Global change is transforming Earth’s ecological communities with severe consequences for the functions and services they provide. In temperate grasslands, home to a mesmerising diversity of invertebrates controlling multiple ecosystem processes and services, land-use intensification and climate change are two of the most important global-change drivers. While we know a lot about their independent effects on grassland biodiversity and ecosystem functioning, little is known about how these stressors interact. Moreover, most research on biodiversity change focuses on decreasing biomass or species richness, while a major aspect is commonly ignored – altered ecological interactions. This is problematic because these interactions represent and control many important ecosystem processes, such as predation, herbivory or decomposition. Networks of trophic interactions, so-called food webs, link the structure and functioning of ecological communities and unravel mechanistic relationships between environmental change, ecological communities and ecosystem multifunctionality – the ability of a system to simultaneously support multiple processes. Consequently, we need to study how ecological interactions and the food webs they comprise respond to environmental change and to multiple interacting global-change drivers. Fortunately, novel tools offer unprecedented opportunities in studying trophic interactions and their impact on ecosystem processes. In addition, we know far more about how global change impacts the aboveground world than its belowground counterpart. However, belowground communities are just as important for the overall functioning of terrestrial ecosystems. Thus, to comprehensively understand global-change impacts on temperate grasslands, we need to study above- and belowground multitrophic interactions and ecosystem processes together, also accounting for their interdependencies. Here, we propose to use the Global Change Experimental Facility (GCEF, Bad Lauchstädt, Germany) to study joint impacts of land-use intensity and climate change on above-belowground multitrophic interactions and ecosystem multifunctionality in a temperate grassland global-change experiment. We will combine novel approaches to assessing trophic interactions and basal-resource dependency with an innovative method to quantify energy flux through ecological interaction networks. We will disentangle separate and interactive effects of land use and climate change and unravel how global-change driven modifications in multitrophic interactions mechanistically translate into altered ecosystem processes and multifunctionality – above and below the ground. Combining a field-experimental approach with novel molecular and quantitative techniques will allow for a leap forward in our understanding of global-change impacts on temperate grasslands, which will be crucial to manage and conserve these important ecosystems

Data from: Conversion of rainforest to oil palm and rubber plantations alters energy channels in soil food webs

In the last decades lowland tropical rainforest has been converted in large into plantation systems. Despite the evident changes above ground, the effect of rainforest conversion on the channeling of energy in soil food webs was not studied. Here we investigated community-level neutral lipid fatty acid profiles in dominant soil fauna to track energy channels in rainforest, rubber and oil palm plantations in Sumatra, Indonesia. Abundant macrofauna including Araneae, Chilopoda and Diplopoda contained high amounts of plant and fungal biomarker fatty acids (FAs). Lumbricina had the lowest amount of plant, but the highest amount of animal-synthesized C20 polyunsaturated FAs as compared to other soil taxa. Mesofauna detritivores (Collembola and Oribatida) contained high amounts of algal biomarker FAs. The differences in FA profiles between taxa were evident if data were analysed across land-use systems, suggesting that soil fauna of different size (macro- and mesofauna) are associated with different energy channels. Despite that, rainforest conversion changed the biomarker FA composition of soil fauna at the community level. Conversion of rainforest into oil palm plantations enhanced the plant energy channel in soil food webs and reduced the bacterial energy channel; conversion into rubber plantations reduced the AMF-based energy channel. The changes in energy distribution within soil food webs may have significant implications for the functioning of tropical ecosystems and their response to environmental changes. At present, these responses are hard to predict considering the poor knowledge on structure and functioning of tropical soil food webs

Characterization of intact polar lipids in soils for assessing their origin

Soil and root samples were taken at the Jena Experiment, a large grassland biodiversity experiment located in the Saale valley near Jena (east Thuringia, Germany, 50°55'N, 11°35'E, 130 m above sea level). In 2002, the experiment was established with a total number of 81 grassland plots of 20 × 20 m (Roscher et al., 2004). The soil type is Eutric Fluvisol and the soil texture changes from sandy loam to silty clay with increasing distance to the Saale river (FAO-Unesco, 1997; Fischer et al., 2014). In June 2016, three surface soil samples (0-10 cm) from each plot were collected, combined to reduce the spatial heterogeneity, and homogenized. The soil samples were sieved (2 mm mesh size). Fine roots (if present) were picked using steel tweezers and stored at −20 ℃. The root samples were taken separately from six plots with different combinations of four functional groups (grass, legume, tall herb, small herb; Table S1). The roots were washed, freeze-dried and frozen. All fungal strains used originate from Jena Microbial Resource Collection (JRMC), University of Jena and HKI, Germany. The saprotrophic fungi Schizophyllum commune FSU:3214xFSU:2896 and Mucor plumbeus JMRC:SF:013709 were cultivated in Petri dishes on solid complex yeast medium (CYM; Schwalb and Miles, 1967) and the mycorrhizal fungi Tricholoma vaccinum JMRC:FSU:4731 and Pisolithus tinctorius FSU:10019 on modified Melin Norkrans b (MMNb) medium (Kottke et al., 1987) at room temperature for 2 and 5 days for the fast growing M. plumbeus and S. commune and 2 and 3 weeks for the slow growing P. tinctorius and T. vaccinum (Table S1). Further six bacterial strains were chosen for this study: Streptomyces acidiscabies E13 (JMRC:ST:033552 from JRMC), Streptomyces mirabilis P16B-1 (Schmidt et al., 2009), Bacillus subtilis DSM-10, Agrobacterium tumefaciens DSM-30150, Pseudomonas fluorescens DSM-50090 (DSMZ, Braunschweig, Germany), and Acetobacter xylinum NQ5 (ATCC 53582; ATCC, USA European Office at Wesel, Germany). The strains were cultivated for 2 to 5 days in Petri dishes on minimal medium (MM; Schmidt et al. 2009) at 28 °C. The collembolans species Heteromurus nitidus (Templeton, 1835) and Folsomia candida Willem, 1902 were taken from laboratory cultures fed with baker's yeast (Saccharomyces cerevisiae; Table S1). Laboratory cultures were maintained in glass jars filled with moist potting soil at 15 °C in darkness and kept moist with distilled water. Before analysis, collembolans were starved for three days to empty their guts; subsequently they were frozen and stored in methanol. Polysphondylium pallidum strain was from the Stallforth Lab at Leibniz Institute for Natural Product Research and Infection Biology in Jena (Germany). Amoebae were cultured (xenically) in the presence of the bacterium Klebsiella aerogenes as food. Briefly, amoebal spore suspension (from previously collected sori) was added to the surface of SM/5 agar plate seeded with 1 X 108 CFU/ml food bacterium K. aerogenes. Plates were incubated at 22°C for 7 to 10 days for mature fruiting bodies to appear. The entire cell mass of amoebal fruiting bodies was carefully collected using a sterile inoculation loop and suspended in KK2 buffer. This cell mass was washed clean of any attached bacteria using the same buffer. Resulting amoebal cells were then subjected to further analysis. Before analyses, roots, fungi, collembolans and amoebae were frozen in liquid nitrogen. They were ground into fine powder and extracted using the same protocol as for the soil samples. Cultured bacteria were collected from Petri dish plates, weighed and extracted using the same protocol