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
Molecular gut content analysis via diagnostic PCR or high-throughput sequencing (metabarcoding) of consumers allows unravelling of feeding interactions in a wide range of animals. This is of ...particular advantage for analyzing the diet of small invertebrates living in opaque habitats such as the soil. Due to their small body size, which complicates dissection, microarthropods are subjected to whole-body DNA extraction-step before their gut content is screened for DNA of their food. This poses the problem that body surface contaminants, such as fungal spores may be incorrectly identified as ingested food particles for fungivorous species. We investigated the effectiveness of ten methods for body surface decontamination in litter-dwelling oribatid mites using Steganacarus magnus as model species. Furthermore, we tested for potential adverse effects of the decontamination techniques on the molecular detection of ingested prey organisms. Prior to decontamination, oribatid mites were fed with an oversupply of nematodes (Plectus sp.) and postmortem contaminated with fungal spores (Chaetomium globosum). We used diagnostic PCR with primers specific for C. globosum and Plectus sp. to detect contaminants and prey, respectively. The results suggest that chlorine bleach (sodium hypochloride, NaClO, 5%) is most efficient in removing fungal surface contamination without significantly affecting the detection of prey DNA in the gut. Based on these results, we provide a standard protocol for efficient body surface decontamination allowing to trace the prey spectrum of microarthropods using molecular gut content analysis.
Forest soil food webs have been assumed to be fueled substantially by root-derived resources. However, until today the flux of root-derived resources into soil animals has been investigated virtually ...exclusively using isotope labeling experiments, whereas studies on the consequences of disrupting the flux of root-derived resources into the soil animal food web are scarce. We here investigated the importance of root-derived resources for a wide range of soil animals by interrupting the resource flux into the soil of different forest types in Central Europe using a trenching experiment. We recorded the abundance of soil animal taxa varying in body size (micro-, meso-, and macrofauna) 1 and 3 years after root trenching, and quantified changes in biomass, species composition, and trophic shift using stable isotopes and NLFA analysis. Among the microfauna groups studied (trophic groups of Nematoda) only the abundance of plant feeding nematodes showed a trend in being decreased by -58% due to root trenching. Major soil mesofauna groups, including Collembola and Oribatida, suffered to a similar extent from root trenching with their abundance and biomass being reduced by about 30–40%. The soil macrofauna groups studied (Diplopoda, Isopoda, Chilopoda, Araneae, Coleoptera) generally were only little affected by root trenching suggesting that they rely less on root-derived resources than micro- and in particular mesofauna. Notably, the community structure of micro-, meso-, and macrofauna was not affected by root trenching. Further, we observed trophic shifts only in 2 out of 10 investigated species with the shifts generally being only minor. The results indicate that soil animal communities are markedly resilient to deprivation of root-derived resources suggesting that links to root-derived resources are non-specific. However, this resilience appears to vary with body size, with mesofauna including both decomposers as well as predators being more sensitive to the deprivation of root-derived resources than microfauna (except for root feeders) and macrofauna. Overall, this suggests that body size constrains the channeling of energy through soil food webs, with root-derived resources in temperate forests being channeled predominantly via soil taxa of intermediate size, i.e., mesofauna.
Nematodes are the most abundant invertebrates in soils and are key prey in soil food webs. Uncovering their contribution to predator nutrition is essential for understanding the structure of soil ...food webs and the way energy channels through soil systems. Molecular gut content analysis of consumers of nematodes, such as soil microarthropods, using specific DNA markers is a novel approach for studying predator–prey interactions in soil. We designed new specific primer pairs (partial 18S rDNA) for individual soil-living bacterial-feeding nematode taxa (Acrobeloides buetschlii, Panagrellus redivivus, Plectus velox and Plectus minimus). Primer specificity was tested against more than 100 non-target soil organisms. Further, we determined how long nematode DNA can be traced in the gut of predators. Potential predators were identified in laboratory experiments including nine soil mite (Oribatida, Gamasina and Uropodina) and ten springtail species (Collembola). Finally, the approach was tested under field conditions by analyzing five mite and three collembola species for feeding on the three target nematode species. The results proved the three primer sets to specifically amplify DNA of the respective nematode taxa. Detection time of nematode DNA in predators varied with time of prey exposure. Further, consumption of nematodes in the laboratory varied with microarthropod species. Our field study is the first definitive proof that free-living nematodes are important prey for a wide range of soil microarthropods including those commonly regarded as detritivores. Overall, the results highlight the eminent role of nematodes as prey in soil food webs and for channelling bacterial carbon to higher trophic levels.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Generalistic interactions between predator and prey may vary with ecosystem type, predator traits, and prey traits, but the interplay of these factors has not been assessed in ground food webs.
We ...investigated trophic interactions of ground‐dwelling spiders across eight forests in European Russia associated with body size, hunting strategy, microhabitat specialization, potential prey type, potential prey population density, and forest type (coniferous vs. broadleaved). We analyzed 128 individual spiders, including juveniles, all identified to the family level with two complementary methods: molecular gut content analysis, and stable isotope analysis of carbon and nitrogen.
The results suggest that feeding frequency of spiders is affected by predator body size and by selection of certain prey type. Stable isotope analysis showed similar trophic niches among spider families, varying moderately with forest type. Larger spiders had higher Δ13C values than smaller ones, but similar Δ15N values, suggesting that different size classes of spiders belong to different food chains. Results based on stable isotope and molecular gut content analyses were weakly linked, indicating them targeting different trophic niche dimensions.
At least for the group‐level interactions, family identity and hunting strategy of predator has little predictive power while predator body size and prey traits affected trophic niche dimensions calling for future studies in this direction. Large spiders feed more and rely on different basal resources than small spiders, suggesting that including small species and juveniles provides a more comprehensive picture of food web organization.
Stable isotope composition and gut content DNA were analysed together in 128 individual spiders in four coniferous and four broadleaved forests in European Russia.
Feeding frequency was affected by predator body size and certain prey types were preferred, while forest type, taxonomy, and hunting strategy had moderate effect on feeding of co‐occurring spiders.
Larger spiders had higher 13C enrichment (resources) than smaller ones, but similar 15 N enrichment (trophic level), suggesting that different size classes of spiders belong to different food chains.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Gut microbiota are determined by both the food ingested and physiological conditions of the host. In soil food webs, detritivore animals occupy various trophic niches, spanning from primary ...decomposers to predators. However, the relative contribution of food resources and species attributes of consumers to gut microbial communities in soil detritivores has not yet been explored. In this study, we investigated gut bacteria and fungi of oribatid mites (Oribatida, Acari), ubiquitous and diverse soil microarthropods feeding on a variety of food resources, to uncover the contribution of host phylogenetic relatedness and trophic niches to the assemblages of gut microbiota. Abundance and community composition of bacteria and fungi were characterized by qPCR and Illumina sequencing, respectively. Gut bacterial communities were more closely correlated with host phylogenetic affinity, whereas gut fungal communities were more closely correlated with the trophic niches of the host. Community phylogenetic analysis suggests that deterministic processes predominated in the assembly of both bacterial and fungal communities in most of the studied oribatid mite species. Integrating phylogenetic distance and trophic niche distance of hosts resulted in the highest correlation coefficients between host species and their gut microbial communities suggesting that both evolutionary history and current trophic niches shape gut microbial communities. Bacteria in the gut may comprise commensals or mutualists facilitating digestion which potentially coevolved with the host, while the fungal community in the gut reflects the trophic niches of the consumer likely suggesting that they form part of the diet and serve as food resources of soil detritivore microarthropods.
•Gut microbiota differed between oribatid mite species living the same habitat.•Gut bacterial communities were determined mainly by host phylogenetic affinity.•Gut fungal communities were influenced in larger part by trophic niche of host.•Deterministic processes predominated in the assembly of gut microbial communities.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
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.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Many bacteria use cyclic di-AMP as a second messenger to control potassium and osmotic homeostasis. In Bacillus subtilis, several c-di-AMP binding proteins and RNA molecules have been identified. ...Most of these targets play a role in controlling potassium uptake and export. In addition, c-di-AMP binds to two conserved target proteins of unknown function, DarA and DarB, that exclusively consist of the c-di-AMP binding domain. Here, we investigate the function of the c-di-AMP-binding protein DarB in B. subtilis, which consists of two cystathionine-beta synthase (CBS) domains. We use an unbiased search for DarB interaction partners and identify the (p)ppGpp synthetase/hydrolase Rel as a major interaction partner of DarB. (p)ppGpp is another second messenger that is formed upon amino acid starvation and under other stress conditions to stop translation and active metabolism. The interaction between DarB and Rel only takes place if the bacteria grow at very low potassium concentrations and intracellular levels of c-di-AMP are low. We show that c-di-AMP inhibits the binding of DarB to Rel and the DarB-Rel interaction results in the Rel-dependent accumulation of pppGpp. These results link potassium and c-di-AMP signaling to the stringent response and thus to the global control of cellular physiology.
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