Genotypic variability enhances the reproducibility of an ecological study

Many scientific disciplines are currently experiencing a “reproducibility crisis” because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduces reproducibility by amplifying impacts of lab-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. We tested this hypothesis using a multi-laboratory microcosm study in which the same ecological experiment was repeated in 14 laboratories across Europe. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the “reproducibility crisis”, deliberately including genetic variation may be a simple solution for increasing the reproducibility of ecological studies performed in controlled environments

Regulation of soil organic matter dynamics and microbial activity by endogeic earthworms

Earthworms are among the most important members of the soil invertebrate fauna in temperate ecosystems. Through burrow construction, mixing of organic matter and mineral soil, comminution of organic matter and casting they beneficially affect soil structure and chemical properties, and thus the biomass, activity and community composition of microorganisms. Microorganisms, particularly bacteria and fungi, are the primarily decomposers of organic matter in soils. Since earthworms control the microbial community they also affect the fate of soil organic matter which may lead either to its mobilization or stabilization. This study investigates the role of different factors presumably controlling the interaction of earthworms and microorganisms with regard to the stabilization and mobilization of soil organic matter. The effect of endogeic earthworms (Octolasion tyrtaeum (Savigny)) and the availability of clay on the mobilization and stabilization of 14C-labelled catechol mixed into an arable and a forest soil was investigated. Production of 14CO2 and accumulation of 14C in humic fractions of casts and the non-processed soils were determined. Octolasion tyrtaeum did not affect 14CO2-C production in the forest soil, but increased it early in the arable soil; clay counteracted the effect of O. tyrtaeum in the arable soil. Clay and O. tyrtaeum did not affect integration of 14C into the humic fractions of the forest soil. In contrast, in the arable soil O. tyrtaeum increased the amount of 14C in the labile fractions, whereas clay increased it in the humin fraction, indicating that endogeic earthworms and clay are only of little importance in soils with high organic matter content, high clay content and high microbial biomass, but contrarily affect phenolic compounds in poor soils. Endogeic earthworms strongly increase microbial activity and thus mineralization of phenolic compounds, whereas clay decreases it by binding phenolic compounds when passing through the earthworm gut. The effect of cutting of shoots of white clover (Trifolium repens L.) and perennial ryegrass (Lolium perenne L.) on the availability of soluble carbon in the rhizosphere, and on the biomass and activity of soil microorganisms and juveniles of the endogeic earthworm species O. tyrtaeum (Savigny) and Aporrectodea caliginosa (Savigny) were studied. Both plant species increased microbial biomass in the soil, but microbial activity remained unaffected. Although defoliation increased the availability of carbon in the rhizosphere as indicated by the increase in microbial biomass, the biomass of both earthworm species decreased during the experiment, suggesting that earthworms were unable to exploit the microbial carbon pool in soil, rather, rhizosphere microorganisms appeared to have effectively competed with endogeic earthworms and exploited root carbon exudates. The interaction of saprophytic fungi and O. tyrtaeum on the translocation and stabilization of litter derived carbon (13C/15N labelled rye leaves) into the upper layer of an arable soil was investigated in a microcosm experiment. Phospholipid fatty acids and ergosterol were used as marker molecules to determine the effects of earthworms on bacterial and fungal abundance and microbial community composition. The results indicate that saprophytic fungi translocate and stabilize litter derived carbon in their mycelial network in the upper mineral soil. Endogeic earthworms reduce fungal biomass by grazing and thereby counteract the fungal stabilization of carbon. In addition, earthworms reduce bacterial biomass in the soil while mainly competing with Gram-negative bacteria for labile carbon resources. The flux of bacterial carbon (13C labelled Serratia marcescens cells) through the soil microbial community as affected by the passage through the gut of endogeic earthworms A. caliginosa was investigated by means of terminal-restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA gene fragments and rRNA stable isotope probing (SIP). Production of 13CO2-C was strongly increased in presence of A. caliginosa and in casts compared to the soil. Microbial communities in casts and soil after one day of incubation were almost similar and consist of eleven different bacterial lineages, with Proteobacteria and Actinobacteria being the most abundant; however they differed in the abundance of Acidobacteria, Firmicutes and Planctomycetes. After six days microbial community in the soil was almost similar to that of casts at day one. The clone library of the casts, in contrast, consisted of only five different lineages and was dominated by members of the phylum Firmicutes, predominantly Staphylococcus spp., indicating that the passage through the gut of endogeic earthworms considerably changes the activity and composition of the microbial community, and the mineralization and incorporation of bacterial carbon. The results of the present study document that endogeic earthworms increase the mineralization of soil organic matter by promoting, feeding on or competing with specific microorganisms in the soil. The effect, however, also depends on abiotic soil conditions such as soil texture

Effects of root and leaf litter identity and diversity on oribatid mite abundance, species richness and community composition.

Habitat heterogeneity is an important driver of aboveground species diversity but few studies have investigated effects on soil communities. Trees shape their surrounding by both leaf litter and roots generating small scale heterogeneity and potentially governing community patterns of soil organisms. To assess the role of vegetation for the soil fauna, we studied whether tree species (Fagus sylvatica L., Acer pseudoplatanus L., Fraxinus excelsior L., Tilia cordata Mill.), markedly differing in leaf litter quality and root associated mycorrhizal symbionts, affect oribatid mite communities by shaping below- and aboveground resources and habitat complexity and availability. Oribatid mite abundance, species richness, community structure and the proportion of litter living and parthenogenetic individuals were analyzed and related to microbial biomass and the amount of remaining litter mass. Although leaf litter species with higher nutritional values decomposed considerably faster, microbial biomass only slightly differed between leaf litter species. Neither root species nor leaf litter species affected abundance, species richness or community structure of oribatid mites. However, root species had an effect on the proportion of parthenogenetic individuals with increased proportions in the presence of beech roots. Overall, the results suggest that identity and diversity of vegetation via leaf litter or roots are of minor importance for structuring oribatid mite communities of a temperate forest ecosystem

Litter composition rather than plant presence affects decomposition of tropical litter mixtures

International audienceLitter decomposition is strongly controlled by litter quality, but the composition of litter mixtures and potential interactions with live plants through root activity may also influence decomposers. In a greenhouse experiment in French Guiana we studied the combined effects of the presence of tropical tree seedlings and of distinct litter composition on mass and nitrogen (N) loss from decomposing litter and on microbial biomass. Different litter mixtures decomposed for 435 days in pots filled with sand and containing an individual seedling from one of four different tree species. We found both additive and negative non-additive effects (NAE) of litter mixing on mass loss, whereas N loss showed negative and positive NAE of litter mixing. If litter from the two tree species, Platonia insignis and Goupia glabra were present, litter mixtures showed more positive and more negative NAE on N loss, respectively. Overall, decomposition, and in particular non-additive effects, were only weakly affected by the presence of tree seedlings. Litter mass loss weakly yet significantly decreased with increasing fine root biomass in presence of Goupia seedlings, but not in the presence of seedlings of any other tree species. Our results showed strong litter composition effects and also clear, mostly negative, non-additive effects on mass loss and N loss. Species identity of tree seedlings can modify litter decomposition, but these live plant effects remain quantitatively inferior to litter composition effects

Leaving your ancestral neighborhood makes you leave your ancestral ecosystem functioning: Decomposition of oak litter

International audienc

Leaving your ancestral neighborhood makes you leave your ancestral ecosystem functioning: Decomposition of oak litter

International audienc

Larger phylogenetic distances in litter mixtures: lower microbial biomass and higher C/N ratios but equal mass loss

International audiencePhylogenetic distances of coexisting species differ greatly within plant communities, but their consequences for decomposers and decomposition remain unknown. We hypothesized that large phylogenetic distance of leaf litter mixtures increases differences of their litter traits, which may, in turn, result in increased resource complementarity or decreased resource concentration for decomposers and hence increased or decreased chemical transformation and reduction of litter. We conducted a litter mixture experiment including 12 common temperate tree species (evolutionarily separated by up to 106 Myr), and sampled after seven months, at which average mass loss was more than 50%. We found no effect of increased phylogenetic distance on litter mass loss or on abundance and diversity of invertebrate decomposers. However, phylogenetic distance decreased microbial biomass and increased carbon/nitrogen (C/N) ratios of litter mixtures. Consistently, four litter traits showed (marginally) significant phylogenetic signal and in three of these traits increasing trait difference decreased microbial biomass and increased C/N. We suggest that phylogenetic proximity of litter favours microbial decomposers and chemical transformation of litter owing to aresource concentration effect. This leads to a new hypothesis: closely related plant species occurring in the same niche should promote and profit from increased nutrient availability

Carbon budgets of top- and subsoil food webs in an arable system

This study assessed the carbon (C) budget and the C stocks in major compartments of the soil food web (bacteria, fungi, protists, nematodes, meso- and macrofauna) in an arable field with/without litter addition. The C stocks in the food web were more than three times higher in topsoil (0-10 cm) compared to subsoil ( > 40 cm). Microorganisms contained over 95% of food web C, with similar contributions of bacteria and fungi in topsoil. Litter addition did not alter C pools of soil biota after one growing season, except for the increase of fungi and fungal feeding nematodes in the topsoil. However, the C budget for functional groups changed with depth, particularly in the microfauna. This suggests food web resilience to litter amendment in terms of C pool sizes after one growing season. In contrast, the distinct depth dependent pattern indicates specific metacommunities, likely shaped by dominant abiotic and biotic habitat properties

Disentangling the root- and detritus-based food chain in the micro-food web of an arable soil by plant removal

<div><p>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.</p></div