Institute of Soil Biology

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity-function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of (i) differentially constructed culturable bacterial communities, and (ii) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.

Soil biodiversity plays a key role in regulating the processes that underpin the delivery of ecosystem goods and services in terrestrial ecosystems. Agricultural intensification is known to change the diversity of individual groups of soil biota, but less is known about how intensification affects biodiversity of the soil food web as a whole, and whether or not these effects may be generalized across regions. We examined biodiversity in soil food webs from grasslands, extensive, and intensive rotations in four agricultural regions across Europe: in Sweden, the UK, the Czech Republic and Greece. Effects of land-use intensity were quantified based on structure and diversity among functional groups in the soil food web, as well as on community-weighted mean body mass of soil fauna. We also elucidate land-use intensity effects on diversity of taxonomic units within taxonomic groups of soil fauna. We found that between regions soil food web diversity measures were variable, but that increasing land-use intensity caused highly consistent responses. In particular, land-use intensification reduced the complexity in the soil food webs, as well as the community-weighted mean body mass of soil fauna. In all regions across Europe, species richness of earthworms, Collembolans, and oribatid mites was negatively affected by increased land-use intensity. The taxonomic distinctness, which is a measure of taxonomic relatedness of species in a community that is independent of species richness, was also reduced by land-use intensification. We conclude that intensive agriculture reduces soil biodiversity, making soil food webs less diverse and composed of smaller bodied organisms. Land-use intensification results in fewer functional groups of soil biota with fewer and taxonomically more closely related species. We discuss how these changes in soil biodiversity due to land-use intensification may threaten the functioning of soil in agricultural production systems.

Summary Results from the pioneering research on the interactions between pH and denitrification in soil from the 1950s to the present are reviewed, the changing perceptions of this complex relationship are discussed, and the current status of the subject is assessed. Facets of this relationship that are analysed in detail include the direct or indirect influence of pH on overall denitrification rates in soils, changes in the composition of gaseous products that depend on pH, methods for measuring the process, the concept of an optimum pH for denitrification, and the adaptation of microbial denitrifying communities to acidic environments. The main conclusions to be drawn are as follows. Total gaseous emissions to the atmosphere (N 2 O, NO and N 2 ) have repeatedly been shown to be less in acidic than in neutral or slightly alkaline soils. This may be attributable to smaller amounts of organic carbon and mineral nitrogen available to the denitrifying population under acid conditions rather than a direct effect of low pH on denitrification enzymes. Numerous laboratory and field studies have demonstrated that the ratio N 2 O:N 2 is increased when the pH of soils is reduced. The relation between soil pH and potential denitrification as determined by various incubation methods remains unclear, results being influenced both by original conditions in soil samples and by unknown changes during incubation. The concept of an optimum pH for denitrification has been frequently proposed, but such a term has little or no meaning without reference to specific attributes of the process.

Intensive land use reduces the diversity and abundance of many soil biota, with consequences for the processes that they govern and the ecosystem services that these processes underpin. Relationships between soil biota and ecosystem processes have mostly been found in laboratory experiments and rarely are found in the field. Here, we quantified, across four countries of contrasting climatic and soil conditions in Europe, how differences in soil food web composition resulting from land use systems (intensive wheat rotation, extensive rotation, and permanent grassland) influence the functioning of soils and the ecosystem services that they deliver. Intensive wheat rotation consistently reduced the biomass of all components of the soil food web across all countries. Soil food web properties strongly and consistently predicted processes of C and N cycling across land use systems and geographic locations, and they were a better predictor of these processes than land use. Processes of carbon loss increased with soil food web properties that correlated with soil C content, such as earthworm biomass and fungal/bacterial energy channel ratio, and were greatest in permanent grassland. In contrast, processes of N cycling were explained by soil food web properties independent of land use, such as arbuscular mycorrhizal fungi and bacterial channel biomass. Our quantification of the contribution of soil organisms to processes of C and N cycling across land use systems and geographic locations shows that soil biota need to be included in C and N cycling models and highlights the need to map and conserve soil biodiversity across the world.

The objective of this study was to investigate how changes in soil pH affect the N(2)O and N(2) emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H(2)SO(4) solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N(2)O and N(2) emissions using the (15)N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG, napA, nirS, nirK, and nosZ denitrification genes. Overall, our results indicate that soil pH is of importance in determining the nature of denitrification end products. Thus, we found that the N(2)O/(N(2)O + N(2)) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N(2)O production were observed. Denitrification activity and N(2)O emissions measured under laboratory conditions were correlated with N fluxes in situ and therefore reflected treatment differences in the field. The size of the denitrifying community was uncoupled from in situ N fluxes, but potential denitrification was correlated with the count of NirS denitrifiers. Significant relationships were observed between nirS, napA, and narG gene copy numbers and the N(2)O/(N(2)O + N(2)) ratio, which are difficult to explain. However, this highlights the need for further studies combining analysis of denitrifier ecology and quantification of denitrification end products for a comprehensive understanding of the regulation of N fluxes by denitrification.

Soil organisms drive major ecosystem functions by mineralising carbon and releasing nutrients during decomposition processes, which supports plant growth, aboveground biodiversity and, ultimately, human nutrition. Soil ecologists often operate with functional groups to infer the effects of individual taxa on ecosystem functions and services. Simultaneous assessment of the functional roles of multiple taxa is possible using food-web reconstructions, but our knowledge of the feeding habits of many taxa is insufficient and often based on limited evidence. Over the last two decades, molecular, biochemical and isotopic tools have improved our understanding of the feeding habits of various soil organisms, yet this knowledge is still to be synthesised into a common functional framework. Here, we provide a comprehensive review of the feeding habits of consumers in soil, including protists, micro-, meso- and macrofauna (invertebrates), and soil-associated vertebrates. We have integrated existing functional group classifications with findings gained with novel methods and compiled an overarching classification across taxa focusing on key universal traits such as food resource preferences, body masses, microhabitat specialisation, protection and hunting mechanisms. Our summary highlights various strands of evidence that many functional groups commonly used in soil ecology and food-web models are feeding on multiple types of food resources. In many cases, omnivory is observed down to the species level of taxonomic resolution, challenging realism of traditional soil food-web models based on distinct resource-based energy channels. Novel methods, such as stable isotope, fatty acid and DNA gut content analyses, have revealed previously hidden facets of trophic relationships of soil consumers, such as food assimilation, multichannel feeding across trophic levels, hidden trophic niche differentiation and the importance of alternative food/prey, as well as energy transfers across ecosystem compartments. Wider adoption of such tools and the development of open interoperable platforms that assemble morphological, ecological and trophic data as traits of soil taxa will enable the refinement and expansion of the multifunctional classification of consumers in soil. The compiled multifunctional classification of soil-associated consumers will serve as a reference for ecologists working with biodiversity changes and biodiversity-ecosystem functioning relationships, making soil food-web research more accessible and reproducible.

Much research focuses on increasing carbon storage in mineral-associated organic matter (MAOM), in which carbon may persist for centuries to millennia. However, MAOM-targeted management is insufficient because the formation pathways of persistent soil organic matter are diverse and vary with environmental conditions. Effective management must also consider particulate organic matter (POM). In many soils, there is potential for enlarging POM pools, POM can persist over long time scales, and POM can be a direct precursor of MAOM. We present a framework for context-dependent management strategies that recognizes soils as complex systems in which environmental conditions constrain POM and MAOM formation.

There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6-16 m) and mapped the distribution of this functional guild in the field. The spatial patterns of soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N(2)O production and relative abundance of some denitrification genes but not on the size of the denitrifier community. Absolute abundance of most denitrification genes was not correlated with the distribution patterns of potential denitrification activity or potential N(2)O production. However, the relative abundance of bacteria possessing the nosZ gene encoding the N(2)O reductase in the total bacterial community was a strong predictor of the N(2)O/(N(2) + N(2)O) ratio, which provides evidence for a relationship between bacterial community composition based on the relative abundance of denitrifiers in the total bacterial community and ecosystem processes. More generally, the presented geostatistical approach allows integrated mapping of microbial communities, and hence can facilitate our understanding of relationships between the ecology of microbial communities and microbial processes along environmental gradients.

Abstract 1. The carbon content and δ 13 C value of soil organic carbon (SOC), microbial biomass (C mic ) and respired CO 2 were measured in a range of grassland soils from tropical and temperate biomes to determine if isotope effect of microbial degradation can induce a shift in isotope composition of SOC and CO 2 . The soil from a depth of 0–2 cm was analysed. C mic was measured using the chloroform fumigation extraction method, while CO 2 was measured in a closed system after 3 and 10 days of incubation. Two soils, temperate and tropical, were used for a long‐term experiment, in which measurements were performed after 3, 10 and 40 days of incubation. 2. SOC and C mic decrease exponentially with increasing mean annual temperature. C mic decreases more slowly than SOC, resulting in a higher proportion of C mic in the SOC of tropical soils relative to temperate soils. 3. The δ 13 C value of C mic and respired CO 2 reflects gross changes in the δ 13 C value of SOC in the corresponding sample. On average, C mic is 13 C‐enriched by c. 2‰ compared with SOC, while respired CO 2 is 13 C‐depleted by c. 2·2‰ compared with C mic . Thus, the observed 13 C‐enrichment in C mic is balanced by a corresponding 13 C‐depletion in respired CO 2 resulting in the δ 13 C value of respired CO 2 being approximately similar to the δ 13 C of SOC. 4. The isotope effect of microbial degradation is of importance in soil. It can be induced by selective utilization of SOC and isotope discrimination during metabolism. Metabolic isotopic discrimination is dependent on the growth stage of the soil microbial population.

Lascaux Cave (Montignac, France) contains paintings from the Upper Paleolithic period. Shortly after its discovery in 1940, the cave was seriously disturbed by major destructive interventions. In 1963, the cave was closed due to algal growth on the walls. In 2001, the ceiling, walls and sediments were colonized by the fungus Fusarium solani. Later, black stains, probably of fungal origin, appeared on the walls. Biocide treatments, including quaternary ammonium derivatives, were extensively applied for a few years, and have been in use again since January 2008. The microbial communities in Lascaux Cave were shown to be composed of human-pathogenic bacteria and entomopathogenic fungi, the former as a result of the biocide selection. The data show that fungi play an important role in the cave, and arthropods contribute to the dispersion of conidia. A careful study on the fungal ecology is needed in order to complete the cave food web and to control the black stains threatening the Paleolithic paintings.

1 The objective of this study was to test the theoretical prediction that the thermal tolerance range for development in insects should be about 20 °C. 2 The data on the thermal requirements for development of 66 species from eight orders of insects was obtained from the literature. The temperatures at which the developmental rates are at their minimum and maximum was obtained for each population by defining the relationship between developmental rate (1/D) and temperature, using either Lactin et al.'s (1995) or Briére et al.'s (1999) model. 3 Thermal windows, i.e. the range in temperature between the minimum and maximum rate of development for individual species, and the relationship between the minimum and maximum temperatures, were examined. 4 The mean thermal window, 19·8 °C with 95% confidence interval 19·1–20·5 and range 13·3−28·6, was influenced by species phylogeny, with the windows narrower for species having a true pupal stage, but not by ecological traits thought to affect species thermal requirements. The relationship between the minimum and maximum temperatures was highly significant and independent of species phylogeny. 5 Theory and this analysis of empirical data indicate that each species of insect can only develop over a limited range of temperatures independent of species traits. In addition, the relationship between the minimum and maximum developmental rates co-vary independent of species phylogeny. This may help identify the precise nature of the physiological mechanism underlying the seasonal development and distribution of insects, and possibly other ectotherms.

Whether bacteria display spatial patterns of distribution and at which level of taxonomic organization such patterns can be observed are central questions in microbial ecology. Here we investigated how the total and relative abundances of eight bacterial taxa at the phylum or class level were spatially distributed in a pasture by using quantitative PCR and geostatistical modelling. The distributions of the relative abundance of most taxa varied by a factor of 2.5-6.5 and displayed strong spatial patterns at the field scale. These spatial patterns were taxon-specific and correlated to soil properties, which indicates that members of a bacterial clade defined at high taxonomical levels shared specific ecological traits in the pasture. Ecologically meaningful assemblages of bacteria at the phylum or class level in the environment provides evidence that deep branching patterns of the 16S rRNA bacterial tree are actually mirrored in nature.

Abstract Rising atmospheric CO 2 concentrations have increased interest in the potential for forest ecosystems and soils to act as carbon (C) sinks. While soil organic C contents often vary with tree species identity, little is known about if, and how, tree species influence the stability of C in soil. Using a 40 year old common garden experiment with replicated plots of eleven temperate tree species, we investigated relationships between soil organic matter (SOM) stability in mineral soils and 17 ecological factors (including tree tissue chemistry, magnitude of organic matter inputs to the soil and their turnover, microbial community descriptors, and soil physicochemical properties). We measured five SOM stability indices, including heterotrophic respiration, C in aggregate occluded particulate organic matter (POM) and mineral associated SOM, and bulk SOM δ 15 N and ∆ 14 C. The stability of SOM varied substantially among tree species, and this variability was independent of the amount of organic C in soils. Thus, when considering forest soils as C sinks, the stability of C stocks must be considered in addition to their size. Further, our results suggest tree species regulate soil C stability via the composition of their tissues, especially roots. Stability of SOM appeared to be greater (as indicated by higher δ 15 N and reduced respiration) beneath species with higher concentrations of nitrogen and lower amounts of acid insoluble compounds in their roots, while SOM stability appeared to be lower (as indicated by higher respiration and lower proportions of C in aggregate occluded POM) beneath species with higher tissue calcium contents. The proportion of C in mineral associated SOM and bulk soil ∆ 14 C, though, were negligibly dependent on tree species traits, likely reflecting an insensitivity of some SOM pools to decadal scale shifts in ecological factors. Strategies aiming to increase soil C stocks may thus focus on particulate C pools, which can more easily be manipulated and are most sensitive to climate change.

Twenty tree ring 13 C / 12 C ratio chronologies from Pinus sylvestris (Scots pine) trees were determined from five locations sampled along the Yenisei River, spaced over a total distance of ∼1000 km between the cities of Turuhansk (66°N) and Krasnoyarsk (56°N). The transect covered the major part of the natural distribution of Scots pine in the region with median growing season temperatures and precipitation varying from 12.2°C and 218 mm to 14.0°C and 278 mm for Turuhansk and Krasnoyarsk, respectively. A key focus of the study was to investigate the effects of variations in temperature, precipitation, and atmospheric CO 2 concentration on long‐ and short‐term variation in photosynthetic 13 C discrimination during photosynthesis and the marginal cost of tree water use, as reflected in the differences in the historical records of the 13 C / 12 C ratio in wood cellulose compared to that of the atmosphere (Δ 13 C c ). In 17 of the 20 samples, trees Δ 13 C c has declined during the last 150 years, particularly so during the second half of the twentieth century. Using a model of stomatal behaviour combined with a process‐based photosynthesis model, we deduce that this trend indicates a long‐term decrease in canopy stomatal conductance, probably in response to increasing atmospheric CO 2 concentrations. This response being observed for most trees along the transect is suggestive of widespread decreases in Δ 13 C c and increased water use efficiency for Scots pine in central Siberia over the last century. Overlying short‐term variations in Δ 13 C c were also accounted for by the model and were related to variations in growing season soil water deficit and atmospheric humidity.

. However, conclusive evidence for their role in stabilising or destabilising soil carbon has not been fully established. Here, we demonstrate that earthworms function like biochemical reactors by converting labile plant compounds into microbial necromass in stabilised carbon pools without altering bulk measures, such as the total carbon content. We show that much of this microbial carbon is not associated with mineral surfaces and emphasise the functional importance of particulate organic matter for long-term carbon sequestration. Our findings suggest that while earthworms do not necessarily affect soil organic carbon stocks, they do increase the resilience of soil carbon to natural and anthropogenic disturbances. Our results have implications for climate change mitigation and challenge the assumption that mineral-associated organic matter is the only relevant pool for soil carbon sequestration.

Animal interactions play an important role in understanding ecological processes. The nature and intensity of these interactions can shape the impacts of organisms on their environment. Because ants and termites, with their high biomass and range of ecological functions, have considerable effects on their environment, the interaction between them is important for ecosystem processes. Although the manner in which ants and termites interact is becoming increasingly well studied, there has been no synthesis to date of the available literature. Here we review and synthesise all existing literature on ant-termite interactions. We infer that ant predation on termites is the most important, most widespread, and most studied type of interaction. Predatory ant species can regulate termite populations and subsequently slow down the decomposition of wood, litter and soil organic matter. As a consequence they also affect plant growth and distribution, nutrient cycling and nutrient availability. Although some ant species are specialised termite predators, there is probably a high level of opportunistic predation by generalist ant species, and hence their impact on ecosystem processes that termites are known to provide varies at the species level. The most fruitful future research direction will be to evaluate the impact of ant-termite predation on broader ecosystem processes. To do this it will be necessary to quantify the efficacy both of particular ant species and of ant communities as a whole in regulating termite populations in different biomes. We envisage that this work will require a combination of methods, including DNA barcoding of ant gut contents along with field observations and exclusion experiments. Such a combined approach is necessary for assessing how this interaction influences entire ecosystems.

Abstract Sulphur ( S ) and nitrogen ( N ) deposition are important drivers of the terrestrial carbon ( C ) and N cycling. We analyzed changes in C and N pools in soil and tree biomass at a highly acidified spruce site in the C zech R epublic during a 15 year period. Total S deposition decreased from 5 to 1.1 g m −2 yr −1 between 1995 and 2009, whereas bulk N deposition did not change. Over the same period, C and N pools in the Oa horizon declined by 116 g C and 4.2 g N m −2 yr −1 , a total decrease of 47% and 42%, respectively. This loss of C and N probably originated from organic matter ( OM ) that had accumulated during the period of high acid deposition when litter decomposition was suppressed. The loss of OM from the Oa horizon coincided with a substantial leaching (1.3 g N m −2 yr −1 at 90 cm) in the 1990s to almost no leaching (<0.02 g N m −2 yr −1 ) since 2006. Forest floor net N mineralization also decreased. This had consequences for spruce needle N concentration (from 17.1 to 11.4 mg kg −1 in current needles), an increase in litterfall C/N ratio (from 51 to 63), and a significant increase in the Oi + Oe horizon C/N ratio (from 23.4 to 27.3) between 1994 and 2009/2010. Higher forest growth and lower canopy defoliation was observed in the 2000s compared to the 1990s. Our results demonstrate that reducing S deposition has had a profound impact on forest organic matter cycling, leading to a reversal of historic ecosystem N enrichment, cessation of nitrate leaching, and a major loss of accumulated organic soil C and N stocks. These results have major implications for our understanding of the controls on both N saturation and C sequestration in forests, and other ecosystems, subjected to current or historic S deposition.

A wide range of plant lines has been propagated by farmers during crop selection and dissemination, but consequences of this crop diversification on plant-microbe interactions have been neglected. Our hypothesis was that crop evolutionary history shaped the way the resulting lines interact with soil bacteria in their rhizospheres. Here, the significance of maize diversification as a factor influencing selection of soil bacteria by seedling roots was assessed by comparing rhizobacterial community composition of inbred lines representing the five main genetic groups of maize, cultivated in a same European soil. Rhizobacterial community composition of 21-day-old seedlings was analysed using a 16S rRNA taxonomic microarray targeting 19 bacterial phyla. Rhizobacterial community composition of inbred lines depended on the maize genetic group. Differences were largely due to the prevalence of certain Betaproteobacteria and especially Burkholderia, as confirmed by quantitative PCR and cloning/sequencing. However, these differences in bacterial root colonization did not correlate with plant microsatellite genetic distances between maize genetic groups or individual lines. Therefore, the genetic structure of maize that arose during crop diversification (resulting in five main groups), but not the extent of maize diversification itself (as determined by maize genetic distances), was a significant factor shaping rhizobacterial community composition of seedlings.

Abstract A model for NO − 3 reduction and diffusion in aggregated soils is presented and used in conjunction with a derived constant, the Thiele modulus, to examine the conditions which could contribute to a NO − 3 diffusion limitation of denitrification. The Thiele modulus is a function of the anaerobic radius of an aggregate, the maximum rate of NO − 3 reduction for a given soil, the K m value for NO − 3 reduction, and the intra‐aggregate NO − 3 diffusion coefficient. Results from this theoretical exercise suggested that the anaerobic radius is the most important factor in determining whether denitrification is limited by NO − 3 diffusion. The model predicts that under anaerobic conditions, only soils with a mean aggregate radius greater than 2 mm will experience a NO − 3 diffusion limitation. This limitation may not be effective in practice if the bulk NO − 3 concentration is much greater (100 times) than the K m for NO − 3 reduction; this appears to often be the case in fertilized soils but may not be the case in soils of natural ecosystems. Under aerobic conditions, a diffusion limitation will exist in most aggregated soils, since only large aggregates have anaerobic microsites (i.e., large anaerobic radii) where denitrification can occur. A carbon limitation, through its lowering of the maximum denitrification rate, lessens the magnitude of any existing NO − 3 diffusion limitation. Diffusive limitations were experimentally examined in two ways. First, the ratio of denitrification rates of anaerobic cores relative to anaerobic slurries were used to indicate the degree of any substrate supply limitation; the slurry rates were always greater suggesting either NO − 3 or carbon was limiting. Second, soil cores were preincubated with either NO − 3 or a diffusible carbon source (succinate) at 4°C to allow diffusion but to suppress biological responses. These results revealed that carbon, rather than NO − 3 , was limiting denitrification rates in this clay loam soil. These experimental results were in agreement with model predictions.

The potential applicability of the leaf radiative transfer model PROSPECT (version 3.01) was tested for Norway spruce (Picea abies (L.) Karst.) needles collected from stress resistant and resilient trees. Direct comparison of the measured and simulated leaf optical properties between 450–1000 nm revealed the requirement to recalibrate the PROSPECT chlorophyll and dry matter specific absorption coefficients k ab(λ) and k m(λ). The subsequent validation of the modified PROSPECT (version 3.01.S) showed close agreement with the spectral measurements of all three needle age‐classes tested; the root mean square error (RMSE) of all reflectance (ρ) values within the interval of 450–1000 nm was equal to 1.74%, for transmittance (τ) it was 1.53% and for absorbance (α) it was 2.91%. The total chlorophyll concentration, dry matter content, and leaf water content were simultaneously retrieved by a constrained inversion of the original PROSPECT 3.01 and the adjusted PROSPECT 3.01.S. The chlorophyll concentration estimated by inversion of both model versions was similar, but the inversion accuracy of the dry matter and water content was significantly improved. Decreases in RMSE from 0.0079 g cm−2 to 0.0019 g cm−2 for dry matter and from 0.0019 cm to 0.0006 cm for leaf water content proved the improved performance of the recalibrated PROSPECT version 3.01.S.