Jean-Christophe Lata

Plant Preference for Ammonium versus Nitrate: A Neglected Determinant of Ecosystem Functioning?

Although nitrogen (N) availability is a major determinant of ecosystem properties, little is known about the ecological importance of plants’ preference for ammonium versus nitrate (β) for ecosystem functioning and the structure of communities. We modeled this preference for two contrasting ecosystems and showed that β significantly affects ecosystem properties such as biomass, productivity, and N losses. A particular intermediate value of β maximizes the primary productivity and minimizes mineral N losses. In addition, contrasting β values between two plant types allow their coexistence, and the ability of one type to control nitrification modifies the patterns of coexistence with the other. We also show that species replacement dynamics do not lead to the minimization of the total mineral N pool nor the maximization of plant productivity, and consequently do not respect Tilman’s R* rule. Our results strongly suggest in the two contrasted ecosystems that β has important consequences for ecosystem functioning and plant community structure.

Biological Nitrification Inhibition--A Novel Strategy to Regulate Nitrification in Agricultural Systems

Human activity has had the single largest influence on the global nitrogen (N) cycle by introducing unprecedented amounts of reactive-N into ecosystems. A major portion of this reactive-N, applied as fertilizer to crops, leaks into the environment with cascading negative effects on ecosystem functions and contributes to global warming. Natural ecosystems use multiple pathways of the N-cycle to regulate the flow of this element. By contrast, the large amounts of N currently applied in agricultural systems cycle primarily through the nitrification process, a single inefficient route that allows much of the reactive-N to leak into the environment. The fact that present agricultural systems do not channel this reactive-N through alternate pathways is largely due to uncontrolled soil nitrifier activity, creating a rapid nitrifying soil environment. Regulating nitrification is therefore central to any strategy for improving nitrogen-use efficiency. Biological nitrification inhibition (BNI) is an active plant-mediated natural function, where nitrification inhibitors released from plant roots suppress soil-nitrifying activity, thereby forcing N into other pathways. This review illustrates the presence of detection methods for variation in physiological regulation of BNI-function in field crops and pasture grasses and analyzes the potential for its genetic manipulation. We present a conceptual framework utilizing a BNI-platform that integrates diverse crop science disciplines with ecological principles. Sustainable agriculture will require development of production systems that include new crop cultivars capable of controlling nitrification (i.e., high BNI-capacity) and improved agronomic practices to minimize leakage of reactive-N during the N-cycle, a critical requirement for increasing food production while avoiding environmental damage.

Soil microbial loop and nutrient uptake by plants: a test using a coupled C:N model of plant–microbial interactions

We have developed a spatially explicit model of plant root and soil bacteria interactions in the rhizosphere in order to formalise and study the microbial loop hypothesis that postulates that plants can stimulate the release of mineral N from the soil organic matter by providing low molecular weight C molecules to C-limited microorganisms able to liberate into the soil enzymes that degrade the organic matter. The model is based on a mechanistic description of diffusion of solutes in the soil, nutrient uptake by plants, bacterial activity and bacterial predation. Modelled soil bacterial populations grow, mediate transformations among several forms of nitrogen (mineral and organic) and compete for nitrogen with plants. Our objectives were to see if we could simulate the stimulation of turnover of the microbial loop by exudates and to study the effects of diffusion of C and N in the rhizosphere on these different processes. The model qualitatively mimics most of the characteristics of the microbial loop hypothesis. In particular, (1) plant exudates increase the growth of bacteria in the soil and (2) increase the degradation of soil organic matter and N mineralisation. (3) The increased bacterial biomass induces an increase in predator biomass and, as a result, (4) plant mineral N uptake is increased threefold compared with scenarios without exudation. However, the temporal dynamics simulated by the model are much slower than observed dynamics (the increase in uptake appears after a few months). Taking into consideration the diffusion of C and N containing molecules in soil has large effects on the spatial structure of the bacterial and predator biomass. However, the average biomass of bacteria and predators, N mineralisation and plant N uptake were not affected by these properties. The model provides a quantitative and mechanistic explanation of how plants could benefit from liberating low molecular organic matter and the subsequent stimulation of the microbial loop and increases N mineralisation.

A tale of four stories: soil ecology, theory, evolution and the publication system.

Background Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. Findings We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. Conclusion This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate “particularity” (empirical observations) and “generality” (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary.

Relationships between root density of the African grass Hyparrhenia diplandra and nitrification at the decimetric scale: an inhibition–stimulation balance hypothesis

Previous studies have shown that Lamto savannah exhibits two different types of nitrogen cycle with high and low nitrification sites and suggested that the perennial grass Hyparrhenia diplandra is responsible for this duality at a subpopulation level, with one ecotype being thought to be able to inhibit nitrification. The present work aimed to investigate the relationships between nitrification and the roots of H. diplandra at two scales. (i) Site–scale experiments gave new insight into the hypothesized control of nitrification by H. diplandra tussocks: the two ecotypes exhibited opposite influences, inhibition in a low nitrification site (A) and stimulation in a high nitrification site (B). (ii) Decimetric–scale experiments demonstrated close negative or positive relationships (in sites A or B, respectively) between the roots and nitrification (in the 0–10 cm soil layer), showing an unexpectedly high sensitivity of the nitrification process to root density. In both soils, the correlation between the roots and nitrification decreased with depth and practically disappeared in the 20–30 cm soil layer (where the nitrification potential was found to be very low). Therefore, the impact of H. diplandra on nitrification may be viewed as an inhibition–stimulation balance.

Designing mixtures of varieties for multifunctional agriculture with the help of ecology. A review

The study of natural ecosystems and experiments using mixtures of plant species demonstrates that both species and genetic diversity generally promote ecosystem functioning. Therefore, mixing crop varieties is a promising alternative practice to transform modern high-input agriculture that is associated with a drastic reduction of within-field crop genetic diversity and is widely recognized as unsustainable. Here, we review the effects of mixtures of varieties on ecosystem functioning, and their underlying ecological mechanisms, as studied in ecology and agronomy, and outline how this knowledge can help designing more efficient mixtures. We recommend the development of two complementary strategies to optimize variety mixtures by fostering the ecological mechanisms leading to a positive relationship between biodiversity and ecosystem functioning and its stability through time, i.e., sampling and complementarity effects. (1) In the “trait-blind” approach, the design of high-performance mixtures is based on estimations of the mixing abilities of varieties. While this approach is operational because it does not require detailed trait knowledge, it relies on heavy experimental designs to evaluate mixing ability. (2) The trait-based approach is particularly efficient to design mixtures of varieties to provide particular baskets of services but requires building databases of traits for crop varieties and documenting the relations between traits and services. The performance of mixtures requires eventually to be evaluated in real economic, social, and agronomic contexts. We conclude that the need of a multifunctional low-input agriculture strongly increases the attractiveness of mixtures but that new breeding approaches are required to create varieties with higher mixing abilities, to foster complementarity and selection effects through an increase in the variance of relevant traits and to explore new combinations of trait values.

Root exclusion through trenching does not affect the isotopic composition of soil CO2 efflux

Disentangling the autotrophic and heterotrophic components of soil CO2 efflux is critical to understanding the role of soil system in terrestrial carbon (C) cycling. In this study, we combined a stable C-isotope natural abundance approach with the trenched plot method to determine if root exclusion significantly affected the isotopic composition (δ13C) of soil CO2 efflux (RS). This study was performed in different forest ecosystems: a tropical rainforest and two temperate broadleaved forests, where trenched plots had previously been installed. At each site, RS and its δ13C (δ13CRs) tended to be lower in trenched plots than in control plots. Contrary to RS, δ13CRs differences were not significant. This observation is consistent with the small differences in δ13C measured on organic matter from root, litter and soil. The lack of an effect on δ13CRs by root exclusion could be from the small difference in δ13C between autotrophic and heterotrophic soil respirations, but further investigations are needed because of potential artefacts associated with the root exclusion technique.

Nitrogen Dynamics in the Soil-Plant System

On an annual basis, the concept of primary production limitation by soil nutrient in natural systems is complex because of the very strong link between nutrient availability and plant cover spatial structure and species composition. In old and stable ecosystems, the plant community is probably highly adapted to the level of available nutrients. The latter is itself strongly dependent on plant community structure, and it is not obvious that annual primary production is controlled by the flux of nutrients originating from soil humus mineralization. The spatial pattern of the distribution of mineral nutrients in soil is rarely homogenous: nutrient concentrations vary rapidly at different scales, from meter (presence or absence of trees for example) to micrometer (presence or absence of bacteria). Soil fauna distribution and activity, which modify the physical and chemical environment of micro-organisms, are key factors controlling the soil organic nitrogen storage and mineral nitrogen production. The ability of plants to uptake nutrients is another key factor controlling primary productivity and, in a sense, the real soil fertility is also a function of plant distribution and plant underground architecture. This impact of soil biological characteristics on soil fertility can explain the discrepancy sometimes observed between high productivity and low mineral nutrients content, as in Lamto.

Multifunctionality is affected by interactions between green roof plant species, substrate depth, and substrate type

Summary Green roofs provide ecosystem services through evapotranspiration and nutrient cycling that depend, among others, on plant species, substrate type, and substrate depth. However, no study has assessed thoroughly how interactions between these factors alter ecosystem functions and multifunctionality of green roofs. We simulated some green roof conditions in a pot experiment. We planted 20 plant species from 10 genera and five families (Asteraceae, Caryophyllaceae, Crassulaceae, Fabaceae, and Poaceae) on two substrate types (natural vs. artificial) and two substrate depths (10 cm vs. 30 cm). As indicators of major ecosystem functions, we measured aboveground and belowground biomasses, foliar nitrogen and carbon content, foliar transpiration, substrate water retention, and dissolved organic carbon and nitrates in leachates. Interactions between substrate type and depth strongly affected ecosystem functions. Biomass production was increased in the artificial substrate and deeper substrates, as was water retention in most cases. In contrast, dissolved organic carbon leaching was higher in the artificial substrates. Except for the Fabaceae species, nitrate leaching was reduced in deep, natural soils. The highest transpiration rates were associated with natural soils. All functions were modulated by plant families or species. Plant effects differed according to the observed function and the type and depth of the substrate. Fabaceae species grown on natural soils had the most noticeable patterns, allowing high biomass production and high water retention but also high nitrate leaching from deep pots. No single combination of factors enhanced simultaneously all studied ecosystem functions, highlighting that soil–plant interactions induce trade‐offs between ecosystem functions. Substrate type and depth interactions are major drivers for green roof multifunctionality.

Trace element concentrations along a gradient of urban pressure in forest and lawn soils of the Paris region (France)

The concentration, degree of contamination and pollution of 7 trace elements (TEs) along an urban pressure gradient were measured in 180 lawn and wood soils of the Paris region (France). Iron (Fe), a major element, was used as reference element. Copper (Cu), cadmium (Cd), lead (Pb) and zinc (Zn) were of anthropogenic origin, while arsenic (As), chromium (Cr) and nickel (Ni) were of natural origin. Road traffic was identified as the main source of anthropogenic TEs. In addition, the industrial activity of the Paris region, especially cement plants, was identified as secondary source of Cd. Soil characteristics (such as texture, organic carbon (OC) and total nitrogen (tot N) contents) tell the story of the soil origins and legacies along the urban pressure gradient and often can explain TE concentrations. The history of the land-use types was identified as a factor that allowed understanding the contamination and pollution by TEs. Urban wood soils were found to be more contaminated and polluted than urban lawns, probably because woods are much older than lawns and because of the legacy of the historical management of soils in the Paris region (Haussmann period). Lawn soils are similar to the fertile agricultural soils and relatively recently (mostly from the 1950s onwards) imported from the surrounding of Paris, so that they may be less influenced by urban conditions in terms of TE concentrations. Urban wood soils are heavily polluted by Cd, posing a high risk to the biological communities. The concentration of anthropogenic TEs increased from the rural to the urban areas, and the concentrations of most anthropogenic TEs in urban areas were equivalent to or above the regulatory reference values, raising the question of longer-term monitoring.