Christophe Robin

Divergent composition but similar function of soil food webs of individual plants: plant species and community effects

Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa/groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon mineralization or food web stability. Hence, the composition and structure of entire soil food webs vary at the scale of individual plants and are strongly influenced by the species identity of the plant. However, the ecosystem functions these food webs provide are determined by the identity of the entire plant community.

Desorption kinetics of PAHs from aged industrial soils for availability assessment

Persistent organic pollutants (POPs), such as polycyclic aromatic hydrocarbons (PAHs), may be found in high concentrations in soils of former industrial sites including manufactured gas plants or coking plants. Techniques using moderate solvent extraction, biological tests or solid phase extraction have proved useful for pollution availability estimation. However, more accurate and reliable measurement tools specifically adapted to low concentrations are still needed. Based on a solid-liquid extraction using a Tenax® resin, we suggest a protocol to assess the bioavailability of PAHs, dedicated to aged industrial wasteland soils. Desorption kinetics were measured on three representative contaminated industrial soils. Results were modeled using a first order two-compartment model that provided an estimate of the rapidly desorbing fraction, which was considered to be available, over a 30 h extraction period. In conclusion, this method, allowing the measurement of the available fraction, might prove more relevant than the total concentration value when assessing soil contamination related risks. It may also predict achievable bioremediation performances.

Fine-scale spatial genetic structure of the black truffle (Tuber melanosporum) investigated with neutral microsatellites and functional mating type genes.

The genetic structure of ectomycorrhizal (ECM) fungal populations results from both vegetative and sexual propagation. In this study, we have analysed the spatial genetic structure of Tuber melanosporum populations, a heterothallic ascomycete that produces edible fruit bodies. Ectomycorrhizas from oaks and hazels from two orchards were mapped and genotyped using simple sequence repeat markers and the mating type locus. The distribution of the two T. melanosporum mating types was also monitored in the soil. In one orchard, the genetic profiles of the ascocarps were compared with those of the underlying mycorrhizas. A pronounced spatial genetic structure was found. The maximum genet sizes were 2.35 and 4.70 m in the two orchards, with most manifesting a size < 1 m. Few genets persisted throughout two seasons. A nonrandom distribution pattern of the T. melanosporum was observed, resulting in field patches colonized by genets that shared the same mating types. Our findings suggest that competition occurs between genets and provide basic information on T. melanosporum propagation patterns that are relevant for the management of productive truffle orchards.

Carbon Transfer from the Host to Tuber melanosporum Mycorrhizas and Ascocarps Followed Using a 13C Pulse-Labeling Technique

Truffles ascocarps need carbon to grow, but it is not known whether this carbon comes directly from the tree (heterotrophy) or from soil organic matter (saprotrophy). The objective of this work was to investigate the heterotrophic side of the ascocarp nutrition by assessing the allocation of carbon by the host to Tuber melanosporum mycorrhizas and ascocarps. In 2010, a single hazel tree selected for its high truffle (Tuber melanosporum) production and situated in the west part of the Vosges, France, was labeled with 13CO2. The transfer of 13C from the leaves to the fine roots and T. melanosporum mycorrhizas was very slow compared with the results found in the literature for herbaceous plants or other tree species. The fine roots primarily acted as a carbon conduit; they accumulated little 13C and transferred it slowly to the mycorrhizas. The mycorrhizas first formed a carbon sink and accumulated 13C prior to ascocarp development. Then, the mycorrhizas transferred 13C to the ascocarps to provide constitutive carbon (1.7 mg of 13C per day). The ascocarps accumulated host carbon until reaching complete maturity, 200 days after the first labeling and 150 days after the second labeling event. This role of the Tuber ascocarps as a carbon sink occurred several months after the end of carbon assimilation by the host and at low temperature. This finding suggests that carbon allocated to the ascocarps during winter was provided by reserve compounds stored in the wood and hydrolyzed during a period of frost. Almost all of the constitutive carbon allocated to the truffles (1% of the total carbon assimilated by the tree during the growing season) came from the host.

Continuous monitoring of rhizosphere respiration after labelling of plant shoots with 14CO2

The present work describes an original method to follow rate of 14CO2 and total CO2 production from rhizosphere respiration after plant shoots had been pulse-labelled with 14CO2. We used a radioactivity detector equipped with a plastic cell for flow detection of beta radiation by solid scintillation counting. The radioactivity detector was coupled with an infrared gas analyser. The flow detection of 14CO2 was compared to trapping of 14CO2 in NaOH and counting by liquid scintillation. First, we demonstrated that NaOH (1 M) trapped 95% of the CO2 of a gaseous sample. Then, we determined that the counting efficiency of the radioactivity flow cell was 41% of the activity of gaseous samples as determined by trapping in NaOH (1 M) and by counting by static liquid scintillation. The sensitivity of the 14CO2- flow detection was 0.08 Bq mL−1 air and the precision was 2.9% of the activity measured compared to 0.9% for NaOH trapping method. We presented two applications which illustrate the relevance of 14CO2-flow detection to investigations using 14C to trace photoassimilates within the plant-soil system. First, we examined the kinetics of 14CO2 production when concentrated acid is added to NaH14CO3. This method is the most commonly used to label photoassimilates with 14C. Then, we monitored 14CO2 activity in rhizosphere respiration of 5-week old maize cultivated in soil and whose shoots had been pulse-labelled with 14CO2. We conclude that alkali traps should be used for a cumulative determination of 14CO2 because they are cheap and accurate. On the other hand, we demonstrated that the flow detection of 14CO2 had a finer temporal resolution and was consequently a relevant tool to study C dynamics in the rhizosphere at a short time scale.

Carbon Metabolism Enzyme Activities and Carbon Partitioning in Pinus halepensis Mill, exposed to Mild Drought and Ozone

Summary Since several years, accelerated decline of Aleppo pine ( Pinus halepensis ) forests has been observed in mediterranean areas. In fact, the combination of various environmental factors (photochemical oxidants, drought, high light, ...) was suspected to cause this decline. In this study, three year-old Aleppo pines were exposed during 3 months to ozone fumigation (100 ppb) combined or not with mild drought to study the effects of these combined factors on some sequences linked to carbon partitioning and primary carbon metabolism within the tree. After a cumulative ozone exposure of 132ppm·h, ozone induced a significant decrease in specific activity of the whole-plant (−38%) combined with a disequilibrium of the carbon transfer between root and shoot in favour of the shoots (non significant). Moreover, while the same cumulative dose of ozone had no effect on total Rubisco activity in one year-old needles, mitochondfial NAD malic enzyme activity increased significantly (+32%). By combining ozone with mild drought, the ozone-induced responses of all the parameters were significantly amplified and Rubisco activity was significantly decreased (by 44%). These results allowed us to conclude that at 132ppm·h, ozone alone led to an increase in dark respiration. Moreover, by the combination of ozone and mild drought, a decrease carbon fixation capacity was associated to a decrease of the carbon transfered to the toots, leading to a reduced root growth. Thus, there are indications that high levels of ozone during the summer months may impair the ability of Pinus halepensis to withstand severe water stress in its natural environment.

How does nitrogen availability alter rhizodeposition in Lolium multiflorum Lam. during vegetative growth

The objective of this work was to determine if the impact of nitrogen (N) on the release of organic carbon (C) into the soil by roots (rhizodeposition) correlated with the effect of this nutrient on some variables of plant growth. Lolium multiflorum Lam. was grown at two levels of N supply, either in sterile sand percolated with nutrient solution or in non-sterile soil. The axenic sand systems allowed continuous quantification of rhizodeposition and accurate analysis of root morphology whilst the soil microcosms allowed the study of 14C labelled C flows in physico-chemical and biological conditions relevant to natural soils. In the axenic sand cultures, enhanced N supply strongly increased the plant biomass, the plant N content and the shoot to root ratio. N supply altered the root morphology by increasing the root surface area and the density of apices, both being significantly positively correlated with the rate of organic C release by plant roots before sampling. This observation is consistent with the production of mucilage by root tips and with mechanisms of root exudation reported previously in the literature, i.e. the passive diffusion of roots solutes along the root with increased rate behind the root apex. We proposed a model of root net exudation, based on the number of root apices and on root soluble C that explained 60% of the variability in the rate of C release from roots at harvest. The effects of N on plant growth were less marked in soil, probably related to the relatively high supply of N from non-fertiliser soil-sources. N fertilization increased the shoot N concentration of the plants and the shoot to root ratio. Increased N supply decreased the partitioning of 14C to roots. In parallel, N fertilisation increased the root soluble 14C and the 14C recovered in the soil per unit of root biomass, suggesting a stimulation of root exudation by N supply. However, due to the high concentration of N in our unfertilised plants, this stimulation was assumed to be very weak because no significant effect of N was observed on the microbial C and on the bacterial abundance in the rhizosphere. Considering the difficulties in evaluating rhizodeposition in non sterile soil, it is suggested that the root soluble C, the root surface area and the root apex density are additional relevant variables that should be useful to measure along with the variables that are commonly determined when investigating how plant functioning impacts on the release of C by roots (i.e soil C, C of the microbial biomass, rhizosphere respiration).

Black truffle-associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles

Although truffles are cultivated since decades, their life cycle and the conditions stimulating ascocarp formation still remain mysterious. A role for bacteria in the development of several truffle species has been suggested but few is known regarding the natural bacterial communities of Périgord Black truffle. Thus, the aim of this study was to decipher the structure and the functional potential of the bacterial communities associated to the Black truffle in the course of its life cycle and along truffle maturation. A polyphasic approach combining 454-pyrosequencing of 16S rRNA gene, TTGE, in situ hybridization and functional GeoChip 3.0 revealed that Black truffle ascocarps provide a habitat to complex bacterial communities that are clearly differentiated from those of the surrounding soil and the ectomycorrhizosphere. The composition of these communities is dynamic and evolves during the maturation of the ascocarps with an enrichment of specific taxa and a differentiation of the gleba and peridium-associated bacterial communities. Genes related to nitrogen and sulphur cycling were enriched in the ascocarps. Together, these data paint a new picture of the interactions existing between truffle and bacteria and of the potential role of these bacteria in truffle maturation.

Protozoa enhance foraging efficiency of arbuscular mycorrhizal fungi for mineral nitrogen from organic matter in soil to the benefit of host plants

Dead organic matter (OM) is a major source of nitrogen (N) for plants. The majority of plants support N uptake by symbiosis with arbuscular mycorrhizal (AM) fungi. Mineralization of N is regulated by microfauna, in particular, protozoa grazing on bacteria. We hypothesized that AM fungi and protozoa interactively facilitate plant N nutrition from OM. In soil systems consisting of an OM patch and a root compartment, plant N uptake and consequences for plant carbon (C) allocation were investigated using stable isotopes. Protozoa mobilized N by consuming bacteria, and the mobilized N was translocated via AM fungi to the host plant. The presence of protozoa in both the OM and root compartment stimulated photosynthesis and the translocation of C from the host plant via AM fungi into the OM patch. This stimulated microbial activity in the OM patch, plant N uptake from OM and doubled plant growth. The results indicate that protozoa increase plant growth by both mobilization of N from OM and by protozoa-root interactions, resulting in increased C allocation to roots and into the rhizosphere, thereby increasing plant nutrient exploitation. Hence, mycorrhizal plants need to interact with protozoa to fully exploit N resources from OM.

Is the C:N ratio a reliable indicator of C allocation to primary and defence-related metabolisms in tomato?

Plant growth and defence are both fuelled by compounds synthesized from a common pool of carbon and nitrogen, implying the existence of a competition for carbon and nitrogen allocation to both metabolisms. The ratio of carbon to nitrogen (C:N) of an organ is often regarded as a convenient indicator of growth and quality. The purpose of this work was to assess whether or not it is possible to extend its use to characterize the trade-off between growth and defence processes. Therefore, we calculated C:N ratios in the pool of resources and in the total plant, and correlated them to the concentrations of diverse compounds of the primary and secondary metabolisms in young tomatoes. Plants were grown hydroponically at N availabilities either limiting (0.1 mM) or not (7 mM) for growth in two glasshouses maintained either under ambient or enriched (700 vpm) air CO(2). These conditions yielded a large array of C:N in fully developed leaves, developing leaves, stem and roots, sampled 27, 35 and 47 days after sowing. Growth parameters and tissue concentrations of primary metabolites (carbohydrates, starch), defence-related compounds (polyphenols, glycoalkaloids), lignin, nitrate, ammonium, C and N were analyzed. Net CO(2) exchange rate was also measured at the last sampling date. Low N limited plant growth more than photosynthesis. The C:N in the resource pool was far higher than the total C:N. Starch was the most responsive compound, attaining high concentration under high C:N, whereas lignin remained stable. Chlorogenic acid, rutin, kaempferol-rutinoside and tomatine concentrations correlated positively to C:N. The same patterns were observed for most organs and molecules, except soluble carbohydrates in fully developed leaves whose concentration was not influenced. Among the organs, developing leaves showed the highest concentrations of secondary compounds and were the most responsive to C:N variations. Neither the biochemical nature of the compounds (C-based or N- containing metabolites) nor the calculation mode of C:N, influenced the patterns observed. Within the range of N availabilities considered (up to N limitation but not deficiency), the C:N can be considered as a good indicator of the secondary compounds concentrations in organs, especially for those involved in the chemical defence.