Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites.

Soil microbial communities play a key role in plant nutrition and stress tolerance. This is particularly true in sites contaminated by trace metals, which often have low fertility and stressful conditions for woody plants in particular. However, we have limited knowledge of the abiotic and biotic factors affecting the richness and composition of microbial communities inhabiting the rhizosphere of plants in contaminated sites. Using high-throughput amplicon sequencing, we studied the rhizospheric bacterial and fungal community structures of 14 woody plant families planted in three contrasting sites contaminated by metals (Pb, Cd, Zn, Mn, Fe, S). The rhizospheric bacterial communities in the given sites showed no significant difference between the various woody species but did differ significantly between sites. The Proteobacteria phylum was dominant, accounting for over 25 % of the overall relative abundance, followed by Actinobacteria, Bacteroidetes and Gemmatimonadetes. Site was also the main driver of fungal community composition, yet unlike bacteria, tree species identity significantly affected fungal communities. The Betulaceae, Salicaceae and Fagaceae families had a high proportion of Basidiomycota, particularly ectomycorrhizal fungi, and the lowest diversity and richness. The other tree families and the unplanted soil harboured a greater abundance of Ascomycota and Mucoromycota. Consequently, for both bacteria and fungi, the site effect significantly impacted their community richness and composition, while the influence of plants on the richness and composition of rhizospheric microbial communities stayed consistent across sites and was dependent on the microbial kingdom. Finally, we highlighted the importance of considering this contrasting response of plant rhizospheric microbial communities in relation to their host identity, particularly to improve assisted revegetation efforts at contaminated sites.

Mycorrhizal inoculation effects on growth and the mycobiome of poplar on two phytomanaged sites after 7-year-short rotation coppicing.

Aims: Afforestation of trace-element contaminated soils, notably with fast growing trees, has been demonstrated to be an attractive option for bioremediation due to the lower costs and dispersion of contaminants than conventional cleanup methods. Mycorrhizal fungi form symbiotic associations with plants, contributing to their tolerance towards toxic elements and actively participating to the biorestoration processes. The aim of this study was to deepen our understanding on the effects of mycorrhizal inoculation on plant development and fungal community at two trace-element contaminated sites (Pierrelaye and Fresnes-sur-Escaut, France) planted with poplar (Populus trichocarpa x Populus maximowiczii). Methods: The 2 sites were divided into 4 replicated field blocks with a final plant density of 2200 tree h-1. Half of the trees were inoculated with a commercial inoculum made of a mix of mycorrhizal species. The sites presented different physico-chemical characteristics (e.g., texture: sandy soil versus silty-loam soil and organic matter: 5.7% versus 3.4% for Pierrelaye and Fresnes-sur-Escaut, respectively) and various trace element contamination levels. Results: After 7 years of plantation, inoculation showed a significant positive effect on poplar biomass production at the two sites. Fungal composition study demonstrated a predominance of the phylum Ascomycota at both sites, with a dominance of Geopora Arenicola and Mortierella elongata, and a higher proportion of ectomycorrhizal and endophytic fungi (with the highest values observed in Fresnes-sur-Escaut: 45% and 28% for ECM and endophytic fungi, respectively), well known for their capacity to have positive effects on plant development in stressful conditions. Furthermore, Pierrelaye site showed higher frequency (%) of mycorrhizal tips for ectomycorrhizal fungi (ECM) and higher intensity (%) of mycorrhizal root cortex colonization for arbuscular mycorrhizal fungi (AMF) than Fresnes-sur-Escaut site, which translates in a higher level of diversity. Conclusions: Finally, this study demonstrated that this biofertilization approach could be recommended as an appropriate phytomanagement strategy, due to its capacity to significantly improve poplar productivity without any perturbations in soil mycobiomes.

The effect of earthworms on plant response in metal contaminated soil focusing on belowground-aboveground relationships.

Contaminated soils are lands in Europe deemed less favourable for conventional agriculture. To overcome the problem of their poor fertility, bio-fertilization could be a promising approach. Soil inoculation with a choice of biological species (e.g. earthworm, mycorrhizal fungi, diazotroph bacteria) can be performed in order to improve soil properties and promote nutrients recycling. However, questions arise concerning the dynamics of the contaminants in an inoculated soil. The aim of this study was to highlight the soil-plant-earthworm interactions in the case of a slightly contaminated soil. For this purpose, a pot experiment in controlled conditions was carried out during 2 months with a Cd, Zn, and Cu contaminated sandy soil, including conditions with or without earthworms (Aporrectodea caliginosa) and with or without plants (Lolium perenne). The three components of the trace element bioavailability were studied to understand the belowground-aboveground relationships and were quantified as followed: i) environmental availability in soils by measuring trace element concentrations in soil solution, ii) environmental bioavailability for organisms by measuring trace element concentrations in depurated whole earthworms bodies and in the plant aerial biomass, and iii) toxicological bioavailability, by measuring survival rate and body weight changes for earthworms and biomass for plants. The results showed that earthworm inoculation increased the content of all studied TE in soil solution. Moreover, lower concentrations of Cd and Zn were found in plants in the presence of earthworms while the bioavailability decreased when compared to the condition without plants. The trace element bioaccumulation in earthworms did not produce a direct toxicity, according to the earthworm survival rate and body weight results. Finally, our pot experiment confirmed that even in contaminated soils, the presence of A. caliginosa promotes plant adaptation and improves biomass production, reducing trace element uptake.

Fungal and bacterial outbreak in the wine vinification area in the Saint-Marcel show cave.

In the Saint-Marcel cave (France), wood barrels and thousands of bottles containing red wine were stored for vinification. After storage began, a fungal and bacterial outbreak occurred, and the area was invaded by numerous types of mold colonizing the cave ceilings and all objects related to human activities (the stairwell and oenological materials). In this study, using the metabarcoding approach, we have studied the microbial outbreak and have linked the identified microorganisms to oenological activity. Both 16S and ITS primers were used to sequence the samples collected from the cave. The results showed that the dominant microorganisms proliferating in the cave were related to wine vinification. For instance, Zasmidium cellare, a strain known for living in dark and ethanol-rich environments, was the dominant fungus on the cave stairwell. Furthermore, Guehomyces pullulans, a cold-adapted yeast used for juice clarification, was recorded as the major species on the blackened limestone ceilings. These findings reveal a complex community structure in the studied cave based on the assembly of bacteria and fungi. Finally, our results demonstrate that oenological activities could seriously affect cave preservation, changing the natural microbial communities populating cave environments.

Poplar rotation coppice at a trace element-contaminated phytomanagement site: A 10-year study revealing biomass production, element export and impact on extractable elements.

Growing lignocellulosic crops on marginal lands could compose a substantial proportion of future energy resources. The potential of poplar was explored, by devising a field trial of two hectares in 2007 in a metal-contaminated site to quantify the genotypic variation in the growth traits of 14 poplar genotypes grown in short-rotation coppice and to assess element transfer and export by individual genotypes. Our data led us to conclusions about the genotypic variations in poplar growth on a moderately contaminated site, with the Vesten genotype being the most productive. This genotype also accumulated the least amounts of trace elements, whereas the Trichobel genotype accumulated up to 170 mg Zn kg-1 DW in the branches, with large variation being exhibited among the genotypes for trace element (TE) accumulation. Soil element depletion occurred for a range of TEs, whereas the soil content of major nutrients and the pH remained unchanged or slightly increased after 10 years of poplar growth. The higher TE content of bark tissues compared with the wood and the higher proportion of bark in branches compared with the wood led us to recommend that only stem wood be harvested, instead of the whole tree, which will enable a reduction in the risks encountered with TE-enriched biomass in the valorization process.

Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data.

In recent decades, show caves have begun to suffer from microorganism proliferation due to artificial lighting installations for touristic activity. In addition to the aesthetic problem, light encourages microorganisms that are responsible for physical and chemical degradation of limestone walls, speleothems and prehistoric paintings of cultural value. Microorganisms have previously been described by microscopy or culture-dependent methods, but data provided by new generation sequencing are rare. The authors identified, for the first time, microorganisms proliferating in one Swiss and in four French show caves using three different primers. The results showed that both photosynthetic and non-photosynthetic bacteria were the dominant taxa present in biofilms. Microalgae were heavily represented by the Trebouxiophyceae, Eustigmatophyceae and Chlorophyceae groups. Twelve diatoms were also recorded, with dominance of Syntrichia sp. (96.1%). Fungi were predominantly represented by Ascomycota, Zygomycota and Basidiomycota, fully half of the sampled biofilms where Fungi were detected. Comparing microbial communities from bleach-treated caves to those in untreated caves showed no significant difference except for a low-level change in the abundance of certain taxa. These findings provided by Illumina sequencing reveal a complex community structure in the 5 caves based on the assembly of bacteria, cyanobacteria, algae, diatoms, fungi and mosses.

Soil plant interactions of Populus alba in contrasting environments.

The effects of the Populus alba tree on different biochemical soil properties, growing in a contaminated area, were studied for two years under field conditions. Two types of trace element contaminated soils were studied: a neutral contaminated soil (NC) and an acid contaminated soil (AC). One neutral non-contaminated area was studied as control. Soil samples were collected at depths of 0-20 cm and 20-40 cm. Leaves and litter samples were analysed. The addition of organic matter, through root exudates and litter, contributed to an increase in soil pH, especially in acid soil. Microbial Biomass Carbon (MBC) was significantly increased by the presence of the trees in all studied areas, especially in the upper soil layer. Similar results were also observed for protease activity. Both MBC and Protease activity were more sensitive to contamination than ß-glucosidase activity. These changes resulted in a decrease of available trace element concentrations in soil and in an improvement of soil quality after a 2-year study. The total concentration of Cd and Zn in soil did not increase over time due to litter deposition. Analysis of P. alba leaves did not show a significant nutritional imbalance and trace element concentrations were normal for plants, except for Cd and Zn. These results indicate that P. alba is suitable for the improvement of soil quality in riparian contaminated areas. However, due to the high Cd and Zn concentrations in leaves, further monitoring of this area is required.

Lignite reduces the solubility and plant uptake of cadmium in pasturelands.

Repeated application of Cd-rich phosphate fertilizers can lead to the accumulation of this nonessential element in soil. This can result in increased plant uptake, with possible breaches of food or feed safety standards. We aimed to determine whether lignite (brown coal) can reduce Cd solubility and plant uptake in New Zealand pasture soils. In batch sorption experiments, we tested the capacity of lignite and lignite-soil mixtures to sorb Cd at various soil pH and Cd loadings. Over a pH range of 4-7, Cd sorption by lignite was 1-2 orders of magnitude greater than by a typic immature pallic soil containing 2% carbon. The addition of 5 wt % lignite to a range of soils revealed that lignite addition was most effective in reducing soluble Cd in soils with low pH. In a greenhouse experiment, we tested the effect of lignite on the accumulation of Cd and other elements by perennial ryegrass, Lolium perenne (L.). The addition of just 1 wt % lignite to the aforementioned soil reduced plant Cd uptake by 30%, without adversely affecting biomass or the uptake of essential nutrient elements including copper and zinc. This may be due to preferential binding of Cd to organic sulfur in lignite.