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.
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•Saint-Marcel cave has suffered of a fungal outbreak.•Oenological activities were suspected to lead to uncontrolled fungal proliferation.•High throughput sequencing has been used to assess microorganism communities.•Dominant microorganisms proliferating in the cave were related to wine vinification.
This study deals with approaches for a social-ecological friendly European bioeconomy based on biomass from industrial crops cultivated on marginal agricultural land. The selected crops to be ...investigated are: Biomass sorghum, camelina, cardoon, castor, crambe, Ethiopian mustard, giant reed, hemp, lupin, miscanthus, pennycress, poplar, reed canary grass, safflower, Siberian elm, switchgrass, tall wheatgrass, wild sugarcane, and willow. The research question focused on the overall crop growth suitability under low-input management. The study assessed: (i) How the growth suitability of industrial crops can be defined under the given natural constraints of European marginal agricultural lands; and (ii) which agricultural practices are required for marginal agricultural land low-input systems (MALLIS). For the growth-suitability analysis, available thresholds and growth requirements of the selected industrial crops were defined. The marginal agricultural land was categorized according to the agro-ecological zone (AEZ) concept in combination with the marginality constraints, so-called ‘marginal agro-ecological zones’ (M-AEZ). It was found that both large marginal agricultural areas and numerous agricultural practices are available for industrial crop cultivation on European marginal agricultural lands. These results help to further describe the suitability of industrial crops for the development of social-ecologically friendly MALLIS in Europe.
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.
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.
Growing industrial crops on marginal lands has been proposed as a strategy to minimize competition for arable land and food production. In the present study, eight experimental sites in three ...different climatic zones in Europe (Mediterranean, Atlantic and Continental), seven advanced industrial crop species giant reed (two clones), miscanthus (M. × giganteus and two new seed‐based hybrids), saccharum (one clones), switchgrass (one variety), tall wheatgrass (one variety), industrial hemp (three varieties) and willow (eleven clones), and six marginality factors alone or in combination (dryness, unfavorable texture, stoniness, shallow soil, topsoil acidity, heavy metal and metalloid contamination) were investigated. At each site, biophysical constraints and low‐input management practices were combined with prevailing climatic conditions. The relative yield of a site‐specific low‐input system compared with the site‐specific control was from small to large (i.e. from −99% in industrial hemp in the Mediterranean to +210% in willow in the Continental zone), due to the genotype‐by‐management interaction along with climatic variation between growing seasons. Genotype selection and improved knowledge on crop response to changing environmental, site‐specific biophysical constraint and input application has been detected as key to profitably grow industrial crops on marginal areas. This study may act to provide hints on how to scale up investigated cropping systems, through low‐input practices, under similar environmental and soil conditions tested at each site. However, further attention to detail on the agronomy of early plant development and management in larger multi‐year and multi‐location field studies with commercially scalable agronomies are needed to validate yield performances, and thereby to inform on the best industrial crop options.
Growing industrial crops on marginal lands has been proposed as a strategy to minimize competition for arable land and food production. This study can bring an advancement to knowledge on the suitability of certain industrial crops to marginal and contaminated soils to mitigate indirect land‐use change (i‐LUC) in accordance with the RED II and to meet the European Green Deal towards an EU climate neutral in 2050. It ultimately can assist to make general recommendations of the most appropriate crop and management options at the different regions, climates, soils and marginal land types.
The increasing production of waste that is landfilled might contribute to sources of potentially toxic elements; this is the case of residual red gypsum tailings, a by-product of titanium dioxide ...extraction. Revegetation of the site is essential, and phytoextraction of Mn may render the operations economically profitable. This study aimed to apply phytomanagement techniques in order to increase the plant development for revegetation and an optimal Mn phytoextraction using silver birch, the most abundant plant species on the site. To increase the availability of nutrients from the tailings, amendments that reduce the pH, such as pine bark, Miscanthus straw, white peat and ericaceous compost, were mixed with residual red gypsum and birches were allowed to grow for 3 months. The pine bark and ericaceous compost showed a maximum decrease in pH, allowing up to 1400 mg kg-1 dry matter of Mn to be phytoextracted by the silver birch. However, some nutrient competition was found in the treatment of pine bark, which affected biomass production by reducing it by half compared to control.. Further amendment additions may be needed to take advantage of the pine bark capabilities as a nutrient and Mn solubilizing treatment in residual red gypsum.
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.
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•Earthworms improve plant biomass production.•Earthworms increase the mobility of trace elements in soil.•The chelating compounds produced by plants decreased in presence of earthworms.•The fingerprint of roots drives the pot system and limited earthworm growth.
Capsule:Earthworm inoculation in marginal contaminated soil improves aerial plant biomass production and impacts trace element fluxes between compartments.
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.
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•Rhizospheric fungal and bacterial communities were assessed at three different sites.•Fungal communities are mainly driven by soil parameters and tree species.•Two groups of tree species were identified as a function of their fungal communities.•Uncultured and rhizospheric soils shared the same bacterial communities.•The fungal communities differed depending on the site at which the trees were cultivated.
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.
•Bacteria, cyanobacteria, algae, diatoms, fungi and mosses were sequenced.•Bacteria were the most abundant organisms present in the biofilms.•23S primer provided an overview of the mosses present in biofilms.•This study showed the low efficiency of chemical treatment over time.
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