Numerous studies address the distribution and the diversity of dark septate endophytes (DSEs) in the literature, but little is known about their ecological role and their effect on host plants, ...especially in metal-polluted soils. Seven DSE strains belonging to Cadophora, Leptodontidium, Phialophora and Phialocephala were isolated from roots of poplar trees from metal-polluted sites. All strains developed on a wide range of carbohydrates, including cell-wall-related compounds. The strains evenly colonized birch, eucalyptus and ryegrass roots in re-synthesis experiments. Root and shoot growth promotion was observed and was both plant and strain dependent. Two Phialophora and Leptodontidium strains particularly improved plant growth. However, there was no correlation between the level of root colonization by DSEs and the intensity of growth promotion. All strains produced auxin and six also stimulated plant growth through the release of volatile organic compounds (VOCs). SPME-GC/MS analyses revealed four major VOCs emitted by Cadophora and Leptodontidium. The strains exhibited growth at high concentrations of several metals. The ability of metal-resistant DSE strains to produce both soluble and volatile compounds for plant growth promotion indicates interesting microbial resources with high potential to support sustainable production of bioenergy crops within the context of the phytomanagement of metal-contaminated sites.
Metal-tolerant dark septate endophytic fungi can use complex carbon sources and promote plant growth through the release of auxin and volatile organic compounds.
Revegetation of the tailings dumps produced by various industrial activities is necessary to prevent dust storms and erosion and represents a great challenge for ecological restoration. Little is ...known about the microbial colonisation and community structure of revegetated tailings following site exploitation. Here, we report the sequencing of 16S rRNA and internal transcribed spacer (ITS) fungal RNA gene amplicons from chlor-alkali residue and from an adjacent undisturbed soil to define the composition and assembly of the rhizosphere microbial communities. After quality filtering, a total of 72,373 and 89,929 bacterial sequences and 122,618 and 111,209 fungal sequences remained for community analysis from undisturbed soil and tailings dump samples, respectively. These reads were affiliated with 45 bacterial and 9 fungal phyla and 113 bacterial and 35 fungal classes. We observed a clear dominance of Gammaproteobacteria at our study site (24% of total sequences), especially of the Pseudomonas genera (72% of Gammaproteobacteria sequences), together with the dominance of a few fungal taxa, such as Hebeloma and Geopora. However, we also noticed that the core microbiome comprised 64.4% and 62.4% of the bacterial and fungal genera, respectively, despite marked differences in soil physico-chemical properties. A heatmap of correlations between soil parameters and taxa confirmed that approximately 50% of the 33 dominant taxa colonised both types of soil. We further demonstrated that the global bacterial-fungal network topology of the dump approximated that of the undisturbed soil. Our approach illuminates the importance of studying more than just a single component of the microbial community and represents a step forward in uncovering the microbial ecology of disturbed environments beyond what is generally found in conventional studies. Our study also provides novel global community proxies that have led us to conclude that environmental filtering is more likely to occur through the activity of tree roots rather than as a result of specific soil characteristics and could be an important force in the assembly of at least some microbial communities.
•We report the sequencing of 16S RNA and ITS fungal RNA genes from a chlor-alkali dump.•We observed a clear dominance of the Pseudomonas genera (72% of γ-proteobacteria).•The core microbiome comprised 64.4% and 62.4% of the bacterial and fungal genera.•Environmental filtering is more likely to occur through the activity of tree roots.
As a consequence of increased pressure on environment in Europe and beyond, the extent and variety of forms of environmental damage has broadened widely over the last decades. One key way to tackle ...this problem is, evidently, to ensure that damage that arise is properly repaired. Whilst provisions to secure environmental liability have been implemented in the EU context through the Environmental Liability Directive, the effectiveness of this Directive is still limited. In France, in order to surpass current impasses, the 2016 Biodiversity Law was recently enacted (adopted on August 8th, 2016), which creates a specific regime in French civil law for remedying ecological damage (defined as damage caused to nature itself). Three years after the introduction of France’s new approach to ecological damage, the present article reflects on the legal innovations and challenges of the reform, and explains how the new regime proceeds to remedy ecological damage. A key challenge here, as will be discussed, is that nature as such has not been recognised as having legal personality under the French legal system, which has traditionally been a key hurdle for securing compensation for environmental loss in the first place under tort law.
Mercury (Hg) is a highly toxic metal with no known biological function, and it can be highly bioavailable in terrestrial ecosystems. Although fungi are important contributors to a number of soil ...processes including plant nutrient uptake and decomposition, little is known about the effect of Hg on fungi. Fungi accumulate the largest amount of Hg and are the organisms capable of the highest bioaccumulation of Hg. While referring to detailed mechanisms in bacteria, this mini-review emphasizes the progress made recently on this topic and represents the first step towards a better understanding of the mechanisms underlying Hg tolerance and accumulation in fungal species and hence on the role of fungi within the Hg cycle at Hg-contaminated sites.
Key points
•
The fungal communities are more resilient than bacterial communities to Hg exposure.
• The exposure to Hg is a threat to microbial soil functions involved in both C and nutrient cycles.
• Fungal (hyper)accumulation of Hg may be important for the Hg cycle in terrestrial environments.
• Understanding Hg tolerance and accumulation by fungi may lead to new remediation biotechnologies.
The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, ...diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments.
Display omitted
•Two anthropospheric soils displayed contrasting physico-chemical characteristics.•Fungal and bacterial communities were assessed through Illumina Miseq sequencing.•Root microbial communities were well separated from soil microbial communities.•Ascomycota dominated the fungal community in unplanted soils and Pierrelaye site.•The ectomycorrhizal (mostly Basidiomycota) community dominated at Leforest.
The European Union has some of the world's most ambitious and highly developed environmental laws on its books, but their effectiveness is severely compromised by non‐compliance. With the UNECE ...Aarhus Convention (1998), Europe launched an innovative legal experiment, democratizing environmental enforcement by conferring third party citizens and environmental non‐governmental organizations (ENGOs) with legal rights of access to environmental information, public participation, and access to justice in environmental matters. Based on some 2000 surveys and over 150 interviews with stakeholders from three Member States – France, Ireland, and the Netherlands – we adopt a holistic, 360° perspective, capturing the views of regulated parties, NGOs, and the general public on this private governance experiment. Our data provide important new insights into the practical effectiveness of Europe's laws enabling private environmental enforcement, its (intended and unintended) effects on farmers' compliance decisions in the vital area of nature conservation, and how law might be used to stimulate pro‐environmental predispositions.
Private ‘bottom-up’ enforcement has been central to the efforts of the European Union (EU) to promote effective compliance with its ambitious environmental laws. This approach is strengthened by the ...EU's implementation of the Aarhus Convention, which aims to democratize environmental enforcement by conferring citizens and environmental non-governmental organizations (ENGOs) with legal rights of access to environmental information, rights of public participation, and rights of access to justice (the so-called ‘Aarhus mechanisms’). This article empirically assesses the extent to which the Aarhus mechanisms empower ENGOs to take an active role in the private enforcement of the EU Habitats and Birds Directives. Based on 75 surveys and 30 interviews with ENGOs from three Member States (France, Ireland, the Netherlands), we apply regulatory intermediary theory to show how European ENGOs play a vital role in intermediating between (i) EU Member States and their citizens, (ii) the EU and individual citizens, and even (iii) the EU and its Member States. We bring new empirical insights into the role of law as an enabler of regulatory intermediaries, and its potential as a tool for orchestrating regulatory intermediaries.
This study aimed to isolate, identify, and characterise metal-tolerant fungi colonising poplar roots at a metal-contaminated phytoremediation site. Poplar roots were colonised by arbuscular ...mycorrhizal, ectomycorrhizal, and endophytic fungi, and the species were determined by ITS molecular analyses. Eight different isolates were successfully isolated into pure culture. Three isolates belonging to the Helotiales (P02, P06) and the
Serendipita vermifera
species (P04) were highly tolerant to metals (Cd, Zn, Pb, and Cu) compared to the mycorrhizal
Hebeloma
isolates. The three isolates degraded complex carbohydrates, such as xylan and cellulose, indicating that they could partially degrade root cell walls and penetrate into cells. This hypothesis was confirmed by further in vitro re-synthesis experiments, which showed that the three isolates colonised root tissues of poplar plantlets whereas two of them formed microsclerotia-like structures. Taken together, these results suggest an endophytic lifestyle of these isolates. This is the first evidence of
S. vermifera
as a root endophyte of poplar. A new endophytic putative species belonging to the Helotiales and closely related to
Leohumicola
is also reported. Interestingly, and when compared to mock-inoculated plants, both P06 and P04 isolates increased the number of root tips of inoculated poplar plantlets in vitro. Moreover, the
S. vermifera
P04 isolate also increased the shoot biomass. The results are discussed in relation to the potential use of endophytic strains for tree-based phytoremediation of metal-contaminated sites.
Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at ...characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps.
Despite a long history of use in phytomanagement strategies, the impacts of poplar trees on the structure and function of microbial communities that live in the soil remain largely unknown. The ...current study combined fungal and bacterial community analyses from different management regimes using Illumina-based sequencing with soil analysis. The poplar phytomanagement regimes led to a significant increase in soil fertility and a decreased bioavailability of Zn and Cd, in concert with changes in the microbial communities. The most notable changes in the relative abundance of taxa and operational taxonomic units unsurprisingly indicated that root and soil constitute distinct ecological microbial habitats, as exemplified by the dominance of Laccaria in root samples. The poplar cultivar was also an important driver, explaining 12% and 6% of the variance in the fungal and bacterial data sets, respectively. The overall dominance of saprophytic fungi, e.g. Penicillium canescens, might be related to the decomposition activities needed at the experimental site. Our data further highlighted that the mycorrhizal colonization of poplar cultivars varies greatly between the species and genotypes, which is exemplified by the dominance of Scleroderma under Vesten samples. Further interactions between fungal and bacterial functional groups stressed the potential of high-throughput sequencing technologies in uncovering the microbial ecology of disturbed environments.
Laccaria dominates the poplar root fungal community on a contaminated soil.
PDF
