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Maintaining astronaut health throughout long-duration spaceflight is essential to the feasibility of a manned mission to Mars. The ground-based Mars500 experiment investigated long-duration health by isolating six astronauts for 520 days, the longest controlled human confinement study conducted to date. After 520 days, astronauts had uniform strength and lean body mass losses, and increased fasting plasma glucose, calprotectin, and neutrophil levels characteristic of intestinal inflammation but previous analyses revealed no common significant changes in gut microbiota. This study reanalysed data from early (days 7–45) and late (days 420–520) faecal samples and identified 408 exact sequence variants (ESVs), including 213 shared by all astronauts. Thirty-two ESVs were significantly differentially abundant over time, including depletion of keystone resistant starch degrading, anti-inflammatory and insulin sensitivity-associated species, such as Faecalibacterium prausnitzii, Ruminococcus bromii, Blautia luti, Anaerostipes hadrus, Roseburia faecis, and Lactobacillus rogosae, and enrichment of yet-to-be-cultured bacteria. Additionally, the extraordinary experimental confinement allowed observation of microbiota potentially shared between astronauts and their habitat. Forty-nine species were shared, representing 49% and 12% of the human and environmental microbiome diversity, respectively. These findings reveal the microbiota which significantly altered in relative abundance throughout confinement, including species known to influence inflammation and host glucose homeostasis consistent with astronaut symptoms. Identification of microbiome alterations after 520 days of isolation represents a missing piece connecting Mars500 astronaut physiological studies. Knowledge of the impact of long-term confinement upon the human microbiome helps to improve our understanding of how humans interact with their habitats and is a valuable step forward towards enabling long-duration spaceflight.

Phytoextraction potential of a co-planting system was evaluated using a shrub and an herbaceous species and compared with monocultures. A greenhouse experiment with Salix interior and Trifolium pratense grown in combination or alone was conducted for 120 days in soil either uncontaminated or contaminated with wood preservatives containing mixed chromated copper arsenate and pentachlorophenol (PCP). The results showed that the plant species produced similar amounts of dry biomass per pot in monoculture and co-planting, whether growing in contaminated or uncontaminated soil. Arsenic (As), chromium (Cr) and copper (Cu) concentrations in root tissue of S. interior increased 8.6%, 65.9% and 4.5%, respectively, in co-planting compared to its monoculture. T. pratense had superior concentration of As (14% higher) in root tissue when co-planted. However, the higher trace elements concentrations in the plant tissues did not translate into measurable differences in total trace element removal per pot, except for As. The bioconcentration factor for Cu and As was high in the belowground portions of the plants in co-planting. PCP levels in the soil decreased to values near the limit of detection in all treatments. These results suggest that co-planting S. interior with T. pratense could lead to higher phytoextraction potential than monoculture.

Widely used as wood preservatives for the last century, Pentachlorophenol (PCP) and chromated copper arsenate (CCA) have been shown to leach from treated surfaces and contaminate soil of wood storage sites. We performed a four-year field phytoremediation trial in southern Quebec (Canada) on a site contaminated with PCP and CCA with the following objectives: (1) assess the potential of willow, fescue, alfalfa and Indian mustard to tolerate and translocate CCA and PCP residues in their aerial tissues, (2) investigate the possibility of phytoextraction of dioxins and furans, and (3) test the effect of nitrogen fertilizer on phytoremediation performance. We showed that while nitrogen fertilization increased the chlorophyll content of plants, it did not result in a significantly greater plant biomass. We also showed that plants grown in the presence of PCP/CCA residues were able to translocate and concentrate trace elements in their aerial tissues, but also dioxins and furans (PCDD/F). This suggests that plants grown on sites polluted by PCP might contain dioxins and furans and should be treated as contaminated by these toxic chemicals. Finally, the reduction of soil contaminants at the end of the trial suggests that phytoremediation is a promising approach for decontaminating such sites.

Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterized. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge and post-treatment effluent were characterized. From 3163 exact sequence variants (ESVs), 860 were annotated to species-level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially human-associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human-associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease-producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human-associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species-level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem.

Summary Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.

Soil contamination with toxic metalloids, such as arsenic, can represent a substantial human health and environmental risk. Some plants are thought to tolerate soil toxicity using root exudation, however, the nature of this response to arsenic remains largely unknown. Here, white lupin plants were exposed to arsenic in a semi-hydroponic system and their exudates were profiled using untargeted liquid chromatography tandem mass spectrometry. Arsenic concentrations up to 1 ppm were tolerated and led to accumulation of 12.9 μg As g-1 dry weight (DW) and 411 μg As g-1 DW in aboveground and belowground tissues, respectively. From 193 exuded metabolites, 34 were significantly differentially abundant due to 1 ppm arsenic, including depletion of glutathione disulphide and enrichment of phytochelatins and coumarins. Significant enrichment of phytochelatins in exudates of arsenic-treated plants was further confirmed using exudate sampling with strict root exclusion. The chemical tolerance toolkit in white lupin included nutrient acquisition metabolites as well as phytochelatins, the major intracellular metal-binding detoxification oligopeptides which have not been previously reported as having an extracellular role. These findings highlight the value of untargeted metabolite profiling approaches to reveal the unexpected and inform strategies to mitigate anthropogenic pollution in soils around the world. This article is protected by copyright. All rights reserved.

The addition of organic matter (OM) containing glyphosate during compost production, through the introduction of contaminated plant residues or sewage sludge, presents a risk of hindering the proper OM breakdown carried out by microorganisms and causing the accumulation of glyphosate or aminomethylphosphonic acid (AMPA). To measure the effect of glyphosate and glyphosate-based herbicide (GBH) on OM decomposition as well as the dissipation of glyphosate to AMPA during composting, a controlled-environment experiment was conducted using mesocosm-scale vessels. Analytical-grade (AG) glyphosate (150 mg kg

The use of willow plantations can be a sustainable approach for treating primary municipal wastewater, potentially reducing both the environmental and economic burdens associated with conventional treatment. However, the impact of wastewater irrigation upon the willow biorefinery potential has not yet been established. To investigate this effect, three-year-old field grown willows were harvested from plots kept as either controls or irrigated with primary municipal wastewater effluent at 29.5 million L ha−1 yr−1. Biomass compositional analysis, ionic liquid pretreatment and enzymatic saccharification were assessed and differential abundance of persistent extractable phytochemicals was evaluated using untargeted metabolite profiling. Glucan significantly increased by 8% in wastewater treated trees, arabinose and galactose were significantly decreased by 8 and 29%, respectively, while xylose, mannose and lignin content were unaltered. Ionic liquid pretreatment and enzymatic saccharification efficiencies did not vary significantly, releasing >95% of the cell wall glucose and recovering 35% of the lignin. From a total of 213 phytochemical features, 83 were significantly depleted and 14 were significantly enriched due to wastewater irrigation, including flavonoids and lignan derivatives. Considered alongside increased biomass yield from wastewater irrigation (+200%), lignocellulosic bioenergy yields increased to 8.87 t glucose ha−1 yr−1 and 1.89 t ha−1 yr−1 recovered lignin, while net extractives yields increased to 1.48 t ha−1 yr−1, including phytochemicals of interest. The maintenance of glucose accessibility after low-cost ionic liquid pretreatment is promising evidence that sustainable lignocellulose bioenergy production can complement wastewater treatment. Untargeted metabolite assessment revealed some of the phytochemical toolkit employed by wastewater irrigated willows, including accumulation of flooding and salinity tolerance associated flavonoids glabraoside A and glabrene. The extractable phytochemicals underpin a novel high biomass phenotype in willow and, alongside lignocellulosic yields, could help enhance the economic feasibility of this clean wastewater treatment biotechnology through integration with sustainable biorefinery.

Phytoremediation is becoming recognised as a promising environmental approach to decontaminate land. However, establishing large-scale plantations for phytoremediation purposes can bear prohibitive costs. In order to deliver large-scale phytoremediation projects, easily implemented plant establishment solutions need to be available to practitioners. Here, we present a novel planting technology based on willow microcuttings for the rapid establishment of phytoremediation plantations. An experiment was performed testing the effect of microcutting planting density and diversity on various growth parameters including aboveground biomass yields. After two growing seasons, aboveground dry biomass reached an equivalent of 23.1 t/ha. Willow microcutting planting density and diversity did not significantly affect biomass yields, although other growth parameters (survival, stand density and mean stem height) differed across treatments. Our results suggest that this willow microcutting planting technology is viable at large-scale, robust across willow species and represents a lower cost alternative to more traditional planting technologies.

Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.

Plant survival and growth are essential parameters in monitoring the effectiveness of phytoremediation protocols for brownfields decontamination. The ability of different willow cultivars to survive and adapt to contamination in polluted soils can vary according to the nature and concentration of the contaminants. The objectives of this study were to identify which cultivars had the highest yields, and to determine whether the origin of the cuttings influences survival, growth and phytoextraction potential of willow cultivars when grown on polluted soil. Survival, growth and phytoextraction of trace elements (Cd, Cr, Cu, Ni, Pb, Zn) were compared for ten willow cultivars planted in a highly organic-contaminated industrial environment versus in uncontaminated soil. Variations in cultivar response according to cutting origin (contaminated site or not) were also analysed for each site. Results show that, Salix nigra ˈ5005ˈ was very productive in an extremely contaminated environment. Salix eriocephala ˈS25ˈ also performed exceptionally well, as it produced large root biomass (nearly twice that the other cultivars). The highest concentration of cadmium was found in S. x dasyclados ˈSV1ˈ; cultivars S. purpurea x S. miyabeana ˈMillbrookˈ and S. eriocephala ˈS25ˈ exhibited the highest concentrations of chromium. Cultivar ˈS25ˈ was also the most effective at concentrating copper, and S. miyabeana ˈSX67ˈ was the most efficient at phytoextracting zinc. The origin of the cuttings did not have a significant influence on survival, growth or phytoextraction, except for ˈMillbrookˈ: individuals originating from the contaminated environment produced significantly more aboveground biomass when grown in a contaminated environment, compared to individuals who had never been in contact with contaminants. These results could help build more effective phytoremediation protocols for highly contaminated environments by identifying willow cultivars and cutting selection techniques appropriate for specific environments.

Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa were observed between willow species, mostly in contaminated soils. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for Salix eriocephala, S. miyabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. caprea to contamination, and the superior tolerance of S. miyabeana and S. purpurea to soil contamination at that site. The root metatranscriptomes of two species were compared and revealed that plants transcripts are mainly influenced by willow species, while microbial transcripts mainly responded to contamination. A comparison of the rhizosphere and root metatranscriptomes in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, mainly because of large shifts in the rhizosphere metatranscriptome.

Short rotation coppice willow (Salix sp.) is well established as an effective phytoremediation crop and is also emerging as an attractive lignocellulosic bioenergy option. The prospect of integrating value-added renewable chemicals as a supplementary component of the crop’s value is explored here in terms of absolute phenolic yields, extractable from field cultivated mature biomass. Five willow cultivars, selected as leading biomass yielding cultivars, were cultivated at four field sites in Quebec, Canada: Salix x dasyclados ‘SV1’, Salix viminalis ‘SV5027’, Salix miyabeana ‘SX61’, ‘SX64’, ‘SX67’. Substantial and significant cultivar variation was observed in groups of compounds including hydroxycinnamic acids and derivatives, benzoic acids derivatives, flavonols and condensed tannins in concentration per ton of biomass and/or yield per hectare per year. The highest phenolic yields were produced by Salix miyabeana ‘SX67’ cultivated at St-Roch at 5.43 (±0.60) kg ha−1 yr−1, which also produced 35.54 (±4.10) kg ha−1 yr−1 condensed tannins. These phenolic yields suggest further exploration of renewable chemicals production as a supplement to other biomass end-uses could be worthwhile. Such flexibility would help provide important advantages for weathering renewables policy and market uncertainty as well as improve the feasibility and competitiveness of sustainable biomass production as part of an integrated green technology platform.

Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in randomized block design with two factors: 1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and 2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in petroleum hydrocarbons contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.

Municipal wastewater treatment using willow ‘phyto’-filtration has the potential for reduced environmental impact compared to conventional treatment practices. However, the physiological adaptations underpinning tolerance to high wastewater irrigation in willow are unknown. A one-hectare phytofiltration plantation established using the Salix miyabeana cultivar ‘SX67’ in Saint-Roch-de-l'Achigan, Quebec, Canada, tested the impact of unirrigated, potable water or two loads of primary effluent wastewater 19 and 30 ML ha−1 yr−1. A nitrogen load of 817 kg N ha−1 from wastewater did not increase soil pore water nitrogen concentrations beyond Quebec drinking water standards. The willow phytofiltration phenotype had increased leaf area (+106–142%) and leaf nitrogen (+94%) which were accompanied by significant increases in chlorophyll a + b content. Wastewater irrigated trees had higher stomatal sizes and a higher stomatal pore index, despite lower stomatal density, resulting in increased stomatal conductance (+42–78%). These developmental responses led to substantial increases in biomass yields of 56–207% and potable water controls revealed the nitrogen load to be necessary for the high productivity of 28–40 t ha−1 yr−1 in wastewater irrigated trees. Collectively, this study suggests phytofiltration plantations could treat primary effluent municipal wastewater at volumes of at least 19 million litres per hectare and benefit from increased yields of sustainable biomass over a two-year coppice cycle. Added-value cultivation practices, such as phytofiltration, have the potential to mitigate negative local and global environmental impact of wastewater treatment while providing valuable services and sustainable bioproducts.

Fast growing, high biomass willows (Salix sp.) have been extensively used for the phytoremediation of trace element-contaminated environments, as they have an extensive root system and they tolerate abiotic stressors such as drought and metal toxicity. Being dual mycorrhizal plants, they can engage single or simultaneous symbiotic associations with both arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (EM) fungi, which can improve overall plant health and growth. The aim of this study was to test the effect of these mycorrhizal fungi on the growth and trace element (TE) extraction potential of willows. A field experiment was carried out where we grew Salix miyabeana clone SX67 on the site of a decommissioned industrial landfill, and inoculated the shrubs with an AM fungus Rhizophagus irregularis, an EM fungus Sphaerosporella brunnea, or a mixture of both. After two growing seasons, the willows inoculated with the EM fungus S. brunnea produced significantly higher biomass. Ba, Cd and Zn were found to be phytoextracted to the aerial plant biomass, where Cd presented the highest bioconcentration factor values in all treatments. Additionally, the plots where the willows received the S. brunnea inoculation showed a significant decrease of Cu, Pb, and Sn soil concentrations. AM fungi inoculation and dual inoculation did not significantly influence biomass production and soil TE levels.

Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.

Background One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life. Methods Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. ‘Fish Creek’ roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed. Results The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation. Conclusions Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered. Electronic supplementary material The online version of this article (10.1186/s40168-018-0432-5) contains supplementary material, which is available to authorized users.

Trace element (TE) contaminated land represents an important risk to the environment and to human health worldwide. These soils usually contain a variety of TEs which can be a challenge for plant-based remediation options. As individual plant species often possess a limited range of TE remediation abilities, functional complementarity principles could be of value for remediation of soil contaminated by multiple TEs using assemblages of species. Monocultures and polycultures of Festuca arundinacea, Medicago sativa and Salix miyabeana were grown for 4months in aged-polluted soil contaminated by Ag, As, Cd, Cr, Cu, Pb, Se and Zn. Above and belowground biomass yields, root surface area (RSA) and TE tissue concentrations were recorded. In monoculture, the greatest aboveground biomass was produced by S. miyabeana (S), the greatest belowground biomass was from M. sativa (M) and F. arundinacea (F) produced the highest RSA. The polycultures of F+M, F+S and F+M+S produced among the highest values across all three traits. F. arundinacea monoculture and its combination with S. miyabeana (F+S) accumulated the highest amounts of total TEs in belowground tissues, whereas the most effective combination (or monoculture) for aboveground extraction yields varied depending on the TE considered. The crops demonstrated complementarity in their biomass allocation patterns as well as facilitative interactions. When considering contamination with a particular TE, the best phytomanagement approach could include a specific monoculture option; however, when above and belowground biomass allocation patterns, TE-remediation abilities as well as nitrogen accessibility are considered, co-cropping all three species (F+M+S) was the most robust scenario for remediation of multiple-TE contaminated land. By more effectively addressing a diversity of TE, species assemblage approaches could represent an important advancement towards enabling the use of plants to address contaminated-land issues worldwide.

Key message: Highly tolerant and productive willow cultivars have been identified as potential candidates for phytoremediation of contaminated soil with petroleum hydrocarbons (PHs) in southern Quebec, Canada. Abstract: Tolerance of Salix to various organic and inorganic contaminants has been well documented and can vary widely among genotypes. In this study, we compared the responses and tolerances of 11 willow cultivars grown in soil contaminated with petroleum hydrocarbons. The study aimed to identify cultivars with the best performance and capacity to establish under these conditions. Using cuttings of the selected willow genotypes, a high-density field experiment was set up on a former industrial site encompassing two distinct sectors: one contaminated (900 m2), and the other uncontaminated (2,400 m2), which was used as control following a randomized block design. Trees were monitored over two growing seasons by recording a series of growth parameters and physiological measurements (leaf area, chlorophyll concentration, stomatal conductance and nutrient concentration). Genotypic differences explained most of the responses of cultivars observed to soil contamination. S. miyabeana (SX67 and SX61) achieved the highest biomass production, while S. nigra (S05) and S. acutifolia (S54) had the highest photosynthetic capacity. While the cultivars S. × dasyclados (SV1), S. purpurea (‘Fish Creek’) and S. caprea (S365) appeared to be negatively affected by the presence of contaminants, the establishment and development of S05, S. eriocephala (S25) and S. purpurea × S. miyabeana (‘Millbrook’) was much less influenced by soil pollution. Our results will help to guide cultivar selection in future phytoremediation projects.

We present the development of a high throughput phase contrast screening system based on LWFA Xray sources for plant imaging. We upgraded the INRS laser-betatron beam line and we illustrate its imaging potential through the innovative development of new tools for addressing issues relevant to global food security. This initiative, led by the Global Institute of Food Security (GIFS) at the U of Saskatchewan, aims to elucidate that part of the function that maps environmental inputs onto specific plant phenotypes. The prospect of correlating phenotypic expression with adaptation to environmental stresses will provide researchers with a new tool to assess breeding programs for crops meant to thrive under the climate extremes.

After industrial activities shut down, the brownfields remaining on abandoned sites are often left to revegetate naturally, a process that reflects the site's biotic and abiotic characteristics, including spatial pollutant distribution. The soil of a former decantation basin in Varennes (southern Quebec, Canada) was systematically sampled and described in terms of concentration of PAHs (polycyclic aromatic hydrocarbons), PHs (petroleum hydrocarbons C 10 –C 50 ), various trace metals as well as ruderal plant abundance and diversity. Partial redundancy analysis was used to investigate the effect of heterogeneous pollution on the plant community's spatial distribution. Up to 61% of variance in spontaneous plant distribution was explained by the pollutant dispersion pattern on the study site. These findings provide guidelines for the design of site-specific and within-site remediation or rehabilitation promoting natural processes that are already in progress. They also suggest using local vegetation and a greater diversity of plant species when conditions are conducive as this may have many associated benefits. The resulting design, which promotes development of the local plant community, can be a more cost effective and environmentally sustainable alternative to traditional plant-based remediation approaches.

Minimizing nitrogen (N) fertilization inputs during cultivation is essential for sustainable production of bioenergy and biofuels. The biomass crop willow (Salix spp.) is considered to have low N fertilizer requirements due to efficient recycling of nutrients during the perennial cycle. To investigate how successfully different willow genotypes assimilate and allocate N during growth, and remobilize and consequently recycle N before the onset of winter dormancy, N allocation and N remobilization (to and between different organs) were examined in 14 genotypes of a genetic family using elemental analysis and (15)N as a label. Cuttings were established in pots in April and sampled in June, August and at onset of senescence in October. Biomass yield of the trees correlated well with yields recorded in the field. Genotype-specific variation was observed for all traits measured and general trends spanning these sampling points were identified when trees were grouped by biomass yield. Nitrogen reserves in the cutting fuelled the entirety of the canopy establishment, yet earlier cessation of this dependency was linked to higher biomass yields. The stem was found to be the major N reserve by autumn, which constitutes a major source of N loss at harvest, typically every 2-3 years. These data contribute to understanding N remobilization in short rotation coppice willow and to the identification of traits that could potentially be selected for in breeding programmes to further improve the sustainability of biomass production.

Maintaining the long-term productivity of short-rotation coppice plantations is very important to ensure the large-scale deployment of biomass as a renewable energy source. In Quebec (Canada), willow short rotation coppice has been studied since the early ‘90s, thereby allowing long-term analysis of the dynamic performance of several species and hybrids as well as management practices. In this study, we report on the long-term productivity of two trials maintained in southern Quebec and carried out to compare a) growth and biomass yield of willow Salix viminalis (cultivar 5027) grown for 15 years under fertilized and unfertilized conditions and b) growth of different willow cultivars over three successive rotations (10 years). The first trial showed that after four rotations, sludge-fertilized S. viminalis 5027 produced significantly more biomass, 19.2 odt ha−1 yr−1, whereas unfertilized plots yielded 13.8 odt ha−1 yr−1. The second trial showed that among the wide variety of commercial willow cultivars available, SX64 and SX61 along with some indigenous species (i.e. S25, S365, S546) were the most suitable for short-rotation forestry in southern Quebec.

Biomass produced from dedicated plantations constitutes a source of renewable energy and is expected to play an important role in several countries in the coming decades. The cultivation of woody crops such as willows therefore raises several environmental issues. In North America, several native willows are potentially interesting for biomass producers. Willow trees are diverse but few species used for environmental applications have been the object of molecular genetic studies. Based on the sequenced poplar genome, 24 microsatellite markers were assayed on five native North American willow species: Salix amygdaloides, S. discolor, S. eriocephala, S. interior and S. nigra. Polymorphic microsatellite markers were used to characterize the allele data on the shrub Salix eriocephala, a North American species with economic potential. Eleven markers amplified and confirmed the potential of this species. Analysis of samples from six populations in eastern Canada showed that all markers were variable as well as polymorphic in at least one population. The number of alleles per locus ranged from 1 to 9 (mean 2.95) and showed that these microsatellite markers can be used to assess genetic diversity of North American willow species.

Non‐destructive assessment of root systems is important in order to understand and optimise the potential of resource capture and allocation by the plant. We studied the relationships between electrical capacitance (EC) and the below‐ and above‐ground biomass of willows. Cuttings of Salix viminalis × Salix schwerinii cv. Olof were maintained in pots and root development was followed up using a portable capacitance meter over the course of 2.5 months. Pot observations were compared with excavation of two‐year‐old established trees. A strong significant linear relationship (R 2 = 0.81, p < 0.001) was obtained between EC and root biomass (dry weight [DW]) for the pot experiment. EC also showed good correlations with stem and leaf biomass, as well as with stem height. In the excavated willow trees, there was a strong logarithmic relationship between EC and root biomass (R 2 = 0.66, p < 0.001). These results suggest that EC is a good estimator of below‐ground biomass in willow and may become useful in...

Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.

The aim of our study, conducted as a pot experiment, was to assess the potential of willow (Salix miyabeana), alfalfa (Medicago sativa), tall fescue (Festuca arundinacea), and Indian mustard (Brassica juncea) to remediate two brownfield soils differentially contaminated with Ag, Cu and Zn (up to 113.60, 47.50, and 117.00 mg kg(-1) respectively). While aboveground Ag accumulation was highest in B. juncea (4.60 ± 2.58 mg kg(-1)), lower levels were also measured in M. sativa and F. arundinacea. Cu accumulation was observed in all species, but only in underground parts, and was highest in F. arundinacea (269.20 ± 74.75 mg kg(-1)), with a bioconcentration factor of 13.85. Salix miyabeana was found to have the highest Zn aerial tissue concentration (119.96 ± 20.04 mg kg(-1)). Because of its high Ag uptake, the remediation potential of B. juncea should be evaluated more extensively on the site from which we excavated the soil for this study. Given the multiple forms of contamination on the site and the differential specie-related uptake evident in our findings, we hypothesize that an optimal plantation allowing expression of complementary remediation functions would include B. juncea for extraction of Ag, in combination with F. arundinacea for stabilization of Cu and S. miyabeana for extraction of Zn.

The application of nitrogen-containing fertilisers is one approach used to increase growth rates and productivity of forest tree plantations. However, the effects of nitrogen fertilisation on wood properties have not been systematically assessed. The aim of this work was to document the impacts of nitrogen fertilisation on wood formation and secondary xylem fibre properties. We used three fertilisation treatments in which the level of ammonium nitrate was adjusted to 0, 1 and 10 mM in a complete nutrient solution applied daily over a period of 28 days in standardised greenhouse experiments with clonal material of Populus trichocarpa (Torr and Gray) × deltoides (Bartr. ex Marsh). We showed that there was a short-term and repeatable response in which xylem fibre morphology and secondary cell wall structure adapt to a shift in N availability. Under high-nitrogen exposure, xylem fibres were 17% wider and 18% shorter compared to the adequate nitrogen treatment. A very significant thickening of the fibre cell walls was also observed throughout the stem of trees receiving the high-N treatment. It appeared that cell wall structure was greatly affected by the high-N treatment as fibres developed a modified inner cell wall layer. Histological observations indicated that the internal cell wall layer was enriched in cellulose and chemical determinations showed that wood contained more holocellulose. Together, these results indicate that the response of poplar to nitrogen availability may involve marked effects on secondary xylem formation.

Sustainable and inexpensive production of biomass is necessary to make biofuel production feasible, but represents a challenge. Five short rotation coppice (SRC) willow cultivars, selected for high biomass yield, were cultivated on sites at four diverse regions of Quebec to determine their bioenergy potential in contrasting environments. Wood composition and anatomical traits were characterized. Tree height and stem diameter were measured to evaluate growth performance of the cultivars according to the diverse pedoclimatic conditions. Each cultivar showed very specific responses to its environment. While no significant variation in lignin content was observed between sites, there was variation between cultivars. Surprisingly, the pattern of substantial genotype variability in stem density was maintained across all sites. However, wood anatomy did differ between sites in a cultivar (producing high and low density wood), suggesting a probable response to an abiotic stress. Furthermore, twice as many cellulose-rich G-fibers, comprising over 50 % of secondary xylem, were also found in the high density wood, a finding with potential to bring higher value to the lignocellulosic bioethanol industry

Background High concentrations of petroleum hydrocarbon (PHC) pollution can be hazardous to human health and leave soils incapable of supporting agricultural crops. A cheap solution, which can help restore biodiversity and bring land back to productivity, is cultivation of high biomass yielding willow trees. However, the genetic mechanisms which allow these fast-growing trees to tolerate PHCs are as yet unclear. Methods Salix purpurea ‘Fish Creek’ trees were pot-grown in soil from a former petroleum refinery, either lacking or enriched with C10-C50 PHCs. De novo assembled transcriptomes were compared between tree organs and impartially annotated without a priori constraint to any organism. Results Over 45 % of differentially expressed genes originated from foreign organisms, the majority from the two-spotted spidermite, Tetranychus urticae. Over 99 % of T.urticae transcripts were differentially expressed with greater abundance in non-contaminated trees. Plant transcripts involved in the polypropanoid pathway, including phenylalanine ammonia-lyase (PAL), had greater expression in contaminated trees whereas most resistance genes showed higher expression in non-contaminated trees. Conclusions The impartial approach to annotation of the de novo transcriptomes, allowing for the possibility for multiple species identification, was essential for interpretation of the crop’s response treatment. The meta-transcriptomic pattern of expression suggests a cross-tolerance mechanism whereby abiotic stress resistance systems provide improved biotic resistance. These findings highlight a valuable but complex biotic and abiotic stress response to real-world, multidimensional contamination which could, in part, help explain why crops such as willow can produce uniquely high biomass yields on challenging marginal land. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0636-9) contains supplementary material, which is available to authorized users.

Previous revision versions of Fig 2, Fig 3, and S1 Fig were incorrectly published. Please view the correct Fig 2, Fig 3, and S1 Fig here. Fig 2 BEAST gene tree of matK and rbcL. Fig 3 BEAST gene tree of ITS.

Salix L. is the largest genus in the family Salicaceae (450 species). Several classifications have been published, but taxonomic subdivision has been under continuous revision. Our goal is to establish the phylogenetic structure of the genus using molecular data on all American willows, using three DNA markers. This complete phylogeny of American willows allows us to propose a biogeographic framework for the evolution of the genus. Material was obtained for the 122 native and introduced willow species of America. Sequences were obtained from the ITS (ribosomal nuclear DNA) and two plastid regions, matK and rbcL. Phylogenetic analyses (parsimony, maximum likelihood, Bayesian inference) were performed on the data. Geographic distribution was mapped onto the tree. The species tree provides strong support for a division of the genus into two subgenera, Salix and Vetrix. Subgenus Salix comprises temperate species from the Americas and Asia, and their disjunction may result from Tertiary events. Subgenus Vetrix is composed of boreo-arctic species of the Northern Hemisphere and their radiation may coincide with the Quaternary glaciations. Sixteen species have ambiguous positions; genetic diversity is lower in subg. Vetrix. A molecular phylogeny of all species of American willows has been inferred. It needs to be tested and further resolved using other molecular data. Nonetheless, the genus clearly has two clades that have distinct biogeographic patterns.

In this preliminary screening study, we tested the phytoextraction potential of nine Canadian native/well-adapted plant species on a soil highly polluted by trace elements (TE) from a copper refinery. Plant physiological parameters and soil cover index were monitored for a 12-week period. At the end of the trial, biomass yield, bioconcentration (BFC) and translocation (TF) factors for the main TE as well as phytoextraction potential were determined. Most plants were severely injured by the high pollution levels, showing symptoms of toxicity including chlorosis, mortality and very low biomass yield. However, Indian mustard showed the highest selenium extraction potential (65 mg m(-2)), even under harsh growing conditions. Based on our results, tall fescue and ryegrass, which mainly stored As, Cu, Pb and Zn within roots, could be used effectively for phytostabilization.

This is a preliminary hydroponic study to test willow sensitivity to silver nitrate, a highly toxic chemical compound. We grew willow cuttings for a period of three weeks in the presence of increasing AgNO(3) concentrations and assessed the response in terms of growth and physiology. We found that AgNO(3) is generally extremely harmful to willow. AgNO(3) concentration as high as 0.027 muM may result in a significant reduction of biomass productivity and a decrease in stomatal conductance over the first week of exposure. However, willows seem able to adapt to high AgNO(3) concentrations on a longer timeline.

Phytoremediation is a cost-effective green alternative to traditional soil remediation technologies, but has experienced varied success in practice. The recent omics revolution has led to leaps in our understanding of soil microbial communities and plant metabolism, and some of the conditions that promote predictable activity in contaminated soils and heterogeneous environments. Combinations of omics tools and new bioinformatics approaches will allow us to understand integrated activity patterns between plants and microbes, and determine how this metaorganism can be modified to maximize growth, appropriate assembly of microbial communities, and, ultimately, phytoremediation activity. Here we provide an overview of how new omics-mediated discoveries can potentially be translated into an effective and reliable environmental technology. © 2014 Etienne Yergeau.

We investigated the short-term response of poplar roots to low and high nitrogen availability in order to elucidate the mechanisms involved in nutrient acquisition. After 28 days of fertilization with low versus high ammonium nitrate, an increase in aboveground biomass was observed accompanied by a decrease in root biomass, reducing the root: shoot ratio after 28 days. These changes in biomass allocation were accompanied by changes in root architecture and altered gene expression. The gene expression response was evaluated after 7 days using a custom cDNA micrarray following transfer to low and high nitrogen supply. We found that 56 sequences were differentially expressed in poplar roots. Many of these 56 genes could be associated with putative roles in development or response to biotic and abiotic stress. A time course analysis of selected cell wall-related genes by RT-qPCR confirmed the expression patterns obtained by microarray and also showed the timing of this differential response. Our results show that patterns of transcript accumulation in roots of poplars are influenced by nitrogen supply, providing evidence of unique nitrogen-adaptative mechanisms.

The production of energy by burning biomass (i.e. bioenergy), either directly or through transformation, is one of the most promising alternative sources of sustainable energy. Contrary to fossil fuels, bioenergy does not necessarily result in a net long-term increase in atmospheric greenhouse gases, particularly when production methods take this concern into account. Converting forests, peatlands, or grasslands to production of food-crop based biofuels may release up to 400 times more CO2 than the annual greenhouse gas (GHG) reductions that these biofuels would provide by displacing fossil fuels. On the other hand, biofuels from biomass grown on degraded and abandoned agricultural lands planted with perennials do not have a negative effect on carbon emissions [1]. In addition, when properly managed, bioenergy can enhance both agricultural and rural development by increasing agricultural productivity, creating new opportunities for revenue and employment, and improving access to modern energy services in rural areas, both in developed and developing countries [2].

Background Short rotation coppice willow is a potential lignocellulosic feedstock in the United Kingdom and elsewhere; however, research on optimising willow specifically for bioethanol production has started developing only recently. We have used the feedstock Salix viminalis × Salix schwerinii cultivar 'Olof' in a three-month pot experiment with the aim of modifying cell wall composition and structure within the stem to the benefit of bioethanol production. Trees were treated for 26 or 43 days with tension wood induction and/or with an application of the cellulose synthesis inhibitor 2,6-dichlorobenzonitrile that is specific to secondary cell walls. Reaction wood (tension and opposite wood) was isolated from material that had received the 43-day tension wood induction treatment. Results Glucan content, lignin content and enzymatically released glucose were assayed. All measured parameters were altered without loss of total stem biomass yield, indicating that enzymatic saccharification yield can be enhanced by both alterations to cell wall structure and alterations to absolute contents of either glucan or lignin. Conclusions Final glucose yields can be improved by the induction of tension wood without a detrimental impact on biomass yield. The increase in glucan accessibility to cell wall degrading enzymes could help contribute to reducing the energy and environmental impacts of the lignocellulosic bioethanol production process.