Poplar clones of different sizes, grown on a heavy metal polluted site, are associated with microbial populations of varying composition

Long-term effects of phytoextraction by a poplar clone on the concentration, fractionation, and transportation of heavy metals in mine tailings

Mine tailings are one of main causes of diffused heavy metal pollution since the heavy metals in there may acquire mobility. The current knowledge of the processes at work in long-term phytoremediation by woody species remains insufficient. Through a 4-year field study, we evaluated the phytoextraction efficiency of Populus deltoides CL. 'Xianglin 90' grown on a mine tailing co-polluted by Cd, Cu, Cr, Ni, Pb, and Zn. The concentrations of Cd, Cu, Ni, Pb, and Zn in the rhizospheric soil were reduced by amounts ranging from 12.86 to 42.19% during the study period. Bioconcentration factors and translocation factors showed that the accumulation of Cd and Zn occurring in the shoots was the most effective. Combined with the considerable biomass produced by poplar, the extracted amounts of Cd and Zn could reach 0.61 g and 10.66 g plant^-1, respectively, in which the shoots account for 77.3% (Cd) and 89.0% (Zn) of the overall extraction amounts. Acid-soluble Cd and Zn increased by 5.49% and 4.29%, respectively, in the rhizosphere compared to the bulk soil, indicating that poplar enhanced the mobility of Cd and Zn in the rhizosphere, which explained its ability for bioaccumulation and root-shoot translocation. Moreover, calculated time required to address the issue of Cd and Zn pollution was theoretically shortened by more than half from 2015 to 2019. This study brings new insights into the long-term effects of phytoextraction on the concentration, fractionation, and transportation of heavy metals and confirms the potential of poplar as a Cd and Zn remediation species.

Pb tolerance and accumulation capabilities of Bidens pilosa L. growing in polluted soils depend on the history of exposure

Phytoremediation, especially phytoextraction, is a good alternative for remediation of soils contaminated with heavy metals. This method requires selection of species for their tolerance, high accumulation levels in harvestable parts, and high biomass production. Bidens pilosa L. has been reported as tolerant to and potentially hyperaccumulator of several heavy metals, including Pb, but with variable results in terms of effectiveness. The aim of this study was to analyse the intra- and interpopulation variability of B. pilosa in response to Pb in individuals from two populations: one historically exposed to Pb and another with no history of exposure. Bidens pilosa L. presented tolerance to Pb pollution in soil, evidenced in a higher survival rate, a better antioxidant response, and an efficient reduction in cell membrane damage mainly due to history of exposure. The period of exposure (30 years) was not long enough to obtain a B. pilosa population that provides seeds for phytoextraction projects, since the average value of total extraction was relatively low. Collecting seeds from a historically exposed population will provide some suitable individuals with Pb accumulation and translocation capabilities, but not a sufficient amount to conduct a large phytoremediation project. The individual accumulator profile of B. pilosa is not related to the physiological behaviour or to the Pb entry into the vascular bundle in root, but to the incorporation of other heavy metals that are micronutrients.

Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North-South transect

Tree root-associated microbiomes are shaped by geographic, soil physico-chemical, and host tree parameters. However, their respective impacts on microbiome variations in soils across larger spatial scales remain weakly studied. We out-planted saplings of oak clone DF159 (Quercus robur L.) as phytometer in four grassland field sites along a European North-South transect. After four years, we first compared the soil microbiomes of the tree root zone (RZ) and the tree root-free zone (RFZ). Then, we separately considered the total microbiomes of both zones, besides the microbiome with significant affinity to the RZ and compared their variability along the transect. Variations within the microbiome of the tree RFZ were shaped by geographic and soil physico-chemical changes, whereby bacteria responded more than fungi. Variations within both microbiomes of the tree RZ depended on the host tree and abiotic parameters. Based on perMANOVA and Mantel correlation tests, impacts of site specificities and geographic distance strongly decreased for the tree RZ affine microbiome. This pattern was more pronounced for fungi than bacteria. Shaping the microbiome of the soil zones in root proximity might be a mechanism mediating the acclimation of oaks to a wide range of environmental conditions across geographic regions.

Characterization of the Belowground Microbial Community in a Poplar-Phytoremediation Strategy of a Multi-Contaminated Soil

Due to their widespread use in industrial applications in recent decades, Polychlorobiphenyls (PCBs) and heavy metals (HMs) are the most common soil contaminants worldwide, posing a risk for both ecosystems and human health. In this study, a poplar-assisted bioremediation strategy has been applied for more than 4 years to a historically contaminated area (PCBs and HMs) in Southern Italy using the Monviso poplar clone. This clone was effective in promoting a decrease in all contaminants and an increase in soil quality in terms of organic carbon and microbial abundance. Moreover, a significant shift in the structure and predicted function of the belowground microbial community was also observed when analyzing both DNA and cDNA sequencing data. In fact, an increase in bacterial genera belonging to Proteobacteria able to degrade PCBs and resist HMs was observed. Moreover, the functional profiling of the microbial community predicted by PICRUSt2 made it possible to identify several genes associated with PCB transformation (e.g., bphAa, bphAb, bphB, bphC), response to HM oxidative stress (e.g., catalase, superoxide reductase, peroxidase) and HM uptake and expulsion (e.g., ABC transporters). This work demonstrated the effectiveness of the poplar clone Monviso in stimulating the natural belowground microbial community to remove contaminants and improve the overall soil quality. It is a practical example of a nature based solution involving synergic interactions between plants and the belowground microbial community.

Soil Microbial Biomass and Community Composition Relates to Poplar Genotypes and Environmental Conditions

Poplars, known for their diversity, are trees that can develop symbiotic relationships with several groups of microorganisms. The genetic diversity of poplars and different abiotic factors influence the properties of the soil and may shape microbial communities. Our study aimed to analyse the impact of poplar genotype on the biomass and community composition of the microbiome of four poplar genotypes grown under different soil conditions and soil depths. Of the three study sites, established in the mid-1990s, one was near a copper smelter, whereas the two others were situated in unpolluted regions, but were differentiated according to the physicochemical traits of the soil. The whole-cell fatty acid analysis was used to determine the biomass and proportions of gram-positive, gram-negative and actinobacteria, arbuscular fungi (AMF), other soil fungi, and protozoa in the whole microbial community in the soil. The results showed that the biomass of microorganisms and their contributions to the community of organisms in the soil close to poplar roots were determined by both factors: the tree-host genotype and the soil environment. However, each group of microorganisms was influenced by these factors to a different degree. In general, the site effect played the main role in shaping the microbial biomass (excluding actinobacteria), whereas tree genotype determined the proportions of the fungal and bacterial groups in the microbial communities and the proportion of AMF in the fungal community. Bacterial biomass was influenced more by site factors, whereas fungal biomass more by tree genotype. With increasing soil depth, a decrease in the biomass of all microorganisms was observed; however, the proportions of the different microorganisms within the soil profile were the result of interactions between the host genotype and soil conditions. Despite the predominant impact of soil conditions, our results showed the important role of poplar genotype in shaping microorganism communities in the soil.

Substitution of manure for chemical fertilizer affects soil microbial community diversity, structure and function in greenhouse vegetable production systems

Soil microbial communities and enzyme activities together affect various ecosystem functions of soils. Fertilization, an important agricultural management practice, is known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research was to make a comparative study of the effects of different nitrogen (N) fertilizer rates and types (organic and inorganic) on soil physicochemical properties, enzyme activities and microbial attributes in a greenhouse vegetable production (GVP) system of Tianjin, China. Results showed that manure substitution of chemical fertilizer, especially at a higher substitution rate, improved soil physicochemical properties (higher soil organic C (SOC) and nutrient (available N and P) contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure application induced a higher fungi/bacteria ratio due to a lower response in bacterial than fungal growth. Also, manure application greatly increased bacterial stress indices, as well as microbial communities and functional diversity. The principal component analysis showed that the impact of manure on microbial communities and enzyme activities were more significant than those of chemical fertilizer. Furthermore, redundancy analysis indicated that SOC and total N strongly influenced the microbial composition, while SOC and ammonium-N strongly influenced the microbial activity. In conclusion, manure substitution of inorganic fertilizer, especially at a higher substitution rate, was more efficient for improving soil quality and biological functions.

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.

Analysis of the bacterial community from high alkaline (pH > 13) drainage water at a brown mud disposal site near Žiar nad Hronom (Banská Bystrica region, Slovakia) using 454 pyrosequencing

Brown mud, as a waste product of the industrial process of aluminum production, represents a great environmental burden due to its toxicity to living organisms. However, some microorganisms are able to survive in this habitat, and they can be used in bioremediation processes. Traditional cultivation methods have a limited capacity to characterize bacterial composition in environmental samples. Recently, next-generation sequencing methods have provided new perspectives on microbial community studies. The aim of this study was to analyze the bacterial community in the drainage water of brown mud disposal site near Žiar nad Hronom (Banská Bystrica region, Slovakia) using 454 pyrosequencing. We obtained 9964 sequences assigned to 163 operational taxonomic units belonging to 10 bacterial phyla. The phylum Proteobacteria showed the highest abundance (80.39%) within the bacterial community, followed by Firmicutes (13.05%) and Bacteroidetes (5.64%). Other bacterial phyla showed an abundance lower than 1%. The classification yielded 85 genera. Sulfurospirillum spp. (45.19%) dominated the bacterial population, followed by Pseudomonas spp. (13.76%) and Exiguobacterium spp. (13.02%). These results indicate that high heavy metals content, high pH, and lack of essential nutrients are the drivers of a dramatic reduction of diversity in the bacterial population in this environment.

Belowground Microbiota and the Health of Tree Crops

Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

Distinct Communities of Poplar Endophytes on an Unpolluted and a Risk Element-Polluted Site and Their Plant Growth-Promoting Potential In Vitro

Numerous studies demonstrated that endophytic microbes can promote plant growth and increase plant stress resistance. We aimed at isolating poplar endophytes able to increase their hosts' fitness both in nutrient-limited and polluted environments. To achieve this goal, endophytic bacteria and fungi were isolated from roots and leaves of hybrid poplars (Populus nigra × P. maximowiczii clone Max-4) on an unpolluted and a risk element-polluted site in the Czech Republic and subsequently screened by a number of in vitro tests. Bacterial communities at the unpolluted site were dominated by Gammaproteobacteria with Pseudomonas sp. as the prominent member of the class, followed by Bacilli with prevailing Bacillus sp., whereas Alphaproteobacteria, mostly Rhizobium sp., prevailed at the polluted site. The fungal endophytic community was dominated by Ascomycetes and highly distinct on both sites. Dothideomycetes, mostly Cladosporium, prevailed at the non-polluted site while unclassified Sordariomycetous fungi dominated at the polluted site. Species diversity of endophytes was higher at the unpolluted site. Many tested endophytic strains solubilized phosphate and produced siderophores, phytohormones, and antioxidants. Some strains also exhibited ACC-deaminase activity. Selected bacteria showed high tolerance and the ability to accumulate risk elements, making them promising candidates for use in inocula promoting biomass production and phytoremediation. Graphical Abstract ᅟ.

Evaluation of bioenergy crop growth and the impacts of bioenergy crops on streamflow, tile drain flow and nutrient losses in an extensively tile-drained watershed using SWAT

Large quantities of biofuel production are expected from bioenergy crops at a national scale to meet US biofuel goals. It is important to study biomass production of bioenergy crops and the impacts of these crops on water quantity and quality to identify environment-friendly and productive biofeedstock systems. SWAT2012 with a new tile drainage routine and improved perennial grass and tree growth simulation was used to model long-term annual biomass yields, streamflow, tile flow, sediment load, and nutrient losses under various bioenergy scenarios in an extensively agricultural watershed in the Midwestern US. Simulated results from bioenergy crop scenarios were compared with those from the baseline. The results showed that simulated annual crop yields were similar to observed county level values for corn and soybeans, and were reasonable for Miscanthus, switchgrass and hybrid poplar. Removal of 38% of corn stover (3.74Mg/ha/yr) with Miscanthus production on highly erodible areas and marginal land (17.49Mg/ha/yr) provided the highest biofeedstock production (279,000Mg/yr). Streamflow, tile flow, erosion and nutrient losses were reduced under bioenergy crop scenarios of bioenergy crops on highly erodible areas and marginal land. Corn stover removal did not result in significant water quality changes. The increase in sediment and nutrient losses under corn stover removal could be offset with the combination of other bioenergy crops. Potential areas for bioenergy crop production when meeting the criteria above were small (10.88km²), thus the ability to produce biomass and improve water quality was not substantial. The study showed that corn stover removal with bioenergy crops both on highly erodible areas and marginal land could provide more biofuel production relative to the baseline, and was beneficial to water quality at the watershed scale, providing guidance for further research on evaluation of bioenergy crop scenarios in a typical extensively tile-drained watershed in the Midwestern U.S.

Microbial community biomass and structure in saline and non-saline soils associated with salt- and boron-tolerant poplar clones grown for the phytoremediation of selenium

Poplar trees (Populus spp.) are often used in bioremediation strategies because of their ability to phytoextract potential toxic ions, e.g., selenium (Se) from poor quality soils. Soil microorganisms may play a vital role in sustaining health of soil and/or tolerance of these trees grown in poor quality soils by contributing to nutrient cycling, soil structure, overall soil quality, and plant survival. The effect of naturally occurring salts boron (B) and Se on soil microbial community composition associated with poplar trees is not known for bioremediation strategies. In this study, three Populus clones 13-366, 345-1, and 347-14 were grown in spring 2006 under highly saline, B, and Se clay-like soils in the west side of the San Joaquin Valley (SJV) of CA, as well as in non-saline sandy loam soils located in the east side of the SJV. After 7 years of growing in the respective soils of different qualities, soil samples were collected from poplar clones grown in saline and non-saline soils to examine and compare soil quality effects on soil microbial community biomass and composition. The phospholipid fatty acid (PLFA) analysis was used to characterize microbial community composition in soils from trees grown at both locations. This study showed that microbial biomass and the amount and proportion of arbuscular mycorrhizal fungal (AMF) community were lower in all three poplar clones grown in saline soil compared to non-saline soil. Amounts of Gram + bacterial and actinomycetes PLFAs were significantly lower in poplar clone 13-366 grown in saline soil compared to non-saline soil; however, they did not differ significantly in poplar clones 347-14 and 345-1. Additionally, amounts of saprophytic fungal, Gram - bacterial and eukaryotic PLFA remained similar at saline and non-saline sites under poplar clones 347-14, 345-1, and 13-366. Therefore, this study suggested that salinity and B do have an impact on microbial biomass and AMF; however, these poplar clones still recycled sufficient amount of nutrients to support and protect saprophytic fungal and bacterial communities from the effects of poor quality soils.

Assessment on cadmium and lead in soil based on a rhizosphere microbial community

The soil ecosystem is easily polluted by heavy metals. Cadmium (Cd) and lead (Pb), as the main pollutants of heavy metals, cause much harm to the soil ecosystem. However, the impact of the two chemicals on rhizosphere microorganisms remains almost unknown. The change of catalase (CAT) activity was consistent with the microbial biomass. 16S rRNA gene sequencing was performed on soil samples to study the toxic effect of heavy metals. On performing sequence analysis at the phylum and family taxonomic levels, 32 identified phyla and 303 families were observed. The dominant phylum was Proteobacteria followed by Bacteroidetes, Acidobacteria, and Actinobacteria. The relative abundance of the dominant phyla was obviously changed under the stress of Cd and Pb, suggesting that the heavy metal input had affected the microbial community structure. At the Order and Family levels, there was different variation of richness and diversity in Cd and Pb group as compared to those in the control group. Furthermore, abundance and similarity analysis showed the differences between Cd and Pb, indicating different toxicology effect on rhizosphere microbial communities because of the unique properties. This study provided a novel insight into the composition of microbial communities of rhizosphere, which could be used to evaluate the soil environment.

Plant-assisted bioremediation of a historically PCB and heavy metal-contaminated area in Southern Italy

A plant-assisted bioremediation strategy was applied in an area located in Southern Italy, close to the city of Taranto, historically contaminated by polychlorinated biphenyls (PCBs) and heavy metals. A specific poplar clone (Monviso) was selected for its ability to promote organic pollutant degradation in the rhizosphere, as demonstrated elsewhere. Chemical and microbiological analyses were performed at the time of poplar planting in selected plots at different distances from the trunk (0.25-1m) and at different soil depths (0-20 and 20-40cm), at day 420. A significant decrease in PCB congeners and a reduction in all heavy metals was observed where the poplar trees were present. No evidence of PCB and heavy metal reduction was observed in the non poplar-vegetated soil. Microbial analyses (dehydrogenase activity, cell viability, microbial abundance) of the autochthonous microbial community showed an improvement in soil quality. In particular, microbial activity generally increased in the poplar-rhizosphere and a positive effect was observed in some cases at up to 1m distance from the trunk and up to 40cm depth. The Monviso clone was effective in promoting both a general decrease in contaminant occurrence and an increase in microbial activity in the chronically polluted area a little more than one year after planting.

Impact of poplar-based phytomanagement on soil properties and microbial communities in a metal-contaminated site

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.

Water extraction kinetics of metals, arsenic and dissolved organic carbon from industrial contaminated poplar leaves

In industrial areas, tree leaves contaminated by metals and metalloids could constitute a secondary source of pollutants. In the present study, water extraction kinetics of inorganic elements (IE: Pb, Zn, Cd, As, Fe and Mn), dissolved organic carbon, pH and biological activity were studied for industrial contaminated poplar leaves. Moreover, the distribution of the IE through the size fractions of the associated top soil was measured. High quantities of Mn, Zn and As and polysaccharides were released in the solution from the strongly contaminated leaves. The kinetic of release varied with time and metal type. The solution pH decreased while dissolved organic contents increased with time after 30 days. Therefore, these contaminated leaves could constitute a source of more available organic metals and metalloids than the initial inorganic process particles. However, the distribution of the IE through the size fractions of the top soil suggested that a great part of the released IE was adsorbed, reducing in consequence their transfers and bioavailability. It's concluded that mobility/bioavailability and speciation of metals and metalloids released from the decomposition of polluted tree leaves depends on soil characteristics, pollutant type and litter composition, with consequences for environmental risk assessment.

Fate of trace elements during the combustion of phytoremediation wood

We investigated the fate of trace elements (TE) in poplar wood on the conversion of biomass to heat in a 0.2 MW combustion unit equipped with a fabric filter. The phytoremediation wood was harvested from a TE-contaminated agricultural site planted with a high-density poplar stand. The combustion technology used in the present experiment allows for an efficient separation of the various ash fractions. The combustion process concentrates Cu, Cr, and Ni in the bottom ash, heat exchanger ash, and cyclone ash fractions. Therefore, the impact of the fabric filter is negligible for these elements. Conversely, Cd, Pb, and Zn are significantly recovered in the emission fraction in the absence of the fabric filter above the emission limits. The use of a fabric filter will allow the concentration of these three TEs in the ashes collected below the filter, thus complying with all regulatory thresholds, i.e., those from the large combustion plant EU directive. Because the TE concentrations in the different fractions differed significantly, it is recommended that these fractions be treated separately, especially when recycling of ashes from phytoremediation wood through application in agriculture is envisaged.