Differentiation between chemo- and radiotoxicity of 137Cs and 60Co on Lemna minor

The uptake and effects of stable Cs and Co on L.minor were extensively studied, together with the effects of gamma radiation using a 137Cs or 60Co source. Innovative is that we combined external irradiation (from 137Cs or 60Co sources) with the direct uptake of certain amounts of stable Cs or Co to simulate the impact of the same mass of a radioisotope compared with that of the stable element. Such approach allows to differentiate between chemo- and radiotoxicity of 137Cs or 60Co, permitting to study the 137Cs and 60Co uptake by L. minor without using high concentrations of these elements in solution. Our results indicate that radiotoxicity of both 137Cs and 60Co has a greater importance compared to their chemotoxicity. This was also supported by the independent action and concentration addition concepts. Both concepts resulted in a good prediction of the dose-response curve of the combination exposure. The maximal removal of 137Cs or 60Co per gram dry matter of L. minor was lower compared with the removal of the corresponding stable isotope. The toxicity of 60Co was higher compared to 137Cs based on EC50 values and uptake data. With respect to the effects on photosynthetic pigments, starch and soluble sugars contents, only starch increased in a concentration- and dose-dependent manner.

Limited effects of crop foliar Si fertilization on a marginal soil under a future climate scenario

Growing crops on marginal lands is a promising solution to alleviate the increasing pressure on agricultural land in Europe. Such crops will however be at the same time exposed to increased drought and pathogen prevalence, on already challenging soil conditions. Some sustainable practices, such as Silicon (Si) foliar fertilization, have been proposed to alleviate these two stress factors, but have not been tested under controlled, future climate conditions. We hypothesized that Si foliar fertilization would be beneficial for crops under future climate, and would have cascading beneficial effects on ecosystem processes, as many of them are directly dependent on plant health. We tested this hypothesis by exposing spring barley growing on marginal soil macrocosms (three with, three without Si treatment) to 2070 climate projections in an ecotron facility. Using the high-capacity monitoring of the ecotron, we estimated C, water, and N budgets of every macrocosm. Additionally, we measured crop yield, the biomass of each plant organ, and characterized bacterial communities using metabarcoding. Despite being exposed to water stress conditions, plants did not produce more biomass with the foliar Si fertilization, whatever the organ considered. Evapotranspiration (ET) was unaffected, as well as water quality and bacterial communities. However, in the 10-day period following two of the three Si applications, we measured a significant increase in C sequestration, when climate conditions where significantly drier, while ET remained the same. We interpreted these results as a less significant effect of Si treatment than expected as compared with literature, which could be explained by the high CO2 levels under future climate, that reduces need for stomata opening, and therefore sensitivity to drought. We conclude that making marginal soils climate proof using foliar Si treatments may not be a sufficient strategy, at least in this type of nutrient-poor, dry, sandy soil.

Endophyte Community Changes in the Seeds of Eight Plant Species following Inoculation with a Multi-Endophytic Bacterial Consortium and an Individual Sphingomonas wittichii Strain Obtained from Noccaea caerulescens

Noccaea caerulescens, a hyperaccumulator plant species known for its metal tolerance and accumulation abilities, harbours a microbiome of interest within its seed. These seed-associated bacteria, often referred to as seed endophytes, play a unique role in seed germination and plant growth and health. This work aimed to address how inoculating seeds of eight different plant species-Medicago sativa (alfalfa), Zea mays (corn), Raphanus sativus (radish), Helianthus annus (sunflower), Cucurbita pepo subsp. pepo (squash), Beta vulgaris subsp. cicla (rainbow chard), Arabidopsis thaliana (thale cress), and Noccaea caerulescens (penny cress)-with a bacterial consortium made from the seed endophytes of N. caerulescens would affect the seed microbiome of each test plant species, as well as inoculation with a strain of the bacterium Sphingomonas wittichii, which was previously isolated from seeds of N. caerulescens. Additionally, we aimed to offer preliminary plant tests in order to determine the best seed treatment plan for future research. The results showed that inoculation with the bacterial consortium held the most potential for increasing plant size (p < 0.001) and increasing germination rate (p < 0.05). The plant that responded best to inoculation was N. caerulescens (penny cress), likely because the microbes being introduced into the seed were not foreign. This paper also offers the first insight into the seed endophytes of Beta vulgaris subsp. cicla, highlighting an abundance of Proteobacteria, Firmicutes, and Actinobacteriota.

Bacteria associated with Zn-hyperaccumulators Arabidopsis halleri and Arabidopsis arenosa from Zn-Pb-Cd waste heaps in Poland as promising tools for bioremediation

To identify metal adapted bacteria equipped with traits positively influencing the growth of two hyperaccumulator plant species Arabidopsis arenosa and Arabidopsis halleri, we isolated bacteria inhabiting rhizosphere and vegetative tissues (roots, basal and stem leaves) of plants growing on two old Zn-Pb-Cd waste heaps in Bolesław and Bukowno (S. Poland), and characterized their potential plant growth promoting (PGP) traits as well as determined metal concentrations in rhizosphere and plant tissues. To determine taxonomic position of 144 bacterial isolates, 16S rDNA Sanger sequencing was used. A metabolic characterization of isolated strains was performed in vitro using PGP tests. A. arenosa and A. halleri accumulate high amounts of Zn in their tissues, especially in stem leaves. Among in total 22 identified bacterial taxa, the highest level of the taxonomical diversity (H' = 2.01) was revealed in A. halleri basal leaf endophytes originating from Bukowno waste heap area. The 96, 98, 99, and 98% of investigated strains showed tolerant to Cd, Zn, Pb and Cu, respectively. Generally, higher percentages of bacteria could synthesize auxins, siderophores, and acetoin as well as could solubilize phosphate. Nine of waste heap origin bacterial strains were tolerant to toxic metals, showed in vitro PGP traits and are potential candidates for bioremediation.

Phytomanagement of trace element polluted fields with aromatic plants: supporting circular bio-economies

Trace elements pollution of soils became a global concern because of their persistence in the environment which can lead to accumulation in food chains up to toxic levels. At the same time, there is a shortage of arable land for growing food, fodder and industrial crops, which highlights the need for remediation/use of polluted land. Restoration of degraded lands has been included as a vital component of UN Sustainable Development Goals (SDGs). We summarize various sources of entry of important trace elements in the environment, available biological reclamation and management strategies and their limitations. Recent advances in phytomanagement approaches using aromatic crops to obtain economically valuable products such as essential oils and revalorize such polluted areas are reviewed. The worldwide application of this strategy in the last 10 years is illustrated through a choropleth map. Finally, the emerging concept of phytomanagement as a restorative and regenerative circular bio-economy is also discussed.

Diversity and potential plant growth promoting capacity of seed endophytic bacteria of the holoparasite Cistanche phelypaea (Orobanchaceae)

Salt marshes are highly dynamic, biologically diverse ecosystems with a broad range of ecological functions. We investigated the endophytic bacterial community of surface sterilized seeds of the holoparasitic Cistanche phelypaea growing in coastal salt marshes of the Iberian Peninsula in Portugal. C. phelypaea is the only representative of the genus Cistanche that was reported in such habitat. Using high-throughput sequencing methods, 23 bacterial phyla and 263 different OTUs on genus level were found. Bacterial strains belonging to phyla Proteobacteria and Actinobacteriota were dominating. Also some newly classified or undiscovered bacterial phyla, unclassified and unexplored taxonomic groups, symbiotic Archaea groups inhabited the C. phelypaea seeds. γ-Proteobacteria was the most diverse phylogenetic group. Sixty-three bacterial strains belonging to Bacilli, Actinomycetes, α-, γ- and β-Proteobacteria and unclassified bacteria were isolated. We also investigated the in vitro PGP traits and salt tolerance of the isolates. Among the Actinobacteria, Micromonospora spp. showed the most promising endophytes in the seeds. Taken together, the results indicated that the seeds were inhabited by halotolerant bacterial strains that may play a role in mitigating the adverse effects of salt stress on the host plant. In future research, these bacteria should be assessed as potential sources of novel and unique bioactive compounds or as novel bacterial species.

Citrate-coated cobalt ferrite nanoparticles for the nano-enabled biofortification of wheat

A pot experiment was conducted in an open greenhouse to explore the use of citrate-coated cobalt ferrite nanoparticles (CoFe₂O₄ NPs) as a source for Fe fortification of three wheat lines (Triticum aestivum L.). Two of the three wheat lines tested differ in their efficiency concerning Zn storage in their grains (efficient and inefficient), and one had inefficient P-absorption. The NPs were supplied by foliar or soil application of Fe at 330 mg L^-1, and 46 or 68 mg kg^-1 soil, respectively. A positive control (Fe-EDTA salt, a conventional iron fertilizer) and a negative control (no fertilization) were also included to compare the efficiency of NP fertilization. Soil fertilization with NPs improved the grain yield and Fe concentration in the grains compared with the foliar application of NPs and conventional Fe fertilizer. Application of soil NPs at 68 mg kg^-1 increased the grain yield by 52% and 21% compared with the control and soil Fe-EDTA treatments, respectively. Likewise, grain Fe concentration increased by 96% and 72% compared with the control and soil Fe-EDTA treatments, respectively. The phytic acid concentration in grains and the phytic acid:Fe ratio decreased by 6% and 62%, respectively, due to the soil application of NPs (68 mg Fe per kg). The Fe grain concentration of lines inefficient for Zn storage and P-uptake in plants from soil fertilized with NPs (68 mg Fe per kg) was 1.37 and 0.26 fold above the target biofortification concentration (60 mg Fe per kg). Cobalt concentration in grains ranged from 9 to 16 mg kg^-1. These concentrations were below the maximum allowable limit of Co in grains (50 mg kg^-1) recommended by FAO and the WHO. Our results showed that Fe supplied as NPs may improve the nutritional quality of wheat grains, and the economic yield. However, there remains a long way to go to achieve effective and economic use of nanotechnology for the nutritional development of wheat.

Effect of selenium and soil pH on cadmium phytoextraction by Urochloa decumbens grown in Oxisol

It has been speculated that selenium (Se) supply can affect cadmium (Cd) 'availability' and increase the Cd tolerance of plants used for phytoextraction, in a pH-dependent process. Thus, we evaluated the interaction Cd-Se and the effects of soil pH in this interaction on plant availability of Cd and phytoextraction efficiency of Urochloa decumbens cv. Basilisk grown in Oxisol. Two soil concentrations of Cd (0.93 and 3.6 mg kg^-1) and Se (<0.2 and 1 mg kg^-1) and two soil pH (0.01 mol L^-1 CaCl₂) conditions (4.1 and 5.7) were considered. At both pH, Se supply increased the exchangeable fraction of Cd and decreased the residual Cd fraction. At pH 4.1, the growth of U. decumbens was impaired by Se addition, regardless of Cd exposure. The lower root growth and tillering of U. decumbens exposed to Cd disappeared at pH 5.7 due to uptake of low Se concentrations. Thus, the toxic or beneficial effects of Se on growth of U. decumbens used for Cd phytoextraction depend on the amount of Se assimilated. The Cd phytoextraction efficiency of U. decumbens was not improved by Se supply, regardless of soil pH. Therefore, we cannot recommend the application of Se to increase Cd phytoextraction by this grass.

Impact of High Salt-Intake on a Natural Gut Ecosystem in Wildling Mice

The mammalian holobiont harbors a complex and interdependent mutualistic gut bacterial community. Shifts in the composition of this bacterial consortium are known to be a key element in host health, immunity and disease. Among many others, dietary habits are impactful drivers for a potential disruption of the bacteria–host mutualistic interaction. In this context, we previously demonstrated that a high-salt diet (HSD) leads to a dysbiotic condition of murine gut microbiota, characterized by a decrease or depletion of well-known health-promoting gut bacteria. However, due to a controlled and sanitized environment, conventional laboratory mice (CLM) possess a less diverse gut microbiota compared to wild mice, leading to poor translational outcome for gut microbiome studies, since a reduced gut microbiota diversity could fail to depict the complex interdependent networks of the microbiome. Here, we evaluated the HSD effect on gut microbiota in CLM in comparison to wildling mice, which harbor a natural gut ecosystem more closely mimicking the situation in humans. Mice were treated with either control food or HSD and gut microbiota were profiled using amplicon-based methods targeting the 16S ribosomal gene. In line with previous findings, our results revealed that HSD induced significant loss of alpha diversity and extensive modulation of gut microbiota composition in CLM, characterized by the decrease in potentially beneficial bacteria from Firmicutes phylum such as the genera Lactobacillus, Roseburia, Tuzzerella, Anaerovorax and increase in Akkermansia and Parasutterella. However, HSD-treated wildling mice did not show the same changes in terms of alpha diversity and loss of Firmicutes bacteria as CLM, and more generally, wildlings exhibited only minor shifts in the gut microbiota composition upon HSD. In line with this, 16S-based functional analysis suggested only major shifts of gut microbiota ecological functions in CLM compared to wildling mice upon HSD. Our findings indicate that richer and wild-derived gut microbiota is more resistant to dietary interventions such as HSD, compared to gut microbiota of CLM, which may have important implications for future translational microbiome research.

Community Profiling of Seed Endophytes from the Pb-Zn Hyperaccumulator Noccaea caerulescens and Their Plant Growth Promotion Potential

Endophytes within plants are known to be crucial for plant fitness, and while their presence and functions in many compartments have been studied in depth, the research on seed endophytes is still limited. This work aimed to characterize the seed endophytic and rhizospheric bacterial community of two Noccaea caerulescens Pb-Zn hyperaccumulator populations, growing on two heavy-metal-polluted sites in Belgium. Cultured representatives were evaluated for their potential to enhance seed germination and root length of the model species Arabidopsis thaliana. The results indicated that the community structure within the seed is conserved between the two locations, comprising mainly of Proteobacteria (seeds), and Actinobacteria in the bulk soil. Root length of A. thaliana was significantly increased when inoculated with Sphingomonas vulcanisoli. The results of this paper offer insights into the importance of the selection of the core seed endophytic microbiome and highlight the precarious symbiotic relationship they have with the plant and seed.

Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIRONAGE Birth Cohort

BACKGROUND

The gut microbiome plays an essential role in human health. Despite the link between air pollution exposure and various diseases, its association with the gut microbiome during susceptible life periods remains scarce.

OBJECTIVES

In this study, we examined the association between black carbon particles quantified in prenatal and postnatal biological matrices and bacterial richness and diversity measures, and bacterial families.

METHODS

A total of 85 stool samples were collected from 4- to 6-y-old children enrolled in the ENVIRonmental influence ON early AGEing birth cohort. We performed 16S rRNA gene sequencing to calculate bacterial richness and diversity indices (Chao1 richness, Shannon diversity, and Simpson diversity) and the relative abundance of bacterial families. Black carbon particles were quantified via white light generation under femtosecond pulsed laser illumination in placental tissue and cord blood, employed as prenatal exposure biomarkers, and in urine, used as a post-natal exposure biomarker. We used robust multivariable-adjusted linear models to examine the associations between quantified black carbon loads and measures of richness (Chao1 index) and diversity (Shannon and Simpson indices), adjusting for parity, season of delivery, sequencing batch, age, sex, weight and height of the child, and maternal education. Additionally, we performed a differential relative abundance analysis of bacterial families with a correction for sampling fraction bias. Results are expressed as percentage difference for a doubling in black carbon loads with 95% confidence interval (CI).

RESULTS

Two diversity indices were negatively associated with placental black carbon [Shannon: -4.38% (95% CI: -8.31%, -0.28%); Simpson: -0.90% (95% CI: -1.76%, -0.04%)], cord blood black carbon [Shannon: -3.38% (95% CI: -5.66%, -0.84%); Simpson: -0.91 (95% CI: -1.66%, -0.16%)], and urinary black carbon [Shannon: -3.39% (95% CI: -5.77%, -0.94%); Simpson: -0.89% (95% CI: -1.37%, -0.40%)]. The explained variance of black carbon on the above indices varied from 6.1% to 16.6%. No statistically significant associations were found between black carbon load and the Chao1 richness index. After multiple testing correction, placental black carbon was negatively associated with relative abundance of the bacterial families Defluviitaleaceae and Marinifilaceae, and urinary black carbon with Christensenellaceae and Coriobacteriaceae; associations with cord blood black carbon were not statistically significant after correction.

CONCLUSION

Black carbon particles quantified in prenatal and postnatal biological matrices were associated with the composition and diversity of the childhood intestinal microbiome. These findings address the influential role of exposure to air pollution during pregnancy and early life in human health. https://doi.org/10.1289/EHP11257.

Quercus ilex Phyllosphere Microbiome Environmental-Driven Structure and Composition Shifts in a Mediterranean Contex

The intra- and interdomain phyllosphere microbiome features of Quercus ilex L. in a Mediterranean context is reported. We hypothesized that the main driver of the phyllosphere microbiome might be the season and that atmospheric pollutants might have a co-effect. Hence, we investigated the composition of epiphytic bacteria and fungi of leaves sampled in urban and natural areas (in Southern Italy) in summer and winter, using microscopy and metagenomic analysis. To assess possible co-effects on the composition of the phyllosphere microbiome, concentrations of particulate matter and polycyclic aromatic hydrocarbons (PAHs) were determined from sampled leaves. We found that environmental factors had a significative influence on the phyllosphere biodiversity, altering the taxa relative abundances. Ascomycota and Firmicutes were higher in summer and in urban areas, whereas a significant increase in Proteobacteria was observed in the winter season, with higher abundance in natural areas. Network analysis suggested that OTUs belonging to Acidobacteria, Cytophagia, unkn. Firmicutes(p), Actinobacteria are keystone of the Q. ilex phyllosphere microbiome. In addition, 83 genes coding for 5 enzymes involved in PAH degradation pathways were identified. Given that the phyllosphere microbiome can be considered an extension of the ecosystem services offered by trees, our results can be exploited in the framework of Next-Generation Biomonitoring.

Phytomanagement of a Lead-Polluted Shooting Range Using an Aromatic Plant Species and Its Effects on the Rhizosphere Bacterial Diversity and Essential Oil Production

This field study aimed to assess the baseline conditions of a long-term shooting range in Argentina polluted with 428 mg kg^-1 lead (Pb) to evaluate the establishment and development of Helianthus petiolaris plants and address the efficacy of the phytomanagement strategy through: (i) element accumulation in plant tissues; (ii) rhizosphere bacterial diversity changes by Illumina Miseq™, and (iii) floral water and essential oil yield, composition, and element concentration by GC-MS and ICP. After one life cycle growing in the polluted sites, in the roots of Helianthus petiolaris plants, Pb concentration was between 195 and 304 mg kg^-1 Pb. Only a limited fraction of the Pb was translocated to the aerial parts. The predominance of the genus Serratia in the rhizosphere of Helianthus petiolaris plants cultivated in the polluted sites and the decrease in the essential oil yield were some effects significantly associated with soil Pb concentration. No detectable Pb concentration was found in the floral water and essential oil obtained. Extractable Pb concentration in the soil reduced between 28% and 45% after the harvest.

Bacterial inoculant-assisted phytoremediation affects trace element uptake and metabolite content in Salix atrocinerea

Natural plant-associated microorganisms are of critical importance to plant growth and survival in field conditions under toxic concentrations of trace elements (TE) and these plant-microbial processes can be harnessed to enhance phytoremediation. The total bacterial diversity from grey willow (Salix atrocinerea) on a brownfield heavily-polluted with lead (Pb) and arsenic (As) was studied through pyrosequencing. Culturable bacteria were isolated and in vitro tested for plant growth-promotion (PGP) traits, arsenic (As) tolerance and impact on As speciation. Two of the most promising bacterial strains - the root endophyte Pantoea sp. AV62 and the rhizospheric strain Rhodococcus erythropolis AV96 - were inoculated in field to S. atrocinerea. This bioaugmentation resulted in higher As and Pb concentrations in both, roots and leaves of bacterial-inoculated plants as compared to non-inoculated plants. In consequence, bacterial bioaugmentation also affected parameters related to plant growth, oxidative stress, the levels of phytochelatins and phenylpropanoids, together with the differential expression of genes related to these tolerance mechanisms to TE in leaves. This study extends our understanding about plant-bacterial interactions and provides a solid basis for further bioaugmentation studies aiming to improve TE phytoremediation efficiency and predictability in the field.

An Alliance of Trifolium repens—Rhizobium leguminosarum bv. trifolii—Mycorrhizal Fungi From an Old Zn-Pb-Cd Rich Waste Heap as a Promising Tripartite System for Phytostabilization of Metal Polluted Soils

The Bolesław waste heap in South Poland, with total soil Zn concentrations higher than 50,000 mg kg^–1, 5,000 mg Pb kg^–1, and 500 mg Cd kg^–1, is a unique habitat for metallicolous plants, such as Trifolium repens L. The purpose of this study was to characterize the association between T. repens and its microbial symbionts, i.e., Rhizobium leguminosarum bv. trifolii and mycorrhizal fungi and to evaluate its applicability for phytostabilization of metal-polluted soils. Rhizobia originating from the nutrient-poor waste heap area showed to be efficient in plant nodulation and nitrogen fixation. They demonstrated not only potential plant growth promotion traits in vitro, but they also improved the growth of T. repens plants to a similar extent as strains from a non-polluted reference area. Our results revealed that the adaptations of T. repens to high Zn-Pb-Cd concentrations are related to the storage of metals predominantly in the roots (excluder strategy) due to nodule apoplast modifications (i.e., thickening and suberization of cell walls, vacuolar storage), and symbiosis with arbuscular mycorrhizal fungi of a substantial genetic diversity. As a result, the rhizobia-mycorrhizal fungi-T. repens association appears to be a promising tool for phytostabilization of Zn-Pb-Cd-polluted soils.

The Effect of Syringic Acid and Phenoxy Herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) on Soil, Rhizosphere, and Plant Endosphere Microbiome

The integration of phytoremediation and biostimulation can improve pollutant removal from the environment. Plant secondary metabolites (PSMs), which are structurally related to xenobiotics, can stimulate the presence of microbial community members, exhibiting specialized functions toward detoxifying, and thus mitigating soil toxicity. In this study, we evaluated the effects of enrichment of 4-chloro-2-methylphenoxyacetic acid (MCPA) contaminated soil (unplanted and zucchini-planted) with syringic acid (SA) on the bacterial community structure in soil, the rhizosphere, and zucchini endosphere. Additionally, we measured the concentration of MCPA in soil and fresh biomass of zucchini. The diversity of bacterial communities differed significantly between the studied compartments (i.e., unplanted soil, rhizospheric soil, and plant endosphere: roots or leaves) and between used treatments (MCPA or/and SA application). The highest diversity indices were observed for unplanted soil and rhizosphere. Although the lowest diversity was observed among leaf endophytes, this community was significantly affected by MCPA or SA: the compounds applied separately favored the growth of Actinobacteria (especially Pseudarthrobacter), while their simultaneous addition promoted the growth of Firmicutes (especially Psychrobacillus). The application of MCPA + SA together lead also to enhanced growth of Pseudomonas, Burkholderia, Sphingomonas, and Pandoraea in the rhizosphere, while SA increased the occurrence of Pseudomonas in leaves. In addition, SA appeared to have a positive influence on the degradative potential of the bacterial communities against MCPA: its addition, followed by zucchini planting, significantly increased the removal of the herbicide (50%) from the soil without affecting, neither positively nor negatively, the plant growth.

Glutathione Is Required for the Early Alert Response and Subsequent Acclimation in Cadmium-Exposed Arabidopsis thaliana Plants

Pollution by cadmium (Cd) is a worldwide problem, posing risks to human health and impacting crop yield and quality. Cadmium-induced phytotoxicity arises from an imbalance between antioxidants and pro-oxidants in favour of the latter. The Cd-induced depletion of the major antioxidant glutathione (GSH) strongly contributes to this imbalance. Rather than being merely an adverse effect of Cd exposure, the rapid depletion of root GSH levels was proposed to serve as an alert response. This alarm phase is crucial for an optimal stress response, which defines acclimation later on. To obtain a better understanding on the importance of GSH in the course of these responses and how these are defined by the rapid GSH depletion, analyses were performed in the GSH-deficient cadmium-sensitive 2-1 (cad2-1) mutant. Cadmium-induced root and leaf responses related to oxidative challenge, hydrogen peroxide (H2O2), GSH, ethylene, and 1-aminocyclopropane-1-carboxylic acid (ACC) were compared between wild-type (WT) and mutant Arabidopsis thaliana plants. Although the cad2-1 mutant has significantly lower GSH levels, root GSH depletion still occurred, suggesting that the chelating capacity of GSH is prioritised over its antioxidative function. We demonstrated that responses related to GSH metabolism and ACC production were accelerated in mutant roots and that stress persisted due to suboptimal acclimation. In general, the redox imbalance in cad2-1 mutant plants and the lack of proper transient ethylene signalling contributed to this suboptimal acclimation, resulting in a more pronounced Cd effect.

Effects of environmental parameters on Lemna minor growth: An integrated experimental and modelling approach

Pollution of surface waters is a worldwide problem for people and wildlife. Remediation and phytoremediation approaches can offer a solution to deal with specific scenarios. Lemna minor, commonly known as duckweed, can absorb and accumulate pollutants in its biomass. To evaluate if L. minor could be applied for phytoremediation purposes, it is necessary to further investigate its remediation capability and to identify which parameters affect the remediation process. Such a model must include both plant growth and pollutant exchange. A remediation model based on a robust experimental study can help to evaluate L. minor as a proper remediation strategy and to predict the outcome of a L. minor based remediation system. To set up this model, this paper focusses on a detailed experimental study and a comprehensive mathematical modelling approach to represent L. minor growth as a function of biomass, temperature, light irradiation and variable nutrient concentrations. The influence of environmental conditions on L. minor growth was studied, by composing 7 days growth curves. Plants were grown under predefined environmental conditions (25°C, 14h photoperiod, 220 μmol m^-2 s^-1 light intensity and a modified Hoagland solution with 23.94 mg N L^-1 and 3.10 mg P L^-1 (N:P ratio of 7.73)) as standard for all experiments. The influence of different temperatures (6, 10, 15, 20, 25, 30 and 35°C), light intensities (63, 118, 170, 220 and 262 μmol m^-2 s^-1), photoperiods (12h and 14h) and N:P ratios (1.18, 3.36, 7.73 and 29.57) were tested in the model. As a result, a growth model was optimised using separate datasets for temperature, light intensity, photoperiod and nutrients and validated by further integrated testing. The growth model is a stable platform for application in phytoremediation of radionuclides in contaminated water, to be extended in future studies with information of pollutant uptake, pollutant-nutrient interactions and transfer to the biomass.

Exploring the Microbiome Analysis and Visualization Landscape

Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.

Dynamics of skin microvascular blood flow in 4-6-year-old children in association with pre- and postnatal black carbon and particulate air pollution exposure

BACKGROUND

A growing body of evidence indicates that cardiovascular health in adulthood, particularly that of the microcirculation, could find its roots during prenatal development. In this study, we investigated the association between pre- and postnatal air pollution exposure on heat-induced skin hyperemia as a dynamic marker of the microvasculature.

METHODS

In 139 children between the ages of 4 and 6 who are followed longitudinally within the ENVIRONAGE birth cohort, we measured skin perfusion by Laser Doppler probes using the Periflux6000. Residential black carbon (BC), particulate (PM₁₀ and PM_2.5) air pollution, and nitrogen dioxide (NO₂) levels were modelled for each participant's home address using a high-resolution spatiotemporal model for multiple time windows. We assessed the association between skin hyperemia and pre- and postnatal air pollution using multiple regression models while adjusting for relevant covariates.

RESULTS

Residential BC exposure during the whole pregnancy averaged (IQR) 1.42 (1.22-1.58) µg/m³, PM₁₀ 18.88 (16.64 - 21.13) µg/m³, PM_2.5 13.67 (11.5 - 15.56) µg/m³ and NO₂ 18.39 (15.52 - 20.31) µg/m³. An IQR increment in BC exposure during the third trimester of pregnancy was associated with an 11.5 % (95% CI: -20.1 to -1.9; p = 0.020) lower skin hyperemia. Similar effect estimates were retrieved for PM₁₀, PM_2.5 and NO₂ (respectively 13.9 % [95% CI: -21.9 to -3.0; p = 0.003], 17.0 % [95% CI: -26.7 to -6.1; p = 0.004] and 12.7% [95 % CI: -22.2 to -1.9; p = 0.023] lower skin hyperemia). In multipollutant models, PM_2.5 showed the strongest inverse association with skin hyperemia. Postnatal exposure to BC, PM₁₀, PM_2.5 or NO₂, was not associated with skin hyperemia at the age of 4 to 6, and did not alter the previous reported prenatal associations when taken into account.

CONCLUSION

Our findings support that BC, particulate air pollution, and NO₂ exposure, even at low concentrations, during prenatal life, can have long-lasting consequences for the microvasculature. This proposes a role of prenatal air pollution exposures over and beyond postnatal exposure in the microvascular alterations which were persistent into childhood.

Are Grasses Really Useful for the Phytoremediation of Potentially Toxic Trace Elements? A Review

The pollution of soil, water, and air by potentially toxic trace elements poses risks to environmental and human health. For this reason, many chemical, physical, and biological processes of remediation have been developed to reduce the (available) trace element concentrations in the environment. Among those technologies, phytoremediation is an environmentally friendly in situ and cost-effective approach to remediate sites with low-to-moderate pollution with trace elements. However, not all species have the potential to be used for phytoremediation of trace element-polluted sites due to their morpho-physiological characteristics and low tolerance to toxicity induced by the trace elements. Grasses are prospective candidates due to their high biomass yields, fast growth, adaptations to infertile soils, and successive shoot regrowth after harvest. A large number of studies evaluating the processes related to the uptake, transport, accumulation, and toxicity of trace elements in grasses assessed for phytoremediation have been conducted. The aim of this review is (i) to synthesize the available information on the mechanisms involved in uptake, transport, accumulation, toxicity, and tolerance to trace elements in grasses; (ii) to identify suitable grasses for trace element phytoextraction, phytostabilization, and phytofiltration; (iii) to describe the main strategies used to improve trace element phytoremediation efficiency by grasses; and (iv) to point out the advantages, disadvantages, and perspectives for the use of grasses for phytoremediation of trace element-polluted soils.

Exploring the Diversity and Aromatic Hydrocarbon Degrading Potential of Epiphytic Fungi on Hornbeams from Chronically Polluted Areas

Plants can ‘catch’ and mitigate airborne pollutants and are assisted by fungi inhabiting their leaves. The structure and function of the fungal communities inhabiting the phyllosphere of hornbeam trees growing in two chronically polluted areas, the oilfield of Bóbrka and the city center of Warsaw, were compared to the ones growing in one nature reserve, the Białowieża National Park. Fungi were isolated and characterized both phylogenetically and functionally for their potential role in air pollution mitigation. Both culture-dependent (e.g., enzyme assays and tolerance tests) and culture-independent methods (e.g., ITS and shotgun sequencings) were used. Furthermore, the degradation potential of the fungi was assessed by gas chromatography mass spectrometry (GC-MS). Shotgun sequencing showed that the phyllosphere fungal communities were dominated by fungi belonging to the phylum Ascomycota. Aureobasidium was the only genus detected at the three locations with a relative abundance ≥1.0%. Among the cultivated epiphytic fungi from Bóbrka, Fusarium sporotrichioides AT11, Phoma herbarum AT15, and Lophiostoma sp. AT37 showed in vitro aromatic hydrocarbon degradation potential with laccase activities of 1.24, 3.62, and 7.2 μU L⁻¹, respectively, and peroxidase enzymes with activities of 3.46, 2.28, and 7.49 μU L⁻¹, respectively. Furthermore, Fusarium sporotrichioides AT11 and Phoma herbarum AT15 tolerated exposure to airborne naphthalene and benzene. Lophiostoma sp. AT37 was the most tolerant to exposure to these pollutants, in line with being the best potential aromatic hydrocarbon degrader isolated in this study.

Unraveling the mechanisms controlling Cd accumulation and Cd-tolerance in Brachiaria decumbens and Panicum maximum under summer and winter weather conditions

We evaluated the mechanisms that control Cd accumulation and distribution, and the mechanisms that protect the photosynthetic apparatus of Brachiaria decumbens Stapf. cv. Basilisk and Panicum maximum Jacq. cv. Massai from Cd-induced oxidative stress, as well as the effects of simulated summer or winter conditions on these mechanisms. Both grasses were grown in unpolluted and Cd-polluted Oxisol (0.63 and 3.6 mg Cd kg^-1 soil, respectively) at summer and winter conditions. Grasses grown in the Cd-polluted Oxisol presented higher Cd concentration in their tissues in the winter conditions, but the shoot biomass production of both grasses was not affected by the experimental conditions. Cadmium was more accumulated in the root apoplast than the root symplast, contributing to increase the diameter and cell layers of the cambial region of both grasses. Roots of B. decumbens were more susceptible to disturbed nutrients uptake and nitrogen metabolism than roots of P. maximum. Both grasses translocated high amounts of Cd to their shoots resulting in oxidative stress. Oxidative stress in the leaves of both grasses was higher in summer than winter, but only in P. maximum superoxide dismutase (SOD) and ascorbate peroxidase (APX) activities were increased. However, CO₂ assimilation was not affected due to the protection provided by reduced glutathione (GSH) and phytochelatins (PCs) that were more synthesized in shoots than roots. In summary, the root apoplast was not sufficiently effective to prevent Cd translocation from roots to shoot, but GSH and PCs provided good protection for the photosynthetic apparatus of both grasses.

Efficient regulation of copper homeostasis underlies accession-specific sensitivities to excess copper and cadmium in roots of Arabidopsis thaliana

The commonly used Arabidopsis thaliana natural accessions Columbia (Col-0) and Wassilewskija (Ws) are known to differ in their metal sensitivity, with Col-0 being more sensitive to copper (Cu) and cadmium (Cd) than Ws. As both Cu and Cd are known to affect Cu homeostasis, it was investigated whether this process is part of an accession-specific mechanism underlying their difference in metal sensitivity. As roots are the first contact point during metal exposure, responses were compared between roots of both accessions of hydroponically grown plants exposed to excess Cu or Cd for 24 and 72 h. Root Cu levels increased in both accessions under Cu and Cd exposure. However, under Cu exposure, the downregulation of Cu transporter (COPT) genes in combination with a more pronounced upregulation of metallothionein gene MT2b indicated that Ws plants coped better with the elevated Cu concentrations. The Cd-induced disturbance in Cu homeostasis was more efficiently counteracted in roots of Ws plants than in Col-0 plants. This was indicated by a higher upregulation of the SPL7-mediated pathway, crucial in the regulation of the Cu homeostasis response. In conclusion, maintaining the Cu homeostasis response in roots is key to accession-specific differences in Cu and Cd sensitivity.

Arsenate-reducing bacteria affect As accumulation and tolerance in Salix atrocinerea

Arsenic (As)-reducing bacteria are able to influence As-speciation and, in this way, change As bio-availability. In consequence, this has an impact on As uptake by plants growing on polluted soil and on the effectiveness of the phytoremediation process. To be able to efficiently utilize these bacteria for As-phytoremediation in the field, a better understanding of the plant-bacterial interactions involved in As-tolerance or toxicity is needed. In this work, seedlings of a clone of Salix atrocinerea derived from a specimen naturally growing on an As-polluted brownfield were grown under gnotobiotic conditions exposed to As, and in the presence or absence of two of its field-associated and in vitro characterized plant growth-promoting (PGP) bacteria. The inoculation with Pantoea sp., induced a moderate reduction of AsV to AsIII in the exposure medium that, together with a coordinated plant response of As uptake, chelation and sequestration, increased As accumulation in roots; which is reflected into a higher phytostabilization. However, inoculation with Rhodococcus erythropolis due to a higher disproportionate reduction of AsV to AsIII in the medium caused less As accumulation in roots that non-bioaugmented plants and despite the lower As content, the concentrations of AsIII present in the medium and the damage suffered in roots and leaves, indicated that As tolerance mechanisms (such as prevention of AsIII uptake and efflux) did not occur in time to avoid physical disturbance and plants growth reduction. Interestingly, by two different metabolic pathways -coordinated by different key transporters mediating As uptake, tolerance, distribution and vacuolar accumulation at the roots- both bacteria limited As accumulation in Salix shoots. Our results provide for the first time a detailed insight in the plant-bacterial responses and physiological changes contributing to As tolerance in S. atrocinerea, that will facilitate the design of effective strategies for exploitation of plant-associated microorganisms for phytoremediation.

Exopolysaccharide Carbohydrate Structure and Biofilm Formation by Rhizobium leguminosarum bv. trifolii Strains Inhabiting Nodules of Trifoliumrepens Growing on an Old Zn-Pb-Cd-Polluted Waste Heap Area

Heavy metals polluting the 100-year-old waste heap in Bolesław (Poland) are acting as a natural selection factor and may contribute to adaptations of organisms living in this area, including Trifolium repens and its root nodule microsymbionts—rhizobia. Exopolysaccharides (EPS), exuded extracellularly and associated with bacterial cell walls, possess variable structures depending on environmental conditions; they can bind metals and are involved in biofilm formation. In order to examine the effects of long-term exposure to metal pollution on EPS structure and biofilm formation of rhizobia, Rhizobium leguminosarum bv. trifolii strains originating from the waste heap area and a non-polluted reference site were investigated for the characteristics of the sugar fraction of their EPS using gas chromatography mass-spectrometry and also for biofilm formation and structural characteristics using confocal laser scanning microscopy under control conditions as well as when exposed to toxic concentrations of zinc, lead, and cadmium. Significant differences in EPS structure, biofilm thickness, and ratio of living/dead bacteria in the biofilm were found between strains originating from the waste heap and from the reference site, both without exposure to metals and under metal exposure. Received results indicate that studied rhizobia can be assumed as potentially useful in remediation processes.

Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane

Background

A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys.

Results

We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria–Bertani (LB), LB01, yeast extract–mannitol (YMA), yeast extract–flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies.

Conclusions

This study gives first insights into the total bacterial community of the H. helix phylloplane, including an evaluation of its culturability using five different growth media. We further provide a collection of 200 bacterial isolates underrepresented in current databases, including the characterization of PGP profiles. Here we highlight the potential of simple strategies to obtain higher microbial diversity from environmental samples and the use of high-throughput sequencing to guide isolate selection from a variety of growth media.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02119-z.

Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation

The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their in vitro degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg^–1 of glyphosate. Most of them also demonstrated a diverse spectrum of in vitro plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of Ochrobactrum haematophilum exhibited different colonization patterns in the rhizoplane compared to an isolate of Rhizobium sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l^–1 in 9 days. In a microcosms experiment with Lotus corniculatus L, O. haematophilum performed better than Rhizobium, with 97% of glyphosate transformed after 20 days. The results suggest that L. corniculatus in combination with to O. haematophilum can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils.

Differential effect of silver nanoparticles on the microbiome of adult and developing planaria

Silver nanoparticles (AgNPs) are widely incorporated in household, consumer and medical products. Their unintentional release via wastewaters raises concerns on their environmental impact, particularly for aquatic organisms and their associated bacterial communities. It is known that the microbiome plays an important role in its host's health and physiology, e.g. by producing essential nutrients and providing protection against pathogens. A thorough understanding of the effects of AgNPs on bacterial communities and on their interactions with the host is crucial to fully assess AgNP toxicity on aquatic organisms. Our results indicate that the microbiome of the invertebrate Schmidtea mediterranea, a freshwater planarian, is affected by AgNP exposure at the tested 10 μg/ml concentration. Using targeted amplification of the bacterial 16S rRNA gene V3-V4 region, two independent experiments on the microbiomes of adult worms revealed a consistent decrease in Betaproteobacteriales after AgNP exposure, mainly attributed to a decrease in Curvibacter and Undibacterium. Although developing tissues and organisms are known to be more sensitive to toxic compounds, three independent experiments in regenerating worms showed a less pronounced effect of AgNP exposure on the microbiome, possibly because underlying bacterial community changes during development mask the AgNP induced effect. The presence of a polyvinyl-pyrrolidone (PVP) coating did not significantly alter the outcome of the experiments compared to those with uncoated particles. The observed variation between the different experiments underlines the highly variable nature of microbiomes and emphasises the need to repeat microbiome experiments, within and between physiological states of the animal.

Long-Term Cd Exposure Alters the Metabolite Profile in Stem Tissue of Medicago sativa

As a common pollutant, cadmium (Cd) is one of the most toxic heavy metals accumulating in agricultural soils through anthropogenic activities. The uptake of Cd by plants is the main entry route into the human food chain, whilst in plants it elicits oxidative stress by unbalancing the cellular redox status. Medicago sativa was subjected to chronic Cd stress for five months. Targeted and untargeted metabolic analyses were performed. Long-term Cd exposure altered the amino acid composition with levels of asparagine, histidine and proline decreasing in stems but increasing in leaves. This suggests tissue-specific metabolic stress responses, which are often not considered in environmental studies focused on leaves. In stem tissue, profiles of secondary metabolites were clearly separated between control and Cd-exposed plants. Fifty-one secondary metabolites were identified that changed significantly upon Cd exposure, of which the majority are (iso)flavonoid conjugates. Cadmium exposure stimulated the phenylpropanoid pathway that led to the accumulation of secondary metabolites in stems rather than cell wall lignification. Those metabolites are antioxidants mitigating oxidative stress and preventing cellular damage. By an adequate adjustment of its metabolic composition, M. sativa reaches a new steady state, which enables the plant to acclimate under chronic Cd stress.

Beneficial features of plant growth-promoting rhizobacteria for improving plant growth and health in challenging conditions: A methodical review

New eco-friendly approaches are required to improve plant biomass production. Beneficial plant growth-promoting (PGP) bacteria may be exploited as excellent and efficient biotechnological tools to improve plant growth in various - including stressful - environments. We present an overview of bacterial mechanisms which contribute to plant health, growth, and development. Plant growth promoting rhizobacteria (PGPR) can interact with plants directly by increasing the availability of essential nutrients (e.g. nitrogen, phosphorus, iron), production and regulation of compounds involved in plant growth (e.g. phytohormones), and stress hormonal status (e.g. ethylene levels by ACC-deaminase). They can also indirectly affect plants by protecting them against diseases via competition with pathogens for highly limited nutrients, biocontrol of pathogens through production of aseptic-activity compounds, synthesis of fungal cell wall lysing enzymes, and induction of systemic responses in host plants. The potential of PGPR to facilitate plant growth is of fundamental importance, especially in case of abiotic stress, where bacteria can support plant fitness, stress tolerance, and/or even assist in remediation of pollutants. Providing additional evidence and better understanding of bacterial traits underlying plant growth-promotion can inspire and stir up the development of innovative solutions exploiting PGPR in times of highly variable environmental and climatological conditions.

Monitoring indoor exposure to combustion-derived particles using plants

Indoor plants can be used to monitor atmospheric particulates. Here, we report the label-free detection of combustion-derived particles (CDPs) on plants as a monitoring tool for indoor pollution. First, we measured the indoor CDP deposition on Atlantic ivy leaves (Hedera hibernica) using two-photon femtosecond microscopy. Subsequently, to prove its effectiveness for using it as a monitoring tool, ivy plants were placed near five different indoor sources. CDP particle area and number were used as output metrics. CDP values ranged between a median particle area of 0.45 × 10² to 1.35 × 10⁴ μm², and a median particle number of 0.10 × 10² to 1.42 × 10³ particles for the indoor sources: control (greenhouse) < milling machine < indoor smokers < wood stove < gas stove < laser printer. Our findings demonstrate that Atlantic ivy, combined with label-free detection, can be effectively used in indoor atmospheric monitoring studies.

Correction to: A novel method for assessing climate change impacts in ecotron experiments

The article was published bearing a typographical error to the second author name listed. The author group regret the error and the name should be referenced and credited as Jakob Zscheischler and not the former.

A novel method for assessing climate change impacts in ecotron experiments

Ecotron facilities allow accurate control of many environmental variables coupled with extensive monitoring of ecosystem processes. They therefore require multivariate perturbation of climate variables, close to what is observed in the field and projections for the future. Here, we present a new method for creating realistic climate forcing for manipulation experiments and apply it to the UHasselt Ecotron experiment. The new methodology uses data derived from the best available regional climate model projection and consists of generating climate forcing along a gradient representative of increasingly high global mean air temperature anomalies. We first identified the best-performing regional climate model simulation for the ecotron site from the Coordinated Regional Downscaling Experiment in the European domain (EURO-CORDEX) ensemble based on two criteria: (i) highest skill compared to observations from a nearby weather station and (ii) representativeness of the multi-model mean in future projections. The time window is subsequently selected from the model projection for each ecotron unit based on the global mean air temperature of the driving global climate model. The ecotron units are forced with 3-hourly output from the projections of the 5-year period in which the global mean air temperature crosses the predefined values. With the new approach, Ecotron facilities become able to assess ecosystem responses on changing climatic conditions, while accounting for the co-variation between climatic variables and their projection in variability, well representing possible compound events. The presented methodology can also be applied to other manipulation experiments, aiming at investigating ecosystem responses to realistic future climate change.

Enhancing the Rice Seedlings Growth Promotion Abilities of Azoarcus sp. CIB by Heterologous Expression of ACC Deaminase to Improve Performance of Plants Exposed to Cadmium Stress

Environmental pollutants can generate stress in plants causing increased ethylene production that leads to the inhibition of plant growth. Ethylene production by the stressed plant may be lowered by Plant Growth-Promoting Bacteria (PGPB) that metabolizes the immediate precursor of ethylene 1-aminocyclopropane-1-carboxylate (ACC). Thus, engineering PGPB with ACC deaminase activity can be a promising alternative to mitigate the harmful effects of pollutants and thus enhance plant production. Here we show that the aromatics-degrading and metal-resistant Azoarcus sp. CIB behaves as a PGP-bacterium when colonizing rice as an endophyte, showing a 30% increment in plant weight compared to non-inoculated plants. The cloning and expression of an acdS gene led to a recombinant strain, Azoarcus sp. CIB (pSEVA237acdS), possessing significant ACC deaminase activity (6716 nmol mg-1 h-1), constituting the first PGPB of the Rhodocyclaceae family equipped with this PGP trait. The recombinant CIB strain acquired the ability to protect inoculated rice plants from the stress induced by cadmium (Cd) exposure and to increase the Cd concentration in rice seedlings. The observed decrease of the levels of reactive oxygen species levels in rice roots confirms such a protective effect. The broad-host-range pSEVA237acdS plasmid paves the way to engineer PGPB with ACC deaminase activity to improve the growth of plants that might face stress conditions.

Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis

BACKGROUND

The beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rhizosphere. Agricultural soils are a likely sink for nanosilver due to its presence in agrochemicals and land-applied biosolids, but a complete assessment of nanosilver's effects on this environment is lacking because the impact on the natural soil microbiome is not known. In a study assessing the use of nanosilver for phytopathogen control with maize, we analyzed the metatranscriptome of the maize rhizosphere and observed multiple unintended effects of exposure to 100 mg kg-1 nanosilver in soil during a growth period of 117 days.

RESULTS

We found several unintended effects of nanosilver which could interfere with agricultural systems in the long term. Firstly, the archaea community was negatively impacted with a more than 30% decrease in relative abundance, and as such, their involvement in nitrogen cycling and specifically, nitrification, was compromised. Secondly, certain potentially phytopathogenic fungal groups showed significantly increased abundances, possibly due to the negative effects of nanosilver on bacteria exerting natural biocontrol against these fungi as indicated by negative interactions in a network analysis. Up to 5-fold increases in relative abundance have been observed for certain possibly phytopathogenic fungal genera. Lastly, nanosilver exposure also caused a direct physiological impact on maize as illustrated by increased transcript abundance of aquaporin and phytohormone genes, overall resulting in a stress level with the potential to yield hormetically stimulated plant root growth.

CONCLUSIONS

This study indicates the occurrence of significant unintended effects of nanosilver use on corn, which could turn out to be negative to crop productivity and ecosystem health in the long term. We therefore highlight the need to include the microbiome when assessing the risk associated with nano-enabled agriculture. Video Abstract.

Glutathione: A key player in metal chelation, nutrient homeostasis, cell cycle regulation and the DNA damage response in cadmium-exposed Arabidopsis thaliana

Glutathione (GSH) is an important player in plant responses to cadmium (Cd) through its dual function as an antioxidant and precursor for metal-chelating phytochelatins (PCs). In addition, it was shown to be involved in cell cycle regulation in Arabidopsis thaliana roots, but its involvement in this process in leaves is largely unknown and has never been evaluated in Cd-exposed plants. This study aimed to elucidate the role of GSH in leaf growth and development, metal chelation, nutrient homeostasis and cell cycle regulation in A. thaliana plants upon prolonged Cd exposure. Responses were compared between wild-type (WT) plants and three GSH-deficient mutants. Our results indicate that PC production remains important in plants exposed to Cd for an extended duration. Furthermore, an important role for GSH in regulating nutrient homeostasis in Cd-exposed plants was revealed. Cell cycle analysis demonstrated that negative effects of Cd exposure on cell division and endoreplication were more pronounced in leaves of the GSH-deficient cadmium-sensitive 2-1 (cad2-1) mutant in comparison to the WT, indicating the involvement of GSH in cell cycle regulation. Finally, a crucial role for GSH in transcriptional activation of the Cd-induced DNA damage response (DDR) was revealed, as the Cd-induced upregulation of DDR-related genes was either less pronounced or completely abolished in leaves of the GSH-deficient mutants.

Bioaugmentation with PGP-trace element tolerant bacterial consortia affects Pb uptake by Helianthus annuus grown on trace element polluted military soils

In this study, we sought to compose consortia of plant growth-promoting (PGP) and trace element tolerant bacteria, to improve plant growth and inhibit uptake and translocation of trace elements, eventually allowing the cultivation of profitmaking crops on trace elements polluted soils, reducing the risks of entrance of these elements into the food chain. Sunflower (Helianthus annuus L.) was grown on two polluted military soils (MS1 and MS2) in greenhouse microcosms and inoculated with three different bacterial consortia (C1, C2, C3). Growth and physiological status of the plants were unaffected during the experiment with the inoculation. After 2 months, plants were harvested. Consortium C2 and C3 decreased Pb shoot bioaccumulation by respectively 80-85% when plants were grown in the MS1 and even to concentrations below detection limit in plants grown in MS2. Differences in uptake and (sub)cellular localization of Pb and Cd in selected bacterial isolates were investigated in vitro by TEM-EDX. Pb absorption was observed by Bacillus wiedmanni ST29 and Bacillus paramycoides ST9 cultures. While adsorption at the bacterial cell wall was observed by Bacillus paramycoides ST9 and retention in the extracellular matrix by Cellulosimicrobium cellulans ST54.

Effects of winter and summer conditions on Cd fractionation and bioavailability, bacterial communities and Cd phytoextraction potential of Brachiaria decumbens and Panicum maximum grown in a tropical soil

The interactions between soil properties, microorganisms, plant species and climate affect cadmium (Cd) availability in tropical soils. In this study, we investigated the effects of simulated summer and winter conditions on Cd fractionation and bacterial communities in Oxisols and on growth of two high biomass production-grasses (Brachiaria decumbens and Panicum maximum) that were evaluated for their Cd phytoextraction potential. We also assessed how these interactions could influence the availability of Cd and its possible phytoextraction by these grasses. The Cd fraction bound to carbonates was higher in the winter conditions, while Cd bound to Fe- and Mn oxides was higher in the summer conditions, which resulted in a higher Cd availability in winter compared to summer conditions. B. decumbens and P. maximum took up more Cd when grown in the winter conditions, but their biomasses were not affected by the higher Cd uptake. The occurrence and relative abundance of bacterial taxa in the bare soil differed from the soils cultivated with grasses, where the Gammaproteobacteria predominated. However, no positive correlations were observed between the rhizosphere bacterial community in the cultivated soils and Cd availability, irrespective of the season conditions.

Suppressor of Gamma Response 1 Modulates the DNA Damage Response and Oxidative Stress Response in Leaves of Cadmium-Exposed Arabidopsis thaliana

Cadmium (Cd) exposure causes an oxidative challenge and inhibits cell cycle progression, ultimately impacting plant growth. Stress-induced effects on the cell cycle are often a consequence of activation of the DNA damage response (DDR). The main aim of this study was to investigate the role of the transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) and three downstream cyclin-dependent kinase inhibitors of the SIAMESE-RELATED (SMR) family in the Cd-induced DDR and oxidative challenge in leaves of Arabidopsis thaliana. Effects of Cd on plant growth, cell cycle regulation and the expression of DDR genes were highly similar between the wildtype and smr4/5/7 mutant. In contrast, sog1-7 mutant leaves displayed a much lower Cd sensitivity within the experimental time-frame and significantly less pronounced upregulations of DDR-related genes, indicating the involvement of SOG1 in the Cd-induced DDR. Cadmium-induced responses related to the oxidative challenge were disturbed in the sog1-7 mutant, as indicated by delayed Cd-induced increases of hydrogen peroxide and glutathione concentrations and lower upregulations of oxidative stress-related genes. In conclusion, our results attribute a novel role to SOG1 in regulating the oxidative stress response and connect oxidative stress to the DDR in Cd-exposed plants.

Phytostabilization of Pb and Cd polluted soils using Helianthus petiolaris as pioneer aromatic plant species

The area of soils polluted with heavy metals is increasing due to industrialization and globalization. Aromatic plant species can be a suitable alternative way for agricultural valorization and phytomanagement of such soils by the commercialization of essential oils avoiding risks for the food chain. The potential of growing Helianthus petiolaris in heavy metal polluted soils was assessed in pot experiments using spiked soils and soils from a shooting range. In terms of phytostabilization, H. petiolaris could grow in soils containing 1000 mg/kg Pb²⁺, 50 mg/kg Cd²⁺, accumulating more than three times the soil Cd content in the aerial parts and translocating significant amounts of Pb to the aerial parts when growing in soils polluted with up to 500 mg/kg Pb. When phytostabilization is considered, phytotoxicity of heavy metals strongly depends on the rhizospheric microbial communities, either by mitigating trace element phytotoxicity or promoting plant growth via phytohormone production. So, the effects of heavy metals on the diversity of the rhizospheric bacterial community were assessed using DNA-fingerprinting.

Modelling the ex situ bioremediation of diesel-contaminated soil in a slurry bioreactor using a hydrocarbon-degrading inoculant

Bioremediation is a soil clean-up technique which exploits the metabolic capacity of microorganisms to degrade soil contaminants. A model was developed to simulate the ex situ bioremediation of a diesel-contaminated soil in a bio-slurry reactor inoculated with a diesel-degrading bacterial strain. Mass transfer processes involving desorption of diesel from soil to water and volatilization of diesel from water, and biodegradation by the bacterial inoculant were included in the model by using Weibull sigmoid kinetics and logistic/Monod kinetics respectively. Model parameters were estimated in batch-based abiotic and biodegradation experiments. Sensitivity analysis revealed the importance of maintaining a high bacterial density in the system for maximum bioremediation efficiency. The model was validated using a pilot bioreactor monitored for 528 h, which removed almost 90% of the diesel present in the system. The results revealed the capacity of the model to predict the bioremediation efficiency under different scenarios by adapting the input parameters to each system.

Fenton-Mediated Biodegradation of Chlorendic Acid - A Highly Chlorinated Organic Pollutant - By Fungi Isolated From a Polluted Site

Chlorendic acid is a recalcitrant, highly chlorinated organic pollutant for which no microbial degrader has yet been identified. To address this knowledge gap, fungi were isolated from bulk soil, rhizosphere, and roots of the common bent (Agrostis capillaris) and the hybrid poplar [Populus deltoides × (Populus trichocarpa × P. deltoides) cv. Grimminge], both of which grow on a chlorendic acid polluted site in Belgium. Isolates were taxonomically identified and phenotypically screened for chlorendic acid degradation. Several fungal isolates could degrade chlorendic acid in liquid media up to 45%. The chlorendic acid degrading fungal isolates produced higher levels of hydroxyl radicals when exposed to the pollutant when compared to non-exposed controls, suggesting that the oxidative degradation of chlorendic acid occurs through production of Fenton-mediated hydroxyl radicals. In addition, the isolated Ascomycete Penicillium sp. 1D-2a degraded 58% of the original chlorendic acid concentration in the soil after 28 days. This study demonstrates that the presence of fungi in a chlorendic acid polluted soil can degrade this highly chlorinated organic pollutant. These results indicate that recalcitrant, seemingly non-biologically degradable organic pollutants, such as chlorendic acid, can be remediated by using bioremediation, which opens new perspectives for in situ bioremediation.

Biodegradation of polycyclic aromatic hydrocarbons by native Ganoderma sp. strains: identification of metabolites and proposed degradation pathways

Since polycyclic aromatic hydrocarbons (PAHs) are mutagenic, teratogenic, and carcinogenic, they are of considerable environmental concern. A biotechnological approach to remove such compounds from polluted ecosystems could be based on the use of white-rot fungi (WRF). The potential of well-adapted indigenous Ganoderma strains to degrade PAHs remains underexplored. Seven native Ganoderma sp. strains with capacity to produce high levels of laccase enzymes and to degrade synthetic dyes were investigated for their degradation potential of PAHs. The crude enzymatic extracts produced by Ganoderma strains differentially degraded the PAHs assayed (naphthalene 34-73%, phenanthrene 9-67%, fluorene 11-64%). Ganoderma sp. UH-M was the most promising strain for the degradation of PAHs without the addition of redox mediators. The PAH oxidation performed by the extracellular enzymes produced more polar and soluble metabolites such as benzoic acid, catechol, phthalic and protocatechuic acids, allowing us to propose degradation pathways of these PAHs. This is the first study in which breakdown intermediates and degradation pathways of PAHs by a native strain of Ganoderma genus were determined. The treatment of PAHs with the biomass of this fungal strain enhanced the degradation of the three PAHs. The laccase enzymes played an important role in the degradation of these compounds; however, the role of peroxidases cannot be excluded. Ganoderma sp. UH-M is a promising candidate for the bioremediation of ecosystems polluted with PAHs.

Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bóbrka (Poland)

Hydrocarbon-degrading bacteria are important resources for use in phytoremediation applications. Yet, for many hydrocarbonoclastic strains the genetic information regarding pollutant degradation and detoxification has not been thoroughly revealed. In this study, hydrocarbon-degrading bacteria were isolated from a long-term oil-polluted soil in Bóbrka, Poland. Pseudomonas spp. was the most dominant species. Of all 69 isolated strains tested in the laboratory using qualitative biochemical assays, 61% showed the capability to use diesel as sole carbon source, 33% could produce indole, 19% produced siderophores, 36% produced organic acids, and 54% were capable of producing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase. From all morphologically and genetically different strains, two representative Pseudomonas spp., strain VI4.1 and VI4T1, were selected for genome sequencing. Genomic analyses indicated the presence of the full naphthalene dioxygenase operon (plasmid and chromosomal), of genes involved in the degradation of BTEX compounds (Benzene, Toluene, Ethylbenzene, Xylene) and alkanes (alkB gene) as well as the anthranilate degradation pathway (strain VI4T1) and terephthalate dioxygenase protein (strain VI4.1). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) analyses confirmed naphthalene and BTEX degradation within seven days. Motility, resistance to abiotic stresses, high and low temperatures, low pH, and salinity were confirmed at the genetic level and experimentally verified. The presence of multiple degradative and plant growth promotion genes, together with the in vitro experimental evidence, indicates the high value of these two strains and their potential use for sustainable site clean-up.

Characterisation of the Carpinus betulus L. Phyllomicrobiome in Urban and Forest Areas

Urban green areas are highly valued by citizens for their contribution to the quality of life in cities. Plants play an important role in mitigating airborne pollutants and are assisted in this role by the metabolic capacities of the millions of microbial cells that colonize leaf surfaces (phyllosphere). Many factors influence phyllosphere microbial community composition and function, but to what extent does airborne pollution in cities impact the composition of microbial communities and their functional degradation genes? Here we describe the characterization of the phyllospheric bacterial communities of Carpinus betulus L. trees (hornbeam) across three locations: the city center of Warsaw (Poland), a forest in a UNESCO World Heritage Site (Białowieża), and a forest in one of the world’s oldest operational oil fields (Bóbrka). C. betulus contained higher particulate matter (PM) concentrations, with higher concentrations of palladium and radon in the PM, on leaves in Warsaw than in the forests. Volatile organic compound (VOC) analyses of sampled air revealed higher concentrations of butanone methyl propanal, butylbenzene, and cyclohexane in Bóbrka than Warsaw and Białowieża, while in Warsaw, xylene and toluene were higher. Shotgun microbiome sequencing uncovered a dominance of Gammaproteobacteria (71%), mainly Pseudomonas spp., Actinobacteria, Alpha- and Betaproteobacteria, and Firmicutes. Community composition and function differed significantly between the forests and Warsaw city center. Statistically more hydrocarbon degradation genes were found in Białowieża compared to Warsaw and Bóbrka, and in vitro tests of diesel degradation and plant growth promotion traits of culturable representatives revealed that Białowieża held the highest number of bacteria with plant beneficial properties and degradation genes. This study provides the first detailed insights into the microbiome of C. betulus and sets the stage for developing to a more integrated understanding of phyllosphere microbiota in cities, and their relationships with human health.

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study

The aerial surfaces of plants harbor diverse communities of microorganisms. The rising awareness concerning the potential roles of these phyllosphere microbiota for airborne pollutant remediation and plant growth promotion, advocates for a better understanding of their community structure and dynamics in urban ecosystems. Here, we characterized the epiphytic microbial communities on leaves of Platanus × hispanica trees in the city centre of Hasselt (Belgium), and the nearby forest area of Bokrijk, Genk (Belgium). We compared the influences of season, site, and air pollutants concentration variations on the tree’s phyllosphere microbiome by determining the intra- and inter-individual variation in leaf bacterial communities. High-throughput amplicon sequencing of the 16S rRNA gene revealed large variation in the bacterial community structure and diversity throughout the years but also allowed to discriminate an environment effect on community assembly. Partial drivers for this environment effect on composition can be correlated with the huge differences in ultrafine particulate matter (UFP) and black carbon on the leaves. A change in bacterial community composition was noted for trees growing in the city center compared to the natural site, and also more human-associated genera were found colonizing the leaves from the city center. These integrated results offer an original and first insight in the Platanus phyllomicrobiota, which can offer new opportunities to use phyllosphere microorganisms to enhance air pollution degradation.

Tobacco, Sunflower and High Biomass SRC Clones Show Potential for Trace Metal Phytoextraction on a Moderately Contaminated Field Site in Belgium

Phytoextraction could be a potential management option for diffusely Cd-Zn-Pb-polluted agricultural land in Northeast Belgium. The use of high yielding crops with a sufficiently high metal accumulation is preferred as these are expected to both gradually decontaminate the soil while generating an income through biomass valorization. To find out which high biomass crop possessed the highest and most constant (in time) phytoextraction potential on these soils, different plant species and different mutants or clones of each species, were evaluated during consecutive years. Biomass production and metal accumulation of pre-selected tobacco somaclonal variants (Nicotiana tabacum L.) and pre-selected sunflower mutants (Helianthus annuus L.) were investigated for two productivity years, while the phytoextraction potential of experimental poplar (Populus) and willow (Salix) in short rotation coppice (SRC) was assessed at the end of the second cutting cycle (after two times four growing seasons). The tobacco clones and the sunflower mutants showed efficient extraction of, respectively, Cd and Zn, while the highest simultaneous extractions of Cd and Zn were gained with some SRC clones. Variation in biomass production and metal accumulation were high for all crops over the years. The highest biomass production was observed for the experimental poplar clone of the crossing type Populus deltoides (P. maximowiczii x P. trichocarpa) with 9.9 ton DW per ha per year. The remediation period to reach legal threshold values for the pseudo-total content of Cd in this specific soil was estimated to be at least 60 years. Combining estimated phytoextraction potential and economic and environmental aspects, the SRC option is proposed as the most suitable crop for implementing metal phytoextraction in the investigated area.