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Rapid and exceptionally small-scale adaptation of the alpine plant Cardamine resedifolia to mining-contaminated soils in multi-stress condition.

The mechanisms by which plants tolerate soil contamination have been studied in details in controlled laboratory conditions, but they still remain largely unexplored in natural conditions where mixtures of contaminants are present in soils and their effects might interact with other environmental variables. This is especially true in high-altitude alpine environments, where abiotic stress is naturally heightened, but which so far have received little attention in environmental pollution studies. As we were interested in the tolerance mechanisms at play on very fine spatiotemporal scales for alpine plants growing under multi-stress conditions, we chose Cardamine resedifolia as our biological model. This plant is indeed frequently found in areas contaminated by Trace Metals and Metalloids and Polycyclic Aromatic Hydrocarbons in high elevation. We studied populations from former copper, silver-lead, and coal mines in alpine environments, along with populations growing on nearby reference soils. We measured genetic variability within populations as well as genetic differentiation between them, and tested for local adaptation to soil contamination using reciprocal transplants. Population pairs showing signs of local adaptation were then examined using genome scans to identify genes potentially under selection. We found high levels of genetic differentiation between populations growing on contaminated and reference soils a few dozen meters apart. In most cases local adaptation was detected, especially in former copper mines. Genome scans identified genes involved in metal stress management as potentially being under selection. This study provides evidence for rapid adaptation to human-induced pollution in alpine plants at remarkably small spatial scales. It offers new insights into the short-term ecological and evolutionary consequences of mining activities in alpine ecosystems, particularly in relation to substrate-driven differentiation.

Alpine plants

Synergistic removal of total petroleum hydrocarbons and antibiotic resistance genes in Yellow River Delta wetlands contaminated soil composting regulated by biogas slurry addition.

The interactive effects between the emerging contaminant antibiotic resistance genes (ARGs) and the traditional pollutant total petroleum hydrocarbons (TPHs) in contaminated soils remain unclear. The synergistic removal of TPHs and ARGs from composted contaminated soil, along with the microbial mechanisms driven by the addition of biogas slurry, have not yet been investigated. This study explored the impact of biogas slurry on the synergistic degradation mechanisms and bacterial community dynamics of ARGs and TPHs in compost derived from contaminated soil. The addition of biogas slurry resulted in a reduction of targeted ARGs and mobile genetic elements (MGEs) by 9.96%-95.70% and 13.32%-97.66%, respectively. Biogas slurry changed the succession of bacterial communities during composting, thereby reducing the transmission risk of ARGs. Pseudomonas, Cellvibrio, and Devosia were identified as core microorganisms in the synergistic degradation of ARGs and TPHs. According to the partial least squares path model, temperature and NO3- indirectly influenced the removal of ARGs and TPHs by directly regulating the abundance and composition of host microbes and MGEs. In summary, the results of this study contribute to the high-value utilization of biogas slurry and provide methodological support for the low-cost remediation of contaminated soils.

Composting

Birnessite-mediated simultaneous remediation of lead and benzo[a]pyrene co-contaminated soils.

It is currently challenging to remediate soils co-contaminated by heavy metals and polycyclic aromatic hydrocarbons. Birnessite is a naturally ubiquitous manganese oxide mineral with strong oxidation and adsorption capacities, but its specific roles in pollutant transformation and interfacial interaction within co-contaminated systems remain elusive. This study investigated the simultaneous remediation of lead (Pb) and benzo[a]pyrene (BaP) in soils by birnessite through incubation experiments and density functional theory calculation. Birnessite treatment decreased CaCl2- and toxicity characteristic leaching procedure-extractable Pb content by 64.3% and 86.6% and reduced the BaP content by 33.8%. Mechanistically, Pb immobilization was primarily driven by spontaneous adsorption, including ion exchange and surface complexation, which facilitated Pb transformation into Fe-Mn oxide-bound fractions. Concurrently, BaP removal occurred via a synergistic pathway involving reactive species and electron transfer processes. Increasing dosage of birnessite promoted Pb immobilization, but had little effect on BaP oxidation. Moreover, the co-existing Pb affected birnessite-mediated BaP adsorption and oxidation by promoting the formation of [BaP-Pb]2+ and [BaP-Pb(H2O)]2+ complexes via cation-π interactions. These complexes were more preferentially adsorbed on birnessite compared with BaP molecules, but exhibited higher electron transfer barriers. The findings provide critical insights into the remediation of co-contaminated soils and the fate of co-existing contaminants.

Birnessite

Proposal of three novel species of the family Xanthobacteraceae: Xanthobacter pollutisoli sp. nov., Xanthobacter luteus sp. nov. and Aquabacter albus sp. nov., isolated from oil-contaminated soils.

Three Gram-stain-negative bacterial strains, KR7-65T, KR7-225T and CN5-332T isolated from oil-contaminated soil in Korea and China were identified. Phylogenetic analysis based on 16S rRNA gene sequences placed the strains within the family Xanthobacteraceae, with KR7-65T and KR7-225T affiliated with the genus Xanthobacter and CN5-332T with the genus Aquabacter. Sequence similarities to type strains of validly published species were below 98.5%. Core genome phylogeny showed that the four strains formed distinct clusters occupying different positions in the phylogenetic tree and exhibited different closest relatives. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization (dDDH) values between KR7-65T and KR7-225T and members of Xanthobacter were 78.7-87.0%, 74.8-87.8% and 22.7-32.3%, respectively, whereas those between CN5-332T and members of Aquabacter were 80.2-80.7%, 79.6-80.5% and 23.4-23.9%, supporting their assignment as novel species. The DNA G+C contents were 68.0, 69.9 and 66.5 mol% for KR7-65T, KR7-225T and CN5-332T, respectively. Strains KR7-65T and KR7-225T contained phosphatidylcholine, phosphatidylglycerol, phosphatidyl monomethyl ethanolamine, diphosphatidylglycerol (DPG) and an unidentified glycolipid as major polar lipids, whereas DPG was absent in strain CN5-332T. The primary fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), cyclo C19 : 0ω8c and C16 : 0. On the basis of phylogenetic, genomic and phenotypic evidence, strains KR7-65T and KR7-225T represent two novel species of the genus Xanthobacter, for which the names Xanthobacter pollutisoli sp. nov. (type strain KR7-65T=KACC 23453T=NBRC 116939T) and Xanthobacter luteus sp. nov. (type strain KR7-225T=KACC 23282T=NBRC 116940T) are proposed. Strain CN5-332T represents a novel species of the genus Aquabacter, for which the name Aquabacter albus sp. nov. (type strain CN5-332T=KACC 23276T=CCTCC AB 2024343T) is proposed.

Phylogeny

Influence of silage contamination by soil upon trace elements availability in sheep.

The influence of soil contamination in silage has been studied in two successive balance trials realized with 12 growing lambs (27 kg). A perennial Rye Grass at the first cycle was offered alone or contaminated with 5% of acid brown soil issued from altered granit rocks. Voluntary intakes and dry matter digestibility were lowered. Similarly copper, zinc and manganese digestibility dropped sharply in spite of a diet enrichment in these elements by the soil.

Animal Feed

Synergic impact mechanisms of cover crop residue on Cd and As availability and native organic carbon mineralization in Cd and As co-contaminated paddy soil.

The synergic impacts of cover crop residue on heavy metal and metalloid availability and soil organic carbon (SOC) mineralization in contaminated paddy soil and the underlying microbial mechanism remain unclear. This study investigated the availability of cadmium (Cd) and arsenic (As) and mineralization of native SOC in paddy soil treated with 0, 0.4 %, 0.8 % and 1.2 % of δ13C-labeled cover crop residue (Astragalus sinicus L.) via 90-day incubation experiments, the related functional genes and functional microbial communities were analyzed using metagenomic binning assembly. Cover crop residue with addition rate from 0.4 % to 1.2 % significantly decreased available Cd by 56 %-85 % but increased available As by 39 %-66 % compared to the control treatment. Cover crop residue resulted in a positive priming effect on native SOC mineralization but benefited SOC sequestration. Cover crop residue increased the abundance of genes encoding iron reductase (mtrABC, pilA, omcB), sulfate reductase (sir, fpr), As(V) reductase (ArsC), organic carbon hydrolases, methanogenesis, and methylotrophy. Genomes associated with Chloroflexota and Bacteroidota encoded all these key pathways, and their abundance increased with cover crop residue application. Cover crop residue decreased soil Eh, dissolved crystalline iron oxides, enriched specific microorganisms, including Chloroflexota and Bacteroidota, and then synergistically promoted the decrease in Cd availability and the increase in As availability and native SOC mineralization in the examined paddy soil. These findings provided practical and feasible guidance for achieving both safe production and carbon sequestration in contaminated paddy fields, highlighting the requirement to cautious utilization of cover crop residue in As-contaminated paddy fileds.

Soil Pollutants

Results of the investigation of soil for contamination with pathogenic leptospires.

In the natural focus of leptospirosis at the lake Nero (Yaroslav region, USSR) 630 samples of soil were investigated for the presence of leptospires. Seven cultures of leptospires were isolated from the soil; five of them were pathogenic (four belonged to the serogroup Grippotyphosa and one to the serogroup Hebdomadis) and two were saprophytic. Among the cultures of pathogenic leptospires isolated from the soil there was observed the same quantitative ratio of serogroups as among cultures obtained from rodents, which suggests that the leptospires circulate from mammals to soil and vice versa.

Animals

Long-term PFOA and cadmium Co-contamination alters soil carbon, nitrogen, and phosphorus cycling: Insights from metagenomics and metabolomics.

The co-existence of perfluorooctanoic acid (PFOA) and cadmium (Cd) in soil poses a combined threat to microbial communities. However, the ecological effects and underlying mechanisms of their long-term combined exposure remain poorly understood. This study conducted a 90-day soil microcosm experiment to systematically investigate the effects of individual and combined effects of PFOA and Cd on microbial communities. Our results demonstrated that combined pollution of PFOA and Cd significantly affected four soil enzyme activities associated with carbon, nitrogen, and phosphorus cycling. It also influenced microbial thermal activity with an IC50 of PFOA at 0.94 mg/kg. The toxic interaction between PFOA and Cd varied with both toxicity indicators and exposure time. At the community level, PFOA and Cd synergistically reduced bacterial diversity and richness, while exerting more complex interactive effects on fungal communities. Metagenomic analysis revealed that PFOA and Cd significantly affected carbon, nitrogen, and phosphorus cycling by inhibiting inorganic phosphorus solubilization genes (gcd, pqqC) and altering key genes in carbon fixation and nitrogen transformation. Metabolomic profiling further demonstrated that PFOA disrupted membrane lipid homeostasis and amino acid metabolism. Meanwhile, the co-existence of Cd exacerbated disturbances in sugar and carbon metabolism. Our findings provide genetic-level insights into microbial responses to long-term PFOA and Cd co-contamination. These results are essential for risk assessment at such co-contamination sites.

Cadmium

Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection.

Remediation of heavy metal-contaminated soil is a global priority, particularly as reclaimed land increasingly intersects with urban development and human exposure. However, the ecological consequences of soil remediation, especially its impact on antimicrobial resistance (AMR) as a global health threat, have remained poorly understood. Here, we combined single-cell Raman-D₂O probing with genome-resolved metagenomics to monitor the dynamics of phenotypic and genotypic resistance to metals and antibiotics during a 120-day remediation of soils with three contamination levels from a lead-zinc smelting site. Although chemical remediation substantially reduced bioavailable metals (by 42%-65%), AMR was not diminished. Instead, both phenotypic activity and gene abundance of metal- and antibiotic-resistant microorganisms increased, resulting in a two- to three-fold increase in AMR-associated health risks. Among 76 metagenome assembled genomes (MAGs) from phenotypic resistance communities, all Cd resistance-associated MAGs harbored multidrug resistance genes, half of which were colocalized with metal resistance determinants, and their prevalence continued to rise with remediation. These findings reveal that although remediation alleviates acute metal toxicity, residual low-concentration bioavailable metals sustain evolutionary selection for resistance, highlighting a disconnect between chemical recovery and biological safety. Moreover, the improved soil nutrient and physiochemical properties of remediated soils further promoted the proliferation of antibiotic-resistant bacteria. This study offers new ecological insights into the unintended consequences of anthropogenic interventions, underscoring the need to integrate biological safety into soil health and safety assessments.

Soil Microbiology

Assessment of antibiotic resistance genes in soils polluted by chemical and technogenic ways with poly-aromatic hydrocarbons and heavy metals.

Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.

Soil Pollutants

Effects of zinc-smelter emissions on forest soil microflora.

Within 2 km of a zinc (Zn) smelter in Palmerton, Pennsylvania, near the Lehigh Water Gap, up to 13.5% Zn by weight has been measured in the O2 horizon of the soil, and up to 8% Zn in the A1 horizon. The total numbers of bacteria, actinomycetes, and fungi (measured by dilution plate counts) were greatly reduced in the most severely Zn-contaminated soils compared with control soils. The reduction of microbial populations may be a partial cause of the decreased rate of litter decomposition at Lehigh Gap. Growth of most bacteria from control sites was reduced by 100 to 200 muM Zn, most actinomycetes by 100 muM Zn, and most fungi by 100 to 1000 muM Zn in thin-Pablum extract agar (TPab). All the tested actinomycetes and non-spore-forming bacteria isolated from Zn-contaminated Lehigh Gap soils were Zn-tolerant, growing normally in media containing 600-2000 muM Zn. Most fungi, regardless of source, were capable of at least 50% of normal growth at 700 muM Zn. Zinc-tolerant bacteria, actinomycetes, and fungi were readily isolated from low-Zn soils, suggesting that selection for Zn tolerance may proceed rapidly. Acidophilic Mortierella species have been selectively eliminated near the smelter, apparently because of elevated soil pH. Peryronellaea glomerata (Corda) Goidanich and Coniothyrium spp. were found only in the high-Zn soils.

Actinomycetales

Complete genomes of 22 bacterial strains isolated from polluted soil microbiota via enrichment on PFAS as a sole carbon source.

A total of 22 bacterial strains were isolated from PFAS-contaminated soil (Veneto, Italy), after a 5-month enrichment using perfluorooctanoic acid and heptafluorobutyric acid. Whole genomes were sequenced and screened with a curated database of dehalogenase-related proteins. All genomes showed potential for fluorinated compound transformation.

Veneto region, Italy

Absence of plant uptake and translocation of polybrominated biphenyls (PBBs).

Studies of polybrominated biphenyl (PBB) uptake by plants have been conducted in hydroponic solutions and in greenhouse experiments with soil. Autoradiograms of corn and soybean seedlings grown in hydroponic solutions showed no translocation of 14C-PBB from 14C-PBB-treated solutions to plant tops or within the leaf from 14C-PBB-treated spots on the upper leaf surface. A significant portion of the 14C-PBB associated with the roots was removed when the roots were dipped in acetone. Three root crops (radishes, carrots, and onions) were grown in two soils, each treated with a mixture of FireMaster BP-6 (PBB) and 14C-PBB to achieve final concentrations of 100 ppm and 100 ppb. All roots showed more PBB when grown in the soil with the lower clay and organic matter content than they did when grown in the soil with more clay and organic matter. In the latter soil (clay loam) no PBB was detected in any roots from the 100 ppb treatment. More PBB was associated with roots of carrot than of radish or onion. Corn leaf whorls containing dust from a PBB contamination soil and washed radishes from a heavily contaminated garden showed no PBB.

Biphenyl Compounds

From ecological threats to environmental solutions: a critical review of invasive plant species for heavy metal phytoremediation.

Heavy metal contamination represents a persistent environmental challenge threatening ecosystem stability, agricultural productivity, and human health. Therefore, the development of sustainable and cost-effective remediation strategies is essential. Phytoremediation, an environmentally compatible approach that utilizes plants and their associated biological processes to reduce contaminant mobility, bioavailability, and toxicity, has gained increasing attention as an alternative to conventional remediation techniques. Among potential phytoremediation candidates, invasive plant species (IPS) have attracted interest due to their rapid growth, high biomass production, extensive root systems, physiological plasticity, and tolerance to stressful environments, including heavy metal contamination. Species such as Alternanthera philoxeroides, Arundo donax, Eichhornia crassipes, and Pistia stratiotes have demonstrated potential for metal uptake, accumulation, immobilization, or tolerance in contaminated ecosystems. This review critically examines the role of invasive plants in heavy metal phytoremediation by evaluating the physiological, biochemical, and ecological traits that influence remediation outcomes. Key mechanisms, including phytoextraction, phytostabilization, rhizosphere-mediated processes, and plant-microbe interactions, are discussed using evidence from contaminated soil and aquatic environments. The potential advantages of invasive plants, particularly their high biomass production and environmental adaptability, are evaluated alongside ecological concerns associated with their utilization. Importantly, invasion success does not necessarily translate into remediation success, and the effectiveness of invasive plants depends on contaminant characteristics, ecosystem conditions, and management practices. Major challenges, including uncontrolled spread, ecosystem disruption, contaminated biomass management, and limited field-scale validation, are critically assessed. Overall, invasive plants represent context-dependent remediation resources rather than universal solutions. Their application requires integrated risk assessment, containment strategies, long-term monitoring, and evidence-based management frameworks to maximize remediation benefits while minimizing ecological risks.

Contamination

Effect of cadmium on fungi and on interactions between fungi and bacteria in soil: influence of clay minerals and pH.

Fungi (Rhizopus stolonifer, Trichoderma viride, Fusarium oxysporum f. sp. conglutinans, Cunninghamella echinulata, and several species of Aspergillus and Penicillium) tolerated higher concentrations of cadmium (Cd) when grown in soil than when grown on laboratory media, indicating that soil mitigated the toxic effects of Cd. In soil amended with clay minerals, montmorillonite provided partial or total protection against fungistatic effects of Cd, whereas additions of kaolinite provided little or no protection. Growth rates of Aspergillus niger were inhibited to a greater extent by 100 or 250 mug of Cd per g in soil adjusted to pH 7.2 than in the same soil at its natural pH of 5.1. However, there were no differences in the growth rates of Aspergillus fischeri with 100 or 250 mug of Cd per g in the same soil, whether at pH 5.1 or adjusted to pH 7.2. Growth of A. niger and A. fischeri in a soil contaminated with a low concentration of Cd (i.e., 28 mug/g), obtained from a site near a Japanese smelter, did not differ significantly from growth in a soil collected some distance away and containing 4 mug of Cd per g. Growth of A. niger in sterile soil amended with 100 mug of Cd per g and inoculated with Bacillus cereus or Agrobacterium tumefaciens was reduced to a greater extent than in the same soil containing 100 mug of Cd per g but no bacteria. The inhibitory effects of Agrobacterium radiobacter to A. niger were slightly reduced in the presence of 100 mug of Cd per g, whereas the inhibitory effects of Serratia marcescens were enhanced.

Antibiosis

Meta-analysis of source identification and apportionment in soil: A systematic review of analytical procedures, receptor modeling, and environmental applications.

Soil pollution poses significant risks to ecosystems and human health, necessitating accurate source identification and apportionment to guide mitigation strategies. This systematic review evaluates the application of Positive Matrix Factorization (PMF) and other receptor models in soil pollution studies, focusing on analytical procedures, tracer indicators, and environmental applications. This review aims to provide a comprehensive framework for conducting soil source apportionment studies, aiding policymakers in designing effective, region-specific environmental management strategies by compiling global trends and methodological insights. The study addresses sampling protocols, emphasizing representativeness and quality control. Data from 500 peer-reviewed publications highlight the dominance of research in China, Eastern Europe, and South Asia, with agricultural soils being the most frequently studied. Key findings reveal that traffic emissions (20.8 %) and industrial activities (19.4 %) are the primary global contributors to soil contamination, with regional variations such as coal combustion in cold climates and agricultural inputs in developing regions. Policy recommendations include stricter industrial regulations, sustainable agricultural practices, and targeted remediation efforts based on source-specific risks.

Soil Pollutants