Successive phytoextraction alters ammonia oxidation and associated microbial communities in heavy metal contaminated agricultural soils

Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone

The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4+ content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.

Variance of soil bacterial community and metabolic profile in the rhizosphere vs. non-rhizosphere of native plant Rumex acetosa L. from a Sb/As co-contaminated area in China

Heavy metals (HMs) contamination poses a serious threat to soil health. However, the rhizosphere effect of native pioneer plants on the soil ecosystem remains unclear. Herein, how the rhizosphere (Rumex acetosa L.) influenced the process of HMs threatening soil micro-ecology was investigated by coupling various fractions of HMs, soil microorganisms and soil metabolism. The rhizosphere effect alleviated the HMs' stress by absorbing and reducing HMs' direct bioavailability, and the accumulation of ammonium nitrogen increased in the rhizosphere soil. Meanwhile, severe HMs contamination covered the rhizosphere effect on the richness, diversity, structure and predicted function pathways of soil bacterial community, but the relative abundance of Gemmatimonadota decreased and Verrucomicrobiota increased. The content of total HMs and physicochemical properties played a more important role than rhizosphere effect in shaping soil bacterial community. Furthermore, As was observed to have a more significant impact compared to Sb. Moreover, plant roots improved the stability of bacterial co-occurrence network, and significantly changed the critical genera. The process influenced bacterial life activity and nutrient cycling in soil, and the conclusion was further supported by the significant difference in metabolic profiles. This study illustrated that in Sb/As co-contaminated area, rhizosphere effect significantly changed soil HMs content and fraction, soil properties, and microbial community and metabolic profiles.

Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil

Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.

Rhizobacteria helps to explain the enhanced efficiency of phytoextraction strengthened by Streptomyces pactum

The ultimate purpose of phytoextraction is not only to remove heavy metals from soil but also to improve soil quality. Here, we evaluated how the joint effect of Streptomyces pactum (strain Act12) and inorganic (Hoagland's solution) and organic (humic acid and peat) nutrients affected the phytoextraction practice of cadmium (Cd) and zinc (Zn) by potherb mustard, and the microbial community composition within rhizosphere was also investigated. The results indicated that the nutrients exerted synergistically with Act12, all increasing the plant biomass and Cd/Zn uptakes. The inoculation of Act12 alone significantly increased dehydrogenase activity of rhizosphere soil (P < 0.05), while urease and alkaline phosphatase activities varied in different dosage of Act12. Combined application of microbial strain with nutrients increased enzymatic activities with the elevated dosage of Act12. 16S ribosomal RNA high-throughput sequencing analysis revealed that Act12 inoculation reduced the diversity of rhizosphere bacteria. The Act12 and nutrients did not change dominant phyla i.e., Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria and Acidobacteria, but their relative abundance differed among the treatments with: Peat > Act12 > Humic acid > Hoagland's solution. Comparatively, Sphingomonas replaced Thiobacillus as dominant genus after Act12 application. The increase in the Sphingomonas and Flavisolibacter abundances under Act12 and nutrients treatments gave rise to growth-promoting effect on plant. Our results revealed the important role for rhizosphere microbiota in mediating soil biochemical traits and plant growth, and our approach charted a path toward the development of Act12 combined with soil nutrients to enhance soil quality and phytoextraction efficiency in Cd/Zn-contaminated soils.

Lead or cadmium co-contamination alters benzene and toluene degrading bacterial communities

Co-contamination of hydrocarbons with heavy metals in soils often complicates and hinders bioremediation. A comprehensive characterization of site-specific degraders at contaminated sites can help determine if in situ bioremediation processes are sufficient. This study aimed to identify differences in benzene and toluene degradation rates and the microbial communities enriched under aerobic conditions when different concentrations of Cd and Pb are introduced. Microcosms were used to study the degradation of 0.23 mM benzene or 0.19 mM toluene under various concentrations of Pb (up to 240 µM) and Cd (up to 440 µM). Soil collected from a stormwater retention basin receiving runoff from a large parking lot was utilized to seed the microcosms. The hydrocarbon degradation time and rates were measured. After further rounds of amendment and degradation of benzene and toluene, 16S rRNA gene amplicon sequencing and quantitative PCR were used to ascertain the microbial communities enriched under the various concentrations of the heavy metals. The initial degradation time for toluene and benzene was 7 to 9 days and 10 to 13 days, respectively. Degradation rates were similar for each hydrocarbon despite the concentration and presence of metal co-contaminant, however, the enriched microbial communities under each condition differed. Microcosms without metal co-contaminant contained a diversity of putative benzene and toluene degrading bacteria. Cd strongly reduced the richness of the microbial communities. With higher levels of heavy metals, genera such as Ralstonia, Cupriavidus, Azoarcus, and Rhodococcus became more dominant under various conditions. The study finds that highly efficient benzene- and toluene-degrading consortia can develop under variations of heavy metal co-contamination, but the consortia are dependent on the heavy metal type and concentrations.

The role of sulfur nutrition in plant response to metal(loid) stress: Facilitating biofortification and phytoremediation

Metal(loid)s contamination poses a serious threat to ecosystem biosafety and human health. Phytoremediation is a cost-effective and eco-friendly technology with good public acceptance, although the process does require a significant amount of time for success. To enhance the phytoremediation efficiency, numerous approaches have been explored, including soil amendments application with chelators to facilitate remediation. Sulfur (S), a macronutrient for plant growth, plays vital roles in several metabolic pathways that can actively affect metal(loid)s phytoextraction, as well as attenuate metal(loid) toxicity. In this review, different forms of S-amendments (fertilizers) on uptake and translocation in plants upon exposure to various metal(loid) are evaluated. Possible mechanisms for S application alleviating metal(loid) toxicity are documented at the physiological, biochemical and molecular levels. Furthermore, this review highlights the crosstalk between S-assimilation and other biomolecules, such as phytohormones, polyamines and nitric oxide, which are also important for metal(loid) stress tolerance. Given the effectiveness and potential of S amendments on phytoremediation, future studies should focus on optimizing phytoremediation efficiency in long-term field studies and on investigating the appropriate S dose to maximize the food safety and ecosystem health.

Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant

Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g^-1, which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant (p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria，Sordariomycetes and Dothideomycetes. Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.

Long-term nickel contamination increased soil fungal diversity and altered fungal community structure and co-occurrence patterns in agricultural soils

Nickel (Ni) contamination imposes deleterious effects on the stability of soil ecosystem. Soil fungal community as a crucial moderator of soil remediation and biochemical processes has attracted more and more research interests. In the present study, soil fungal community composition and diversity under long-term Ni contamination were investigated and fungal interaction networks were built to reveal fungal co-occurrence patterns. The results showed that moderate Ni contamination significantly increased fungal diversity and altered fungal community structure. Functional predictions based on FUNGuild suggested that the relative abundance of arbuscular mycorrhizal fungi (AMF) significantly increased at moderate Ni contamination level. Ni contamination strengthened fungal interactions. Keystone taxa at different Ni contamination levels, such as Penicillium at light contamination, were identified, which might have ecological significance in maintaining the stability of fungal community to Ni stress. The present study provided a deeper insight into the effect of long-term Ni contamination on fungal community composition and co-occurrence patterns, and was helpful to further explore ecological risk of Ni contamination in cultivated field.

Cyanide treatment of mining tailings using suspended biomass and moving bed biomass reactors

Mexico is the top producer of silver and is on the eighth place from producing gold in the world. For instance, the hydrometallurgical extraction process produces wastewater (mining tailing) characterized by being composed with varying concentrations of cyanide and heavy metals. The purpose of this research was to study the biodegradation of cyanide contained in mining tailings by means of a bacterial consortium isolated from a tailings dam. For this purpose, three types of Eckendfelder reactors were used, one with suspended biomass (BS) and two moving bed biofilter reactors, one with biomass immobilized on Kaldnes (BK) supports, and the other on polyurethane cubes (BCP). Three experimental stages were worked; in each of them, the concentrations of total cyanide were varied. In the first one, it was 26 ± 2 mg·L^-1; in the second one 40 ± 4 mg·L^-1; and the third one 55 ± 4 mg·L^-1. During the whole operation, the pH and temperature were maintained at 9.5 units and 25 °C. After 141 days of operation, biodegradation of the total cyanide contained in the mining tailings was 69% (17 mg·L^-1) in the BS reactor, while in the BK reactor, it was 93% (3.9 mg·L^-1) and in the BCP reactor 95% (2.5 mg·L^-1). The predominant families in each of the reactors, as well as their respective relative abundances, were for the BS and for the BK of Cyclobacteriaceae (20.65% and 24.64%) and Rhizobiaceae (18.48% and 14.01%) and Halomonadaceae (46.97%) and Hyphomonadaceae (24.94%) in the BCP.

Response of Rhizosphere Microbial Community in High-PAH-Contaminated Soil Using Echinacea purpurea (L.) Moench

Under polycyclic aromatic hydrocarbon (PAH) pollution conditions (149.17–187.54 mg/kg), we had found the dominant flora of PAHs by observing the response of the soil microbial community after planting purple coneflower (Echinacea purpurea (L.) Moench). In this study, pot experiments were conducted in a growth chamber to explore the changes in the rhizosphere microbial community structure during remediation of heavily PAH-contaminated soil using purple coneflower (Echinacea purpurea (L.) Moench). The phospholipid fatty acid (PLFA) content in the soil was measured during four periods before and after planting, and the results showed that: (i) at 120 days, E. purpurea can regulate the microbial community structure but had no significant effect on soil microbial diversity, (ii) at 120 days, the number of PLFAs characterizing actinomycetes, bacteria, and fungi increased, and both Gram-negative bacteria and Arbuscular mycorrhizal fungi (AMF) were significant with the observed PLFA level (p < 0.05), and (iii) the results indicated that AMF and Gram-negative bacteria represent some of the main factors that can promote the degradation of PAHs. The results obtained in this work are important to future research on PAH-degradation-functional genes and degradation mechanisms of the selection of flora.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (P_N) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and P_N values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH₃ and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Green remediation of toxic metals contaminated mining soil using bacterial consortium and Brassica juncea

Microorganism-assisted phytoremediation is being developed as an efficient green approach for management of toxic metals contaminated soils and mitigating the potential human health risk. The capability of plant growth promoting Actinobacteria (Streptomyces pactum Act12 - ACT) and Firmicutes (Bacillus subtilis and Bacillus licheniformis - BC) in mono- and co-applications (consortium) to improve soil properties and enhance phytoextraction of Cd, Cu, Pb, and Zn by Brassica juncea (L.) Czern. was studied here for the first time in both incubation and pot experiments. The predominant microbial taxa were Proteobacteria, Actinobacteria and Bacteroidetes, which are important lineages for maintaining soil ecological activities. The consortium improved the levels of alkaline phosphatase, β-D glucosidase, dehydrogenase, sucrase and urease (up to 33%) as compared to the control. The bacterial inoculum also triggered increases in plant fresh weight, pigments and antioxidants. The consortium application enhanced significantly the metals bioavailability (DTPA extractable) and mobilization (acid soluble fraction), relative to those in the unamended soil; therefore, significantly improved the metals uptake by roots and shoots. The phytoextraction indices indicated that B. juncea is an efficient accumulator of Cd and Zn. Overall, co-application of ACT and BC can be an effective solution for enhancing phytoremediation potential and thus reducing the potential human health risk from smelter-contaminated soil. Field studies may further credit the understanding of consortium interactions with soil and different plant systems in remediating multi-metal contaminated environments.

Effects of EDTA on adsorption of Cd(II) and Pb(II) by soil minerals in low-permeability layers: batch experiments and microscopic characterization

Ethylenediaminetetraacetic acid (EDTA) can serve as a washing agent in the remediation of low-permeability layers contaminated by heavy metals (HMs). Therefore, batch adsorption experiments, where pure quartz (SM1) and mineral mixtures (SM2) were used as typical soil minerals (SMs) in low-permeability layers, were implemented to explore the effects of different EDTA concentrations, pH, and exogenous chemicals on the HM-SM-EDTA adsorption system. As the EDTA concentration increased, it gradually cut down the maximum Cd adsorption capacities of SM1 and SM2 from approximately 135 to 55 mg/kg and 2660 to 1453 mg/kg; and the maximum Pb adsorption capacities of SM1 and SM2 were reduced from 660 to 306 mg/kg and 19,677 to 19,262 mg/kg, respectively. When the initial mole ratio (MR = moles of HM ions/sum of moles of HM ions and EDTA) was closer to 0.5, the effect of EDTA was more effective. Additionally, EDTA worked well at pH below 7.0 and 4.0 for Cd and Pb, respectively. Low-molecular-weight organic acids (LMWOAs) affected the system mainly by bridging, complexation, adsorption site competition, and reductive dissolution. Cu²⁺, Fe²⁺ ions could significantly increase the Cd and Pb adsorption onto SM2. Notably, there were characteristic changes in mineral particles, including attachment of EDTA and microparticles, agglomeration, connection, and smoother surfaces, making the specific surface area (SSA) decrease from 16.73 to 12.59 m²/g. All findings indicated that EDTA could effectively and economically reduce the HM adsorption capacity of SMs at the reasonable MR value, contact time, and pH; EDTA reduced the HM adsorption capacity of SMs not only by complexation with HM ions but also by decreasing SSA and blocking active sites. Hence, the acquired insight from the presented study can help to promote the remediation of contaminated low-permeability layers in groundwater.

Adaptation of soil fungi to heavy metal contamination in paddy fields-a case study in eastern China

Soil fungi have been widely studied, but the effects of heavy metal contamination at various levels as well as the abundance and diversity of heavy metal tolerant fungi in the contaminated paddy soils are still unknown. The purpose of this study is to analyze the adaptability of fungi at different levels of heavy metal contamination to identify species that have strong adaptability to heavy metals. In this research, the technology of high-throughput sequencing was applied to study fungal communities in severe level (SL), moderate level (ML), light level (LL), and clean level (CL) for soil samples polluted by heavy metal, as well as to analyze the relations between environmental variables and fungal communities. The spearman analysis showed that 6 dominant fungal phyla and 18 dominant fungal genera were significantly correlated with these environmental variables. The α-diversity indexes of the soil fungal community from SL, ML, and CL were, mostly, drastically higher than the LL samples (p < 0.05). Meanwhile, Ascomycota, the main fungal phylum, was spotted to yield a strong tolerance towards heavy metals, especially in ML. The most dominant genera of tolerant fungi in this area, which are Aspergillus, Penicillium, and Fusarium, could absorb and transport the heavy metals with the help of nutrients under certain heavy metal contamination levels. Therefore, this study indicated that some fungi, which have strong biodegradability on heavy metals, can reduce toxicity of heavy metals and create a proper soil environment to grow food crops. Graphical abstract.

Effects of EDDS on the Cd uptake and growth of Tagetes patula L. and Phytolacca americana L. in Cd-contaminated alkaline soil in northern China

Phytoextraction has been considered an effective and environment-friendly method for removing heavy metals from contaminated soil. However, the efficiency, mechanism, and adaptability of phytoextraction by hyperaccumulators in Cd-polluted weakly alkaline soil have not been investigated in detail. In this study, pot experiments were conducted to evaluate the enhanced effects of S,S-ethylenediamine disuccinic acid (EDDS) on phytoextraction in alkaline soil by measuring the degradation kinetic characteristics of EDDS and Cd absorption dynamics of Tagetes patula L. (T. patula) and Phytolacca americana L. (P. americana) for a period of 55 days. Results showed that the half-life of EDDS varied from 4.20-7.07 days and 3.35-4.36 days for T. patula and P. americana, respectively. EDDS-activated Cd reached saturation at a low dosage (1 mM) and a single application of EDDS was found to be better than double applications. The activation of EDDS on Cd applied before 45 days of harvest was better than that before 15 days of harvest, and disappeared after a 35-day application. Correspondingly, the Cd concentration in P. americana and T. patula leaves increased significantly after 3 days of the EDDS application. However, T. patula had a biomass 2.57 times and Cd absorption capacity 10.06 times higher than P. americana. EDDS showed almost no influence on the stem and leaf biomass of T. patula; however, the root weight decreased by 9.44-71.77%. The Cd concentration in T. patula leaves of all the treatments was 1.00-1.81 times that of the control group. In comparison with other treatments, the EDDS application (3 mM) before 15 days of harvest extracted the highest amount of Cd (601.45 μg/pot) in T. patula shoots, reaching 1.40 times that in the control group. Therefore, T. patula might be a more suitable phytoremediator for Cd-polluted alkaline soil than P. americana; the most effective method was the EDDS application (3 mM) before 15 days of harvest.

Prospect of phytoremediation combined with other approaches for remediation of heavy metal-polluted soils

Accumulation of heavy metals in agricultural soils due to human production activities-mining, fossil fuel combustion, and application of chemical fertilizers/pesticides-results in severe environmental pollution. As the transmission of heavy metals through the food chain and their accumulation pose a serious risk to human health and safety, there has been increasing attention in the investigation of heavy metal pollution and search for effective soil remediation technologies. Here, we summarized and discussed the basic principles, strengths and weaknesses, and limitations of common standalone approaches such as those based on physics, chemistry, and biology, emphasizing their incompatibility with large-scale applications. Moreover, we explained the effects, advantages, and disadvantages of the combinations of common single repair approaches. We highlighted the latest research advances and prospects in phytoremediation-chemical, phytoremediation-microbe, and phytoremediation-genetic engineering combined with remediation approaches by changing metal availability, improving plant tolerance, promoting plant growth, improving phytoextraction and phytostabilization, etc. We then explained the improved safety and applicability of phytoremediation combined with other repair approaches compared to common standalone approaches. Finally, we established a prospective research direction of phytoremediation combined with multi-technology repair strategy.

Long-term phytomanagement with compost and a sunflower - Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil

At a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery.