Structural development and assembly patterns of the root-associated microbiomes during phytoremediation

Effects of sertraline hydrochloride with As(III) or Cd on rhizosphere micro-environment and root endophytes in rice

This study investigated the effects of the antidepressant sertraline hydrochloride (Ser-HCI) on rice physiology when combined with arsenic (III) or cadmium. Hydroponic experiments revealed that combined lower concentrations (0.2 and 0.6 mg L-1) of Ser-HCl and As (III) or Cd increased rice biomass and reduced pH and low molecular weight organic acids. The fluorescence intensity was enhanced with Ser-HCl and As-only treatments, with a significant difference (p < 0.05) in the dissolved organic matter index. There was a decrease in endophyte-specific operational taxonomic units, with proteobacteria dominating the rice root endophytes. The addition of Ser-HCl resulted in the Verrucomicrobiota increasing by 6.4 times, which was positively correlated with malic acid and negatively correlated with pH. Functional annotation highlighted alterations in carbohydrate metabolism pathways. This study provides insights into the interactive effects of Ser-HCl on rice when combined with As (III) or Cd, addressing gaps in our understanding of the impact of antidepressants on plant systems.

Distinct planting patterns exert legacy effects on the networks and assembly of root-associated microbiomes in subsequent crops

Soil legacy effects from previous crops can significantly influence plant-soil interactions in crop rotations. However, the microbial mechanism underlying this effect in subsequent root-associated compartments remains unclear. We investigated the effects of planting patterns (four-year continuous maize [MM], three-year winter wheat and one-year maize rotation [WM], and three-year potato and one-year maize rotation [PM]) on the microbial composition and structure of root-associated compartments, the effect of distinct crops on subsequent microbial co-occurrence patterns, and the assembly mechanism by which the root-associated compartments (bulk soil, rhizosphere, and roots) in subsequent crops regulate the microbiome habitat. Compared with MM, the relative abundance of Acidobacteria in WM was 29.7 % lower, whereas that of Bacteroidota in PM was 37.9 % higher in all three compartments. The co-occurrence patterns of the microbial communities exhibited varied responses to different planting patterns. Indicator taxon analysis revealed less shared and specific species in the root bacterial and fungal networks. The planting pattern elicited specific responses from modules within bacterial and fungal co-occurrence networks in all three compartments. Moreover, the planting patterns and root-associated compartments collectively drove the assembly process of root-associated microorganisms. The neutral model showed that, compared with MM, the stochasticity of bacterial assembly decreased under WM and PM but increased for fungal assembly. WM and PM increased the relative effects of the homogenized dispersal of fungal assemblies in roots. We conclude that previous crops exhibit marked legacy effects in the root-associated microbiome. Therefore, soil heritage should not be ignored when discussing microbiome recruitment strategies and co-occurrence patterns in subsequent crops.

Pollution pressure drives microbial assemblages that improve the phytoremediation potential of heavy metals by Ricinus communis

Due to the rapid expansion of industrial activity, soil pollution has intensified. Plants growing in these polluted areas have developed a rhizobiome uniquely and specially adapted to thrive in such environments. However, it remains uncertain whether pollution acts as a sufficiently selective force to shape the rhizobiome, and whether these adaptations endure over time, potentially aiding in long-term phytoremediation. Therefore, in the present study, we aimed to compare whether the microbiome associated with roots from plants germinated in polluted riverbanks will improve the phytoremediation of Cd and Pb under mesocosm experiments compared with plants germinating in a greenhouse. The experimental design was a factorial 2 × 2, i.e., the origin of the plant and the presence or absence of 100 mg/L of Cd and 1000 mg/L of Pb. Our results showed that plants germinated in polluted riverbanks have the capacity to accumulate twice the amount of Pb and Cd during mesocosm experiments. The metagenomic analysis showed that plants from the river exposed to heavy metals at the end of mesocosm experiments were rich in Rhizobium sp. AC44/96 and Enterobacter sp. EA-1, Enterobacter soli, Pantoea rwandensis, Pantoea endophytica. In addition, those plants were uniquely associated with Rhizobium grahamii, which likely contributed to the differences in the levels of phytoremediation achieved. Furthermore, the functional analysis revealed an augmented functional potential related to hormones, metallothioneins, dismutases, and reductases; meanwhile, the plants germinated in the greenhouse showed an unspecific strategy to exceed heavy metal stress. In conclusion, pollution pressure drives stable microbial assemblages, which could be used in future phytostabilization and phytoremediation experiments.

A meta-analysis on crop growth and heavy metals accumulation with PGPB inoculation in contaminated soils

Plant growth-promoting bacteria (PGPB) offer a promising solution for mitigating heavy metals (HMs) stress in crops, yet the mechanisms underlying the way they operate in the soil-plant system are not fully understood. We therefore conducted a meta-analysis with 2037 observations to quantitatively evaluate the effects and determinants of PGPB inoculation on crop growth and HMs accumulation in contaminated soils. We found that inoculation increased shoot and root biomass of all five crops (rice, maize, wheat, soybean, and sorghum) and decreased metal accumulation in rice and wheat shoots together with wheat roots. Key factors driving inoculation efficiency included soil organic matter (SOM) and the addition of exogenous fertilizers (N, P, and K). The phylum Proteobacteria was identified as the keystone taxa in effectively alleviating HMs stress in crops. More antioxidant enzyme activity, photosynthetic pigment, and nutrient absorption were induced by it. Overall, using PGPB inoculation improved the growth performance of all five crops, significantly increasing crop biomass in shoots, roots, and grains by 33 %, 35 %, and 20 %, respectively, while concurrently significantly decreasing heavy metal accumulation by 16 %, 9 %, and 37 %, respectively. These results are vital to grasping the benefits of PGPB and its future application in enhancing crop resistance to HMs.

Bacteria associated with Comamonadaceae are key arsenite oxidizer associated with Pteris vittata root

Pteris vittata (P. vittata), an arsenic (As) hyperaccumulator commonly used in the phytoremediation of As-contaminated soils, contains root-associated bacteria (RAB) including those that colonize the root rhizosphere and endosphere, which can adapt to As contamination and improve plant health. As(III)-oxidizing RAB can convert the more toxic arsenite (As(III)) to less toxic arsenate (As(V)) under As-rich conditions, which may promote plant survial. Previous studies have shown that microbial As(III) oxidation occurs in the rhizospheres and endospheres of P. vittata. However, knowledge of RAB of P. vittata responsible for As(III) oxidation remained limited. In this study, members of the Comamonadaceae family were identified as putative As(III) oxidizers, and the core microbiome associated with P. vittata roots using DNA-stable isotope probing (SIP), amplicon sequencing and metagenomic analysis. Metagenomic binning revealed that metagenome assembled genomes (MAGs) associated with Comamonadaceae contained several functional genes related to carbon fixation, arsenic resistance, plant growth promotion and bacterial colonization. As(III) oxidation and plant growth promotion may be key features of RAB in promoting P. vittata growth. These results extend the current knowledge of the diversity of As(III)-oxidizing RAB and provide new insights into improving the efficiency of arsenic phytoremediation.

The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.

Plant Growth-Promoting Bacteria Influence Microbial Community Composition and Metabolic Function to Enhance the Efficiency of Hybrid pennisetum Remediation in Cadmium-Contaminated Soil

The green and efficient remediation of soil cadmium (Cd) is an urgent task, and plant-microbial joint remediation has become a research hotspot due to its advantages. High-throughput sequencing and metabolomics have technical advantages in analyzing the microbiological mechanism of plant growth-promoting bacteria in improving phytoremediation of soil heavy metal pollution. In this experiment, a pot trial was conducted to investigate the effects of inoculating the plant growth-promoting bacterium Enterobacter sp. VY on the growth and Cd remediation efficiency of the energy plant Hybrid pennisetum. The test strain VY-1 was analyzed using high-throughput sequencing and metabolomics to assess its effects on microbial community composition and metabolic function. The results demonstrated that Enterobacter sp. VY-1 effectively mitigated Cd stress on Hybrid pennisetum, resulting in increased plant biomass, Cd accumulation, and translocation factor, thereby enhancing phytoremediation efficiency. Analysis of soil physical-chemical properties revealed that strain VY-1 could increase soil total nitrogen, total phosphorus, available phosphorus, and available potassium content. Principal coordinate analysis (PCoA) indicated that strain VY-1 significantly influenced bacterial community composition, with Proteobacteria, Firmicutes, Chloroflexi, among others, being the main differential taxa. Redundancy analysis (RDA) revealed that available phosphorus, available potassium, and pH were the primary factors affecting bacterial communities. Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated that strain VY-1 modulated the metabolite profile of Hybrid pennisetum rhizosphere soil, with 27 differential metabolites showing significant differences, including 19 up-regulated and eight down-regulated expressions. These differentially expressed metabolites were primarily involved in metabolism and environmental information processing, encompassing pathways such as glutamine and glutamate metabolism, α-linolenic acid metabolism, pyrimidine metabolism, and purine metabolism. This study utilized 16S rRNA high-throughput sequencing and metabolomics technology to investigate the impact of the plant growth-promoting bacterium Enterobacter sp. VY-1 on the growth and Cd enrichment of Hybrid pennisetum, providing insights into the regulatory role of plant growth-promoting bacteria in microbial community structure and metabolic function, thereby improving the microbiological mechanisms of phytoremediation.

Effects of sulfur nanoparticles on rhizosphere microbial community changes in oilseed rape plantation soil under mercury stress

In the present study, experiments were conducted to assess the influence of nanoscale sulfur in the microbial community structure of metallophytes in Hg-contaminated rhizosphere soil for planting rapeseed. The results showed that the richness and diversity of the rhizobacteria community decreased significantly under Hg stress, but increased slightly after SNPs addition, with a reduction in the loss of Hg-sensitive microorganisms. Moreover, all changes in the relative abundances of the top ten phyla influenced by Hg treatment were reverted when subjected to Hg + SNPs treatment, except for Myxococcota and Bacteroidota. Similarly, the top five genera, whose relative abundance decreased the most under Hg alone compared to CK, increased by 19.05%-54.66% under Hg + SNPs treatment compared with Hg alone. Furthermore, the relative abundance of Sphingomonas, as one of the dominant genera for both CK and Hg + SNPs treatment, was actively correlated with plant growth. Rhizobacteria, like Pedobacter and Massilia, were significantly decreased under Hg + SNPs and were positively linked to Hg accumulation in plants. This study suggested that SNPs could create a healthier soil microecological environment by reversing the effect of Hg on the relative abundance of microorganisms, thereby assisting microorganisms to remediate heavy metal-contaminated soil and reduce the stress of heavy metals on plants.

Biogenic manganese oxides promote metal(loid) remediation by shaping microbial communities in biological aqua crust

Biological aqua crust (biogenic aqua crust-BAC) is a potentially sustainable solution for metal(loid) bioremediation in global water using solar energy. However, the key geochemical factors and underlying mechanisms shaping microbial communities in BAC remain poorly understood. The current study aimed at determining the in situ metal(loid) distribution and the key geochemical factors related to microbial community structure and metal(loid)-related genes in BAC of a representative Pb/Zn tailing pond. Here we showed that abundant metal(loid)s (e.g. Pb, As) were co-distributed with Mn/Fe-rich minerals (e.g. biogenic Mn oxide, FeOOH) in BAC. Biogenic Mn oxide (i.e. Mn) was the most dominant factor in shaping microbial community structure in BAC and source tailings. Along with the fact that keystone species (e.g. Burkholderiales, Haliscomenobacter) have the potential to promote Mn ion oxidization and particle agglomeration, as well as Mn is highly associated with metal(loid)-related genes, especially genes related to As redox (e.g. arsC, aoxA), and Cd transport (e.g. zipB), biogenic Mn oxides thus effectively enhance metal(loid) remediation by accelerating the formation of organo-mineral aggregates in biofilm-rich BAC system. Our study indicated that biogenic Mn oxides may play essential roles in facilitating in situ metal(loid) bioremediation in BAC of mine drainage.

Elevated CO2 and nitrogen addition enhance the symbiosis and functions of rhizosphere microorganisms under cadmium exposure

Soil microbes are fundamental to ecosystem health and productivity. How soil microbial communities are influenced by elevated atmospheric carbon dioxide (eCO2) concentration and nitrogen (N) deposition under heavy metal pollution remains uncertain, despite global exposure of terrestrial ecosystems to eCO2, high N deposition and heavy metal stress. Here, we conducted a four year's open-top chamber experiment to assess the effects of soil cadmium (Cd) treatment (10 kg hm-2 year-1) alone and combined treatments of Cd with eCO2 concentration (700 ppm) and/or N addition (100 kg hm-2 year-1) on tree growth and rhizosphere microbial community. Relative to Cd treatment alone, eCO2 concentration in Cd contaminated soil increased the complexity of microbial networks, including the number links, average degree and positive/negative ratios. The combined effect of eCO2 and N addition in Cd contaminated soil not only increased the complexity of microbial networks, but also enhanced the abundance of microbial urealysis related UreC and nitrifying related amoA1 and amoA2, and the richness of arbuscular mycorrhiza fungi (AMF), thereby improving the symbiotic functions between microorganisms and plants. Results from correlation analysis and structural equation model (SEM) further demonstrated that eCO2 concentration and N addition acted on functions and networks differently. Elevated CO2 positively regulated microbial networks and functions through phosphorus (P) and Cd concentration in roots, while N addition affected microbial functions through soil available N and soil organic carbon (SOC) concentration and microbial network through soil Cd concentration. Overall, our findings highlight that eCO2 concentration and N addition make microbial communities towards ecosystem health that may mitigate Cd stress, and provide new insights into the microbiology supporting phytoremediation for Cd contaminated sites in current and future global change scenarios.

Bacterial seed endophyte and abiotic factors influence cadmium accumulation in rice (Oryza sativa) along the Yangtze River area

Cadmium (Cd) contamination in rice (Oryza sativa) is particularly problematic due to its high risk to human health. Investigating the hidden roles of seed endophytes of rice in influencing Cd accumulation is essential to comprehensively understand the effects of biotic and abiotic factors to food security. Here, the content of Cd in soils and rice (Huanghuazhan) seeds from 19 sites along the Yangtze River exhibited considerable differences. From a biotic perspective, we observed the dominant endophytic bacteria, Stenotrophomonas (7.25 %), contribute to Cd control of rice (below 0.2 mg kg-1). Partial Least Squares (PLS) analysis further suggested that Enterobacteriaceae (15.48 %), altitude and pH were found to be the strong variables that might reduce the Cd uptake of rice. In contrast, Cytophagaceae (0.58 %), latitude and mean annual air pressure had the opposite effect. In pot experiments, after respectively inoculating the isolated endophytic bacteria Stenotrophomonas T4 and Enterobacter R1, N1 (f_Enterobacteriaceae), the Cd contents in shoot decreased by 47.6 %, 21.9 % and 33.0 % compared to controls. The distribution of Cd resistant genes (e.g., czcABC, nccAB, cznA) of Stenotrophomonas, Enterobacteriaceaea and Cytophagaceae further suggested their distinct manners in influencing the Cd uptake of rice. Overall, this study provides new insights into the food security threatened by globally widespread Cd pollution.

Removal, fate, and bioavailability of fluoroquinolone antibiotics in a phytoremediation system with four wetland plants: Combing dynamic DGT and traditional methods

Phytoremediation is considered an effective technology for remediating antibiotic-contaminated water; however, its underlying mechanisms remain poorly understood. Therefore, this study investigated the phytoremediation potential of fluoroquinolone antibiotics (FQs) by different wetland plant species. The phytoremediation rates of ΣFQs were 46-69 %, and rhizosphere microorganism degradation (accounting for 90-93 %) dominated the FQ removal over that of plant uptake and hydrolysis. Dissipation of the FQs in the hydroponic system followed a first-order kinetic model. The joint action of the more powerful absorptive capacity of plants and stronger microbial degradation ability in the rhizosphere was the reason that Cyperus papyrus showed significantly higher FQ phytoremediation rates than the other three plant species, which implied that the plant species is a critical factor affecting phytoremediation efficiency. The FQ distribution in plant tissues decreased from root > stem > leaf, suggesting that FQs were more concentrated in the roots than in the aboveground tissues. Negative correlations between the diffusive gradient in thin films and root concentrations implied that these wetland plant species took up FQs mainly via active transport mechanism (requiring some vectors, perhaps via exudates); whereas, the process of root-to-stem transfer and upward transport represented passive transport, which mainly depended on transpiration. These results facilitate an improved understanding of phytoremediation processes and improve their future applications.

Field-scale differences in rhizosphere micro-characteristics of Cichorium intybus, Ixeris polycephala, sunflower, and Sedum alfredii in the phytoremediation of Cd-contaminated soil

Understanding the intricate interplay between Cd accumulation in plants and their rhizosphere micro-characteristics is important for the selection of plant species with profitable Cd phytoextraction and soil remediation efficiencies. This study investigated the differences in rhizosphere micro-ecological characteristics and Cd accumulation in chicory, Ixeris polycephala, sunflower, and Sedum alfredii in low-moderate Cd-contaminated soil. Data reveal that the dominant organic acids in rhizosphere soil that responded to Cd were oxalic and lactic acids in chicory and Ixeris polycephala, tartaric acid in sunflower, and succinic acid in Sedum alfredii. These unique organic acids could also influence the abundance of specific rhizobacterial communities in rhizosphere soil that were Sphingomonadaceae and Bradyrhizobiaceae in both Sedum alfredii (9.75 % and 2.56 %, respectively) and chicory (8.98 % and 2.82 %, respectively) rhizosphere soil, Xanthomonadaceae in both Sedum alfredii and Ixeris polycephala rhizosphere soil, and Gaiellaceae in chicory rhizosphere soil. In this case, the combined effects of the organic acids and unique rhizobacterial communities by plant species increased the bioavailable concentration of Cd in Sedum alfredii, Ixeris polycephala, and sunflower rhizosphere soil, while decreasing the Cd-DOM concentrations in chicory rhizosphere soil and the water-extractable Cd reduced by 88.02 % compared to the control. Though the capacity for Cd accumulation in the shoots of chicory was weaker than of Sedum alfredii but better than either Ixeris polycephala or sunflower, chicory presented better Cd translocation and harbored Cd mainly as the low toxic chemical form of pectates and proteins-bound Cd and Cd oxalate in its shoot. Generally, chicory, as an economic plant, is suitable for phytoremediation of low-moderate Cd-contaminated soil after Sedum alfredii.

Piriformospora indica alter root-associated microbiome structure to enhance Artemisia annua L. tolerance to arsenic

Microorganisms in the rhizosphere are crucial allies for plant stress tolerance. Recent research suggests that by interacting with the rhizosphere microbiome, microorganisms can aid in the revegetation of soils contaminated with heavy metal(loid)s (HMs). However, it is unknown that how Piriformospora indica influences the rhizosphere microbiome to mitigate arsenic-toxicity in arsenic-enriched environments. Artemisia annua plants were grown in the presence or absence of P. indica and spiked with low (50) and high (150 µmol/L) concentrations of arsenic (As). After inoculation with P. indica, fresh weight increased by 37.7% and 10% in control and high concentration treated plants, respectively. Transmission electron microscopy showed that cellular organelles were severely damaged by As and even disappeared under high concentration. Furthermore, As was mostly accumulated by 5.9 and 18.1 mg/kg dry weight in the roots of inoculated plants treated with low and high concentrations of As, respectively. Additionally, 16 S and ITS rRNA gene sequencing were applied to analyze the rhizosphere microbial community structure of A. annua under different treatments. A significant difference was observed in microbial community structure under different treatments as revealed by non-metric multidimensional scaling ordination. The bacterial and fungal richness and diversity in the rhizosphere of inoculated plants were actively balanced and regulated by P. indica co-cultivation. Lysobacter and Steroidobacter were found to be the As-resistant bacterial genera. We conclude that P. indica inoculation could alter rhizosphere microecology, thereby mitigating As-toxicity without harming the environment.

Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site

Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.

Microbial community assembly of the hyperaccumulator plant Sedum plumbizincicola in two contrasting soil types with three levels of cadmium contamination

Microbial communities are closely related to plant performance and numerous studies have shown their involvement with the growth and development of host plants, resistance to pathogen invasion and adaptation to environmental stress. Here we described in detail the ecological process of the microbial community assembly in hyperaccumulator plant Sedum plumbizincicola. We divided the microbiota into four ecological compartments (bulk soil, rhizosphere, root endosphere and aboveground endosphere). The results showed that host selection strongly controlled the aggregation of microbial community. So that microbes occupied different niches from the bulk soil to the aboveground endosphere, and bacterial diversity and network complexity decreased gradually. Soil types were the second influencing factor, especially for the microbial community in the root endosphere. The SourceTracker analysis further confirmed the vertical migration of microbes from bulk soil to aboveground endosphere. In addition, under the condition of heavy metal pollution, the microbial community of S. plumbizincicola tended to form a microbial pool dominated by Proteobacteria and Actinobacteria. Ellin6067, Sphingomonas, Ralstonia, SC-I-84_uncultured bacterium, Burkholderiaceae_Undibacterium and Pedosphaeraceae_uncultured bacterium etc. were identified as the vital biomarker taxa. Among these genera, the relative abundance of last three was significantly positively correlated with the activation and transfer of cadmium, and they mainly enriched in paddy soil. This study provides evidence for the mechanism by which the microbial community assembly occurs and experience for regulating the microbial community and increasing the accumulation efficiency of potentially toxic metals in S. plumbizincicola.

Exopolysaccharide-producing bacteria enhanced Pb immobilization and influenced the microbiome composition in rhizosphere soil of pakchoi (Brassica chinensis L.)

Lead (Pb) contamination of planting soils is increasingly serious, leading to harmful effects on soil microflora and food safety. Exopolysaccharides (EPSs) are carbohydrate polymers produced and secreted by microorganisms, which are efficient biosorbent materials and has been widely used in wastewater treatment to remove heavy metals. However, the effects and underlying mechanism of EPS-producing marine bacteria on soil metal immobilization, plant growth and health remain unclear. The potential of Pseudoalteromonas agarivorans Hao 2018, a high EPS-producing marine bacterium, to produce EPS in soil filtrate, immobilize Pb, and inhibit its uptake by pakchoi (Brassica chinensis L.) was studied in this work. The effects of strain Hao 2018 on the biomass, quality, and rhizospheric soil bacterial community of pakchoi in Pb-contaminated soil were further investigated. The results showed that Hao 2018 reduced the Pb concentration in soil filtrate (16%–75%), and its EPS production increased in the presence of Pb2+. When compared to the control, Hao 2018 remarkably enhanced pakchoi biomass (10.3%–14.3%), decreased Pb content in edible tissues (14.5%–39.2%) and roots (41.3%–41.9%), and reduced the available Pb content (34.8%–38.1%) in the Pb-contaminated soil. Inoculation with Hao 2018 raised the pH of the soil, the activity of several enzymes (alkaline phosphatase, urease, and dehydrogenase), the nitrogen content (NH4+-N and NO3−-N), and the pakchoi quality (Vc and soluble protein content), while also raising the relative abundance of bacteria that promote plant growth and immobilize metals, such as Streptomyces and Sphingomonas. In conclusion, Hao 2018 reduced the available Pb in soil and pakchoi Pb absorption by increasing the pH and activity of multiple enzymes and regulating microbiome composition in rhizospheric soil.

Sustainability of phytoremediation: Post-harvest stratagems and economic opportunities for the produced metals contaminated biomass

Heavy metals (HMs) are indestructible and non-biodegradable. Phytoremediation presents an opportunity to transfer HMs from environmental matrices into plants, making it easy to translocate from one place to another. The ornate features of HMs' phytoremediation are biophilia and carbon neutrality, compared to the physical and chemical remediation methods. Some recent studies related to LCA also support that phytoremediation is technically more sustainable than competing technologies. However, one major post-application challenge associated with HMs phytoremediation is properly managing HMs contaminated biomass generated. Such a yield presents the problem of reintroducing HMs into the environment due to natural decomposition and release of plant sap from the harvested biomass. The transportation of high yields can also make phytoremediation economically inviable. This review presents the design of a sustainable phytoremediation strategy using an ever-evolving life cycle assessment tool. This review also discusses possible post-phytoremediation biomass management strategies for the HMs contaminated biomass management. These strategies include composting, leachate compaction, gasification, pyrolysis, torrefaction, and metal recovery. Further, the commercial outlook for properly utilizing HMs contaminated biomass was presented.

Effects of microbial agents on cadmium uptake in Solanum nigrum L. and rhizosphere microbial communities in cadmium-contaminated soil

Solanum nigrum L. (S. nigrum) and microbial agents are often used for the remediation of cadmium (Cd)-contaminated soil; however, no studies to date have examined the efficacy of using various microbial agents for enhancing the remediation efficiency of Cd-contaminated soil by S. nigrum. Here, we conducted greenhouse pot experiments to evaluate the efficacy of applying Bacillus megaterium (BM) along with citric acid (BM + CA), Glomus mosseae (BM + GM), and Piriformospora indica (BM + PI) on the ability of S. nigrum to remediate Cd-contaminated soil. The results showed that BM + GM significantly increased the Cd accumulation of each pot of S. nigrum by 104% compared with the control. Application of microbial agents changed the soil microbial communities. Redundancy analysis showed that the activities of Catalase (CAT) and urease (UE), soil organic matter, available N and total Cd were the main influencing factors. By constructing the microbial co-occurrence networks, the soil microbe was divided into four main Modules. BM + GM and BM + PI significantly increased the relative abundance of Module#1 and Module#3, respectively, when compared with the control. Additionally, Module#1 showed a significant positive correlation with translocation factor (TF), which could be regarded as the key microbial taxa. Further research found that Ascomycota, Glomeromycota, Proteobacteria, and Actinobacteria within Module#1 were also significantly correlated with TF, and these key species enriched in BM + GM. Overall, our findings indicate that the BM + GM treatment was the most effective for the remediation of Cd pollution. This treatment method may further affect the rhizosphere microbial community by affecting soil indicators, which might drive the formation of Module#1, thus greatly enhancing the Cd remediation capacity of S. nigrum.

New methodology for assessing the environmental efficiency of transport: Application to the valorization of biomass from phytoremediation

It is known that any environmental remediation process must be approached as a system and that the transport of materials is key to determining its sustainability. The aim of this work is to establish how far it was possible to transport plant material from a phytoextraction process in such a way that the environmental gain of the remediation process is not compromised. In the absence of a general methodology to answer our question, a new methodology based on spatial analysis and the life cycle perspective is proposed to calculate, under different hypotheses and depending on the type of remediation, the maximum distance that a lorry can travel, taking as a limit the distance in which the environmental benefit would be equal to 0. The results obtained show that there are significant differences depending on the type of optimisation proposed for the transport route as well as the type of valorization of the plant material to be carried out. Thus, in the case of bioethanol, biomass could be transported up to 25 km. For biodiesel, it can be shipped over distances between 255 and 415 km and finally, if it is valorized by anaerobic co-digestion, biodigesters up to 267 km away could be sought for the most favourable case.

PPCPs and heavy metals from hydrothermal sewage sludge-derived biochar: migration in wheat and physiological response

Once the sludge was directly used in the farmland, it will have a negative impact on human health through the food chain because sludge contains pollutants. Sewage sludge pyrolysis into biochar is an effective way to realize sludge harmless and resourceful utilization. This research used hydrothermal carbonization method to convert sludge into sludge biochar (SLBC) to reduce the types and contents of pharmaceuticals and personal care products (PPCPs) and available heavy metals. Furthermore, migration of the residual caffeine (Caf), acetaminophen (Ace), and heavy metals (Cr, Pb, Cu, Zn) released from the SLBC in the wheat was assessed. The results showed that the levels of Caf, Ace, Pb, Cu, and Zn accumulated in the shoots were lower than the limit regulated by Drug and Food Additive Use Standard in China (Caf: 150 mg/kg; Ace: 2.5 ~ 5 mg/kg; Pb: 0.3 mg/kg; Cu: 10 mg/kg; Zn: 20 mg/kg). The migration of Cr from roots to shoots was also significantly controlled by SBLC. SBLC delayed the germination time of wheat seeds with increasing in hydrothermal temperature, the germination rate and root length showed a decreasing trend. Evans blue and O₂^- fluorescence staining of root tips also confirmed this conclusion. When the wheat was exposed to the low temperature and dose of SLBC, the chlorophyll contents and growth of wheat can be significantly increased; the oxidative damage of cell plasma membrane and net photosynthetic rate were reduced. However, 0.8 g/L of SLBC made plants suffer abiotic stress and caused oxidative damage to plants, and decreased membrane system stability. The study provides some parameters for sludge to realize resource utilization in the agricultural system.

Diversity, function and assembly of the Trifolium repens L. root-associated microbiome under lead stress

Root-associated microbial layers provide unique niches that drive specific microbe assemblies. While the rhizosphere microbiome has long received much attention, endophytic microbes remain largely elusive. Characterizing metal-tolerant plants' strategies for assembling different root-associated microbial layers is important for optimizing phytoremediation. Here, a pre-stratified rhizo-box assay was conducted with Trifolium repens L. under greenhouse conditions with artificial Pb-contaminated soil. Cultivation compensated for the pollution-driven loss of soil microbial biomass carbon, enzyme activities and abundance. The acid-soluble Pb proportion increased in the rhizosphere (from 6.5-13.7% to 7.1-18.0%) compared with bulk soil. Under stress, root-layer variants were a considerable source of variation in the microbiome, with the endosphere representing a unique and independent niche. A core set of root microbes were selected by T. repens, with Proteobacteria and Actinobacteria composed of diverse plant-growth-promoting bacteria (PGPBs) and metal-tolerant members. Cluster analysis revealed endosphere-enriched genera, with Rhizobium, Nocardioides, Novosphingobium, Phyllobacterium, and Sphingomonas being the most dominant. Finally, inferred microbial metabolic pathways suggested that these potential metal-tolerant PGPB species provide critical services to hosts, enabling them to tolerate and even flourish in contaminated soil. Our results provide novel insights for understanding how root-associated microbes help metal-tolerant plants cope with abiotic stress.

Endophyte colonization enhanced cadmium phytoremediation by improving endosphere and rhizosphere microecology characteristics

This study investigated the phytoremediation efficiency of Cd-contaminated soils by hyperaccumulator P. acinosa and its endophyte B. cereus, and evaluated the variation of rhizosphere/endosphere microecology characteristics. The result showed that endophyte PE31, which could successfully colonize on P. acinosa root, increased plant Cd uptake by 42.90% and 28.85% in low and high Cd contaminated soils by promotion of plant biomass and Cd concentration in plant tissues. The improved phytoremediation may attribute to the endophyte inoculation, which significantly improved the bioavailable heavy metal (HM) percentage, nutrient cycling related enzyme activities and nutrient contents including available potassium, phosphorus and organic matter. Additionally, the relative abundance beneficial bacteria Bacillus (significantly increased by 81.23% and 34.03% in the endosphere, and by 4.86% and 8.54% in rhizosphere in low and high Cd contaminated soils) and Lysobacter, showed positive and close correlation with plant growth and HM accumulation. These results indicated that endophyte inoculation could reshape rhizosphere and endosphere microecology characteristics, which enhanced the potential for phytoremediation of Cd contaminated soils.

Combined Phenanthrene and Copper Pollution Imposed a Selective Pressure on the Rice Root-Associated Microbiome

Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated microbes under flooding conditions remains poorly understood. In this study, greenhouse experiments were conducted to investigate the individual and combined effects of phenanthrene (PHE) and copper (Cu) on rice uptake and root-associated microbial coping strategies. The results showed that more than 90% of phenanthrene was degraded, while the existence of Cu significantly reduced the dissipation of PHE in the rhizosphere, and the coexistence of phenanthrene and copper promoted their respective accumulation in plant roots. Copper played a dominant role in the interaction between these two chemicals. Microbes that can tolerate heavy metals and degrade PAHs, e.g., Herbaspirillum, Sphingobacteriales, and Saccharimonadales, were enriched in the contaminated soils. Additionally, microbes associated with redox processes reacted differently under polluted treatments. Fe reducers increased in Cu-treated soils, while sulfate reducers and methanogens were considerably inhibited under polluted treatments. In total, our results uncover the combined effect of heavy metals and polycyclic aromatic hydrocarbons on the assemblage of root-associated microbial communities in anaerobic environments and provide useful information for the selection of effective root-associated microbiomes to improve the resistance of common crops in contaminated sites.

Effects of copper oxide nanoparticles on Salix growth, soil enzyme activity and microbial community composition in a wetland mesocosm

A model wetland with Salix was established to investigate the effects of CuO nanoparticles (NPs; the equivalent amount of Cu at 0, 100 and 500 mg/kg) on plant, soil enzyme activity and microbial community. Ionic Cu (100, 500 mg/kg) and bulk-sized CuO particles (BPs, 500 mg/kg) were included as controls. The results suggested the CuO NPs at 500 mg/kg and ionic Cu treatments inhibited the plant growth, while CuO NPs at 100 mg/kg and CuO BPs at 500 mg/kg played a facilitating role. CuO NPs significantly decreased the activities of peroxidase and polyphenol oxidase, while ionic Cu treatments increased peroxidase activity, BPs and ionic Cu (500 mg/kg) increased the polyphenol oxidase activity. Bacterial community richness and diversity were reduced in all Cu treatments; however, CuO NPs and BPs at 500 mg/kg significantly increased the richness and diversity of fungal community.Soil microbial community was significantly altered by Cu types and dose. In comparison with ionic Cu and CuO BPs, CuO NPs uniquely enriched the microbial community and the fungal families.Overall, it demonstrate that both particle size and dose regulate the impact of CuO on wetland ecology, which deepens our understanding on the ecological risks of CuO NPs in freshwater forested wetland.

A field study reveals links between hyperaccumulating Sedum plants-associated bacterial communities and Cd/Zn uptake and translocation

Hyperaccumulating ecotypes of Sedum plants are promising Cd/Zn phytoextractors, with potential for leveraging its rhizospheric or endophytic microbiomes to improve phytoremediation efficiency. However, research of bacteria associated with Sedum at field scale is still lacking. Here, we presented a detailed investigation of the bacterial microbiome of hyperaccumulating Sedum ecotypes (S. alfredii and S. plumbizincicola) and a non-hyperaccumulating S. alfredii ecotype, which grow at different soil environments. Moreover, we evaluated the heavy metal uptake and translocation potential of Sedum plants at different locations. The results showed that both HE ecotypes, contrary to the NHE, were efficient for phytoremediation in mine areas and farmlands. For NHE plants, rhizosphere co-occurrence networks were more complex than the networks of other compartments, while networks of HE plants were more complex in bulk soil and roots. The proportion of positive correlations within co-occurrence networks was higher for the HE plants, suggesting a greater potential for mutualistic interactions. Plant compartment and location predominantly shaped the microbiome assembly, and Proteobacteria, Actinobacteria and Acidobacteria dominated the bacterial communities of Sedum plants. Keystone taxa related to Zn hyperaccumulation are similar to those related to Cd hyperaccumulation, and nine bacterial genera had significantly positive correlation with Cd/Zn hyperaccumulation. Taxa, linked to phytoremediation in both mine and farmland (i.e. Actinospica and Streptomyces from Actinobacteria), could be targets for further investigation of their ability to promote metal phytoremediation of Sedum species.

Sustainable remediation of hazardous environmental pollutants using biochar-based nanohybrid materials

Biochar is a well-known carbon material with diversified functionalities and excellent physicochemical characteristics with high wastewater treatment potential. This review aims to summarize recent advancements in the development of biochar and biochar-based nanohybrid materials as a potential tool for the removal of harmful organic compounds such as synthetic dyes/effluents. The formation of biochar using pyrolysis of renewable feedstocks and their applications in various industries are explained hereafter. The characteristics and construction of biochar-based hybrid materials are explained in detail. Diversity of feedstocks, including municipal wastes, industrial byproducts, agricultural, and forestry residues, endows different biochar types with a wide structural variety. The production of cost-effective biochar drives the interest in manipulating biochars and induces desire functionality using nanoscale reinforcements. Various types of biochars, such as magnetic biochar, layered nanomaterial coated biochar, nanometallic oxide composites, chemically and physically functionalized biochar, have been produced. With the aid of nanomaterial, hybrid biochar exhibits a high potential to remove toxic contaminants. Depending upon biochar type, dyes/effluents can be removed via different mechanisms, including the Fenton process, photocatalytic degradation, π-π interaction, electrostatic interaction, and physical adsorption. In conclusion, desired physicochemical features, and tunable surface properties of biochar present high potential material in removing organic dyes and other effluents. The blended biochar with different materials/nanomaterials endows broader development and multi-functional opportunities for treating dyes/effluents.

Soil microbial community and association network shift induced by several tall fescue cultivars during the phytoremediation of a petroleum hydrocarbon-contaminated soil

Biodegradation of soil contaminants may be promoted near plant roots due to the "rhizosphere effect" which may enhance microbial growth and activity. However, the effects of different plant cultivars within a single species on degradation remains unclear. Here, we evaluated the removal of soil total petroleum hydrocarbons (TPHs) by ten different cultivars of tall fescue grass (Festuca arundinacea L.) and their associated rhizosphere microbiomes. TPH removal efficiency across the ten different cultivars was not significantly correlated with plant biomass. Rhizing Star and Greenbrooks cultivars showed the maximum (76.6%) and minimum (62.2%) TPH removal efficiencies, respectively, after 120 days. Significant differences were observed between these two cultivars in the composition of rhizosphere bacterial and fungal communities, especially during the early stages (day 30) of remediation but the differences decreased later (day 90). Putative petroleum-degrading bacterial and fungal guilds were enriched in the presence of tall fescue. Moreover, the complexity of microbial networks declined in treatments with higher TPH removal efficiency. The relative abundances of saprotrophic fungi and putative genes alkB and C12O in bacetria involved in petroleum degradation increased, especially in the presence of Rhizing Star cultivar, and this was consistent with the TPH removal efficiency results. These results indicate the potential of tall fescue grass cultivars and their associated rhizosphere microbiomes to phytoremediate petroleum hydrocarbon-contaminated soils.

A review of root exudates and rhizosphere microbiome for crop production

Increasing crop yields and ensuring food security is a major global challenge. In order to increase crop production, chemical fertilizers and pesticides are excessively used. However, the significance of root exudates is understudied. Beneficial interactions between plant and rhizosphere microbiome are critical for plant fitness and health. In this review, we discuss the application and progress of current research methods and technologies in terms of root exudates and rhizosphere microbiome. We summarize how root exudates promote plant access to nitrogen, phosphorus, and iron, and how root exudates strengthen plant immunity to cope with biotic stress by regulating the rhizosphere microbiome, and thereby reducing dependence on fertilizers and pesticides. Optimizing these interactions to increase plant nutrient uptake and resistance to biotic stresses offers one of the few untapped opportunities to confront sustainability issues in food security. To overcome the limitations of current research, combination of multi-omics, imaging technology together with synthetic communities has the potential to uncover the interaction mechanisms and to fill the knowledge gap for their applications in agriculture to achieve sustainable development.

Towards sustainable agriculture: rhizosphere microbiome engineering

Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.

The rhizosphere of Salix viminalis plants after a phytostabilization process assisted by biochar, compost, and iron grit: chemical and (micro)-biological analyses

Amendments, such as biochar, compost, and iron grit, used in phytostabilization studies, showed positive effects on soil physico-chemical properties, plant growth, and the microbial community. However, assisted phytostabilization studies do not always focus on the rhizosphere area where soil, plants, and microorganisms are affected by the amendments and plants and microorganisms can also interact with each other. The aims of this study were to evaluate the effects of amendment application on the exudation of organic acids by Salix viminalis plant roots, as well as the effects of amendments and plant development on the soil CHNS contents and the microbial community activity and diversity, assessed by measuring enzyme activities and using Biolog EcoPlates^TM tests and next-generation sequencing analyses. The results of the mesocosm experiment showed that soil C, H, and N contents were increased by amendment application, especially biochar and compost, while the one of S decreased. Enzyme activities, microbial activity, and diversity were also increased by the addition of amendments, except iron grit alone. Finally, the quantity of organic acids exuded by roots were little affected by amendments, which could in part explain the reduced effect of plant development on soil chemical and microbiological parameters. In conclusion, this study showed in particular that biochar and compost were beneficial for the soil CHN contents and the microbial community while affecting poorly Salix viminalis root exudates.

Variations of root-associated bacterial cooccurrence relationships in paddy soils under chlorantraniliprole (CAP) stress

Root-associated microbiomes are beneficial for plant development and health. However, the assembly of root-associated bacterial communities and their feedback under chlorantraniliprole (CAP) stress are unclear. This study investigated the response of root-associated bacterial microbiota to CAP dosage during the two developmental phases of rice. The results showed that CAP application had little effect on the bacterial diversity of bulk and rhizosphere soils, whereas that of the endosphere samples demonstrated a large variability. Moreover, the CAP stress exhibited less influence than the plant compartment and developmental stage contributing to microbiome variation. The core bacterial co-occurrence relationships also changed with the CAP application, especially, in the endosphere of the roots. These results further elucidate the impacts of CAP application on root-associated bacterial communities in intensive agricultural ecosystems and provide new insights for CAP ecological risk assessments.

Assembly strategies of the wheat root-associated microbiome in soils contaminated with phenanthrene and copper

Plants can cope with stressful conditions by indirectly regulating root-associated microbial structures. However, the recruitment strategies of the root-associated microbiome in combined organic and inorganic contaminated soils are not well known, especially for common agricultural crops. In this study, we performed greenhouse experiments to investigate the interactive effects of joint copper (Cu) and phenanthrene (PHE) pollution on wheat growth and microbial detoxication processes. Results show that heavy metals did not affect PHE dissipation in the rhizosphere but significantly enhanced the accumulation of PHE in the endosphere. In contrast, the addition of PHE did not influence the absorption of Cu by wheat roots. Cu was the primary factor affecting the variation of microbial communities in cocontaminated treatments among each rhizocompartment while the interactive effects of combined pollutants were only detected in unplanted bulk soil. Microbes are known to degrade polycyclic aromatic hydrocarbons and tolerant heavy metal stress e.g. Novosphingobium, Sphingomonas, Sphingobium and Pseudomonas enriched in the contaminated treatments. Our results provide an integrated understanding of the synthetic effects of combined pollutants on the root-microbial assemblage process in plant-soil systems and offer useful information on the selection of effective bioremediating root-associated microbes for the application of self-remediation by common crops.

Unravelling metabolism and microbial community of a phytobed co-planted with Typha angustifolia and Ipomoea aquatica for biodegradation of doxylamine from wastewater

Pharmaceutical contaminants in environment induce unexpected effects on ecological systems and human; thus, development of efficient technologies for their removal is immensely necessary. In this study, biodegradation and metabolic fate of a frequently found pharmaceutical contaminant, doxylamine by Typha angustifolia and Ipomoea aquatica was investigated. Microbial community of the plant rhizosphere has been identified to understand the important roles of the functional microbes. The plants reduced 48-80.5 % of doxylamine through hydrolysis/dehydroxylation and carbonylation/decarbonylation. A constructed phytobed co-planted with T. angustifolia and I. aquatica removed 77.3 %, 100 %, 83.67 %, and 61.13 % of chemical oxygen demand, total nitrogen, total phosphorus, and doxylamine respectively from real wastewater. High-throughput sequencing of soil and rhizosphere indicated that the phyla Proteobacteria, Bacteroidetes, Firmicutes, Planctomycetes, Actinobacteria, and Cyanobacteria dominated the microbial communities of the phytobed. Current study has demonstrated the applicability of the developed phytobeds for the treatment of doxylamine from municipal wastewater and provide a comprehensive understanding of its metabolism through plant and its rhizospheric microbial communities.

Burkholderia sp. Y4 inhibits cadmium accumulation in rice by increasing essential nutrient uptake and preferentially absorbing cadmium

Microbial remediation of heavy metal-polluted soil is a commonly used method. Burkholderia sp. Y4, isolated from cadmium (Cd)-contaminated rice rhizosphere soil, was investigated for its direct and indirect effects on Cd accumulation in rice by SEM-EDS, FITR and sequencing analysis of the soil bacterial community. Burkholderia sp. Y4 inoculation reduced Cd accumulation in rice roots, rachises, and grains of the two rice varieties T705 and X24 and increased levels of essential elements, especially Fe and Mn, which competitively inhibited Cd transport through cationic channels. Living Burkholderia sp. Y4 cells, rather than non-living ones, could colonize the surface of rice roots and accumulated more Cd through direct biosorption associated with -CO and -NH/-CO bonds of amino acids and proteins. The results of soil microbial community showed that the colonization of externally added Burkholderia sp. Y4 could be maintained over some time to impact the total rhizospheric environment. Burkholderia sp. Y4 inoculation decreased the abundance of microbes involved in the iron cycle (Acidobacteria) as well as of those mediating the transformation of ammonium nitrogen to nitrate nitrogen (Nitrosomonadaceae and Nitrospira). So Burkholderia sp. Y4 inoculation may indirectly change the availability of micronutrients and Cd in rice rhizosphere soil through iron-nitrogen coupled cycles to increase essential nutrient uptake and inhibit Cd accumulation in rice by preferential Cd-biosorption. Therefore, Burkholderia sp. Y4 is potentially suitable for the bioremediation of Cd-contaminated paddy soil.

The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.

Predominance of soil vs root effect in rhizosphere microbiota reassembly

Rhizosphere community assembly is simultaneously affected by both plants and bulk soils and is vital for plant health. However, it is still unclear how and to what extent disease-suppressive rhizosphere microbiota can be constructed from bulk soil, and the underlying agents involved in the process that render the rhizosphere suppressive against pathogenic microbes remain elusive. In this study, the evolutionary processes of the rhizosphere microbiome were explored based on transplanting plants previously growing in distinct disease-incidence soils to one disease-suppressive soil. Our results showed that distinct rhizoplane bacterial communities were assembled on account of the original bulk soil communities with different disease incidences. Furthermore, the bacterial communities in the transplanted rhizosphere were noticeably influenced by the second disease-suppressive microbial pool, rather than that of original formed rhizoplane microbiota and homogenous nontransplanted rhizosphere microbiome, contributing to a significant decrease in the pathogen population. In addition, Spearman's correlations between relative abundances of bacterial taxa and the abundance of Ralstonia solanacearum indicated Anoxybacillus, Flavobacterium, Permianibacter and Pseudomonas were predicted to be associated with disease-suppressive function formation. Altogether, our results showed that bulk soil played an important role in the process of assembling and reassembling the rhizosphere microbiome of plants.

Crop-dependent root-microbe-soil interactions induce contrasting natural attenuation of organochlorine lindane in soils

Plant-specific root-microbe-soil interactions play an indisputable role in microbial adaptation to environmental stresses. However, the assembly of plant rhizosphere microbiomes and their feedbacks in modification of pollution alleviation under organochlorine stress condition is far less clear. This study examined the response of root-associated bacterial microbiomes to lindane pollution and compared the dissipation of lindane in maize-cultivated dry soils and rice-cultivated flooded soils. Results showed that lindane pollution dramatically altered the microbial structure in the rhizosphere soil of maize but had less influence on the microbial composition in flooded treatments regardless of rice growth, when the reductive dechlorination of lindane was actively coupled with natural redox processes under anaerobic conditions. After 30 days of plant growth, lindane residues dissipated much faster in anaerobic than in aerobic environments, with only 1.08 mg kg^-1 lindane remaining in flooded control compared to 12.79 mg kg^-1 in dry control soils. Compared to the corresponding unplanted control, maize growth significantly increased, but rice growth slightly decreased the dissipation of lindane. Our study suggests that opposite impacts would lead to the self-purification of polluted soils during the growth of xerophytic maize and hygrocolous rice. This was attributed to the contrasting belowground micro-ecological processes regarding protection of root tissues and thereby assembly of rhizosphere microbiomes shaped by the xerophytic and hygrocolous crops under different water managements, in response to lindane pollution.

Effects of endophytes inoculation on rhizosphere and endosphere microecology of Indian mustard (Brassica juncea) grown in vanadium-contaminated soil and its enhancement on phytoremediation

We investigated the effects of endophytes inoculation on ecological factors such as root morphology, rhizosphere soil properties, heavy metal speciation, and rhizosphere and endophytic bacterial communities and their role on phytoremediation. Indian mustards were grown for two months in V-contaminated soil with three treatments (control, inoculation with Serratia PRE01 or Arthrobacter PRE05). Inoculation with PRE01 and PRE05 increased organic matter content by 6.94% and 4.6% respectively and significantly increased bioavailability of heavy metals in rhizosphere soils. Despite the endophyte inocula failed to flourish as stable endophytes, they significantly affected the specific composition and diversity of endophytic bacterial communities in roots, with no significant effect on rhizosphere bacterial communities. The test strains could greatly increase plant growth promotion-related biomarkers in the endosphere, especially those associated with Pseudomonas and Microbacterium genera. PICRUSt analysis predicted high relative abundances of functional genes related to environmental information processing especially in the endophytic microbiota. More biomass production (12.0%-17.4%) and total metals uptake (24.2%-32.0%) were acquired in inoculated treatments. We conclude that endophyte PRE01 or PRE05 inoculation could effectively enhance phytoremediation of V-contaminated soil by improving the rhizosphere and endosphere microecology without causing any ecological damage.

Phytoremediation potential of Miscanthus sinensis for mercury-polluted sites and its impacts on soil microbial community

Phytoremediation potential of Miscanthus sinensis and its impacts on soil microbial community and nutrients were evaluated by pot experiment at soil mercury concentration from 1.48 to 706 mg kg^-1. The changes in biomass yield in dry mass, chlorophyll content, and SOD activity indicated Miscanthus sinensis was tolerant to higher levels of soil mercury exposure, and could grow even if at soil mercury up to 706 mg kg^-1. Mercury bioconcentration and translocation factors were close to or greater than 1 when exposed to soil mercury up to 183 mg kg^-1, demonstrating Miscanthus sinensis a potential phytoremediator for mercury-polluted soils. Miscanthus sinensis planting could significantly improve the diversity and abundance of soil microbial community, but might cause potential loss of soil nitrogen and phosphorus in the early and middle of its growth. In a word, the study indicated Miscanthus sinensis was a promising energy crop linking biofuel production and phytoremediation of mercury-contaminated sites.

Effects of bok choy on the dissipation of dibutyl phthalate (DBP) in mollisol and its possible mechanisms of biochemistry and microorganisms

Phytoremediation is an ecologically sustainable method for remediating contaminated soils, however, research on phytoremediation and its mechanisms are still rarely reported. The highest dibutyl phthalate (DBP) dissipation rate was 91% in 0-3mm bok choy rhizosphere via a 45-day rhizo-box experiment, and bok choy could regulate soil nutrients by increasing soil ammonia nitrogen (AN) and available phosphorus (AP). The biochemistry mechanism of interaction between dissolved organic matter (DOM) and DBP was also elucidated by various spectroscopy techniques. It was found that the alkyl ester in DBP produced the fastest response during the binding process, and the aromatic, hydroxyl and phenolic groups of the DOM humic-like substances preceded amide in DOM protein-like substance. It was found that DBP pollution reduced the Chao1 richness and Shannon index of bacteria in black soil via a pot experiment and high-throughput sequencing, which disturbed the metabolic activities and functional diversity of microorganisms in Mollisol. The microbial abundance increased in bok choy amendments, which has a specific microbial community structure and a high abundance of Actinobacteria and Acidobacteria. We concluded that some enriched genera were responsible for DBP dissipation, Alsobacter, Lacibacter, Myceligenerans, Schrenkiella parvula and Undibacterium. The findings of this study revealed that the possible biochemistry and microbial mechanisms of phytoremediation promoting the DBP dissipation in rhizosphere Mollisol and provided more useful information for phytoremediation of organic pollutants.

Assembly of root-associated microbiomes of typical rice cultivars in response to lindane pollution

Organochlorine pesticides have been extensively used for many years to prevent insect diseases of rice (Oryza sativa L.), but little is known about their residual impacts on the underground micro-ecology in anaerobic environment. In this glasshouse study, we characterized the lindane effects on the assembly of root-associated microbiomes of commonly used indica, japonica and hybrid rice cultivars, and their feedback in turn, in modifying lindane anaerobic dissipation during 60 days' rice production. The results showed that rice growth inhibited the anaerobic dissipation of lindane, but was not affected apparently by lindane at initial spiked concentration of 4.62 and 18.54 mg kg^-1 soil. Suppressed removal of lindane in rice planted treatments as compared with that in unplanted control was likely due to inhibited reductive dechlorination induced by a comprehensive effect of radial O₂ secretion of rice root and co-occurring Fe(III) reduction that consumed electron competitively in rice rhizosphere. However, the hybrid cultivar exhibited a less suppression than the conventional cultivars in high polluted soils. Bacteria was more sensitively responded to lindane pollution than fungal taxa, and Actinobacteria, Chloroflexi, Verrucomicrobia and Proteobacteria were the main different phyla between hybrid and conventional cultivars, with a more stable community structure exhibited in the hybrid rice under lindane stress. Our study highlights the assembly and variation of root-associated microbiomes in responses of lindane pollution, and suggests that hybrid rice cultivar might be most competent for cultivation in paddy fields polluted by lindane and other organochlorine pesticides, especially in the area with high residual levels.

Biochar Induces Changes to Basic Soil Properties and Bacterial Communities of Different Soils to Varying Degrees at 25 mm Rainfall: More Effective on Acidic Soils

Biochar and chemical fertilizer have been widely used in agriculture. Most studies have proved that they not only alter soil nutrient content, but also have an impact on soil microbial communities. However, the effects of biochar and chemical fertilizer application on the overall bacterial community in different soil types under rainfall conditions are not yet understood. We took rainfall as a fixed influencing factor and selected four typical soils of China to investigate the bacterial effects of biochar and chemical fertilizer at 25 mm rainfall, and to identify specific differential bacteria and their functions, and to explore the changes of the bacterial community structure of different soil types. The depth of simulated rainfall was 25 mm each time. Yellow-brown soil, fluvo-aquic soil, lou soil, and black soil were chosen for experiment and each soil was divided into four treatments, included non-biochar and non-fertilizer (CK), fertilizer alone (F), biochar alone (C), and combination of biochar and fertilizer (FC). The results indicated that biochar and fertilizer have a more significant effect on bacterial communities in acidic soils. The amendment of biochar and fertilizer alone or together identified 3 (f_Oxalobacteraceae, f_Solibacteraceae_Subgroup_3, f_Sphingomonadaceae), 5 (f_Chitinophagaceae, f_Comamonadaceae, f_Geobacteraceae, f_norank_o_SC-I-84, f_norank_c_OPB35_soil_group), 1 (f_Blastocatellaceae_Subgroup_4) and 0 differential bacteria in yellow-brown soil, fluvo-aquic soil, lou soil, and black soil by statistical test. In yellow-brown soil, the application of biochar alone increased the relative abundance of potential pathogens within the Sphingomonadaceae and reduced the relative abundance of beneficial bacteria in Solibacteraceae, but the addition of biochar and fertilizer together increased the relative abundance of some beneficial bacteria in Oxalobacteraceae. In fluvo-aquic soil, both biochar, and chemical fertilizers promoted the relative abundance of some beneficial bacteria belonging to Chitinophagaceae, Comamonadaceae, and Geobacteraceae that may be involved in nutrient cycling, degradation of plant residues and increase of metal tolerance. The interactions between acidic soil bacterial communities and measured soil parameters including pH, organic matter were found to be statistically significant. Results from this study revealed that it is necessary to formulate biochar and fertilizer application schemes based on different soil types.

Variation of the Bacterial Community in the Rhizoplane Iron Plaque of the Wetland Plant Typha latifolia

The survival of wetland plants in iron, sulfur and heavy metals-rich mine tailing ponds has been commonly attributed to the iron plaque (IP) on the root surface that acts as a protective barrier. However, the contribution of bacteria potentially regulates the iron-sulfur cycle and heavy metal exclusion at the root surface has not been studied in depth, particularly from a microbial ecology perspective. In this study, a pot experiment using Typha latifolia, a typical wetland plant, in non-polluted soil (NP) and tailing soil (T) was conducted. Samples from four zones, comprising non-rhizosphere soil (NR), rhizosphere soil (R) and internal (I) and external (E) layers of iron plaque, were collected from the NP and T and analyzed by 16S rRNA sequencing. Simpson index of the genus level showed greater diversities of bacterial community in the NP and its I zone is the most important part of the rhizosphere. PICRUSt predicted that the I zones in both NP and T harbored most of the functional genes. Specifically, functional genes related to sulfur relay and metabolism occurred more in the I zone in the T, whereas those related to iron acquisition and carbon and nitrogen circulation occurred more in the I zone in the NP. Analysis of dominant bacterial communities at genus level showed highest abundance of heavy metal resistant genus Burkholderia in the E zones in both soils, indicating that heavy metal resistance of Typha latifolia driven by Burkholderia mainly occurred at the external layer of IP. Moreover, many bacterial genera, such as Acidithiobacillus, Ferritrophicum, Thiomonas, Metallibacterium and Sideroxydans, involved in iron and sulfur metabolisms were found in the T and most showed higher abundance in the I zone than in the other zones. This work, as the first endeavor to separate the iron plaque into external and internal layers and investigate the variations of the bacterial communities therein, can provide an insight for further understanding the survival strategy of wetland plants, e.g., Typha latifolia, in extreme environment.