Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling.

Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.

The potential of enhanced phytoremediation to clean up multi-contaminated soil - insights from metatranscriptomics.

This study aimed to (i) investigate the potential for enhanced phytoremediation to remove contaminants from soil historically co-contaminated with petroleum hydrocarbons (PHs) and heavy metals (HMs) and (ii) analyze the expression of crucial bacterial genes and whole metatranscriptomics profiles for better understanding of soil processes during applied treatment. Phytoremediation was performed using Zea mays and supported by the Pseudomonas qingdaonensis ZCR6 strain and a natural biofertilizer: meat and bone meal (MBM). In previous investigations, mechanisms supporting plant growth and PH degradation were described in the ZCR6 strain. Here, ZCR6 survived in the soil throughout the experiment, but the efficacy of PH removal from all soils fertilized with MBM reached 32 % regardless of the bacterial inoculation. All experimental groups contained 2 % (w/w) MBM. The toxic effect of this amendment on plants was detected 30 days after germination, irrespective of ZCR6 inoculation. Among the 17 genes tested using the qPCR method, only expression of the acdS gene, encoding 1-aminocyclopropane-1-carboxylic acid deaminase, and the CYP153 gene, encoding cytochrome P450-type alkane hydroxylase, was detected in soils. Metatranscriptomic analysis of soils indicated increased expression of methane particulated ammonia monooxygenase subunit A (pmoA-amoA) by Nitrosomonadales bacteria in all soils enriched with MBM compared to the non-fertilized control. We suggest that the addition of 2 % (w/w) MBM caused the toxic effect on plants via the rapid release of ammonia, and this led to high pmoA-amoA expression. In parallel, due to its wide substrate specificity, enhanced bacterial hydrocarbon removal in MBM-treated soils was observed. The metatranscriptomic results indicate that MBM application should be considered to improve bioremediation of soils polluted with PHs rather than phytoremediation. However, lower concentrations of MBM could be considered for phytoremediation enhancement. From a broader perspective, these results indicated the superior capability of metatranscriptomics to investigate the microbial mechanisms driving various bioremediation techniques.

Enhancing the phytoextraction efficiency of heavy metals in acidic and alkaline soils by Sedum alfredii Hance: A study on the synergistic effect of plant growth regulator and plant growth-promoting bacteria.

Plant growth regulators (PGR) and plant growth-promoting bacteria (PGPB) have the potential in phytoremediation of heavy metals (HMs) contaminated soils. However, their sole application may not yield the optimal results, thus necessitating the combined application. The present study aimed to enhance the phytoremediation efficiency of Sedum alfredii Hance (S. alfredii) in acidic and alkaline soils through the combination of PGR (Brassinolide, BR) and PGPB (Pseudomonas fluorescens, P. fluorescens). The combination of BR and P. fluorescens (BRB treatment) effectively increased the removal efficiency of S. alfredii for Cd, Pb, and Zn by 355.2 and 155.3 %, 470.1 and 128.9 %, and 408.4 and 209.6 %, in acidic and alkaline soils, respectively. Moreover, BRB treatment led to a substantial increase in photosynthetic pigments contents and antioxidant enzymes activities, resulting in a remarkable increase in biomass (86.71 and 47.22 %) and dry mass (101.49 and 42.29 %) of plants grown in acidic and alkaline soils, respectively. Similarly, BRB treatment significantly elevated the Cd (109.4 and 71.36 %), Pb (174.9 and 48.03 %), and Zn levels (142.8 and 104.3 %) in S. alfredii shoots, along with cumulative accumulation of Cd (122.7 and 79.47 %), Pb (183.8 and 60.49 %), and Zn (150.7 and 117.9 %), respectively. In addition, the BRB treatment lowered the soil pH and DTPA-HMs contents, while augmenting soil enzymatic activities, thereby contributing soil microecology and facilitating the HMs absorption and translocation by S. alfredii to over-ground tissues. Furthermore, the evaluation of microbial community structure in phyllosphere and rhizosphere after remediation revealed the shift in microbial abundance. The combined treatment altered the principal effects on S. alfredii HMs accumulation from bacterial diversity to the soil HMs availability. In summary, our findings demonstrated that synergistic application of BR and P. fluorescens represents a viable approach to strengthen the phytoextraction efficacy of S. alfredii in varying soils.

Anaerobic biodegradation of perfluorooctane sulfonate (PFOS) and microbial community composition in soil amended with a dechlorinating culture and chlorinated solvents.

Perfluorooctane sulfonate (PFOS), one of the most frequently detected per- and polyfluoroalkyl substances (PFAS) occurring in soil, surface water, and groundwater near sites contaminated with aqueous film-forming foam (AFFF), has proven to be recalcitrant to many destructive remedies, including chemical oxidation. We investigated the potential to utilize microbially mediated reduction (bioreduction) to degrade PFOS and other PFAS through addition of a known dehalogenating culture, WBC-2, to soil obtained from an AFFF-contaminated site. A substantial decrease in total mass of PFOS (soil and water) was observed in microcosms amended with WBC-2 and chlorinated volatile organic compound (cVOC) co-contaminants - 46.4 ± 11.0 % removal of PFOS over the 45-day experiment. In contrast, perfluorooctanoate (PFOA) and 6:2 fluorotelomer sulfonate (6:2 FTS) concentrations did not decrease in the same microcosms. The low or non-detectable concentrations of potential metabolites in full PFAS analyses, including after application of the total oxidizable precursor assay, indicated that defluorination occurred to non-fluorinated compounds or ultrashort-chain PFAS. Nevertheless, additional research on the metabolites and degradation pathways is needed. Population abundances of known dehalorespirers did not change with PFOS removal during the experiment, making their association with PFOS removal unclear. An increased abundance of sulfate reducers in the genus Desulfosporosinus (Firmicutes) and Sulfurospirillum (Campilobacterota) was observed with PFOS removal, most likely linked to initiation of biodegradation by desulfonation. These results have important implications for development of in situ bioremediation methods for PFAS and advancing knowledge of natural attenuation processes.

Diversity and functional traits of seed endophytes of Dysphania ambrosioides from heavy metal contaminated and non-contaminated areas.

Seed endophytes played a crucial role on host plants stress tolerance and heavy metal (HM) accumulation. Dysphania ambrosioides is a hyperaccumulator and showed strong tolerance and extraordinary accumulation capacities of multiple HMs. However, little is known about its seed endophytes response to field HM-contamination, and its role on host plants HM tolerance and accumulation. In this study, the seed endophytic community of D. ambrosioides from HM-contaminated area (H) and non-contaminated area (N) were investigated by both culture-dependent and independent methods. Moreover, Cd tolerance and the plant growth promoting (PGP) traits of dominant endophytes from site H and N were evaluated. The results showed that in both studies, HM-contamination reduced the diversity and richness of endophytic community and changed the most dominant endophyte, but increased resistant species abundance. By functional trait assessments, a great number of dominant endophytes displayed multiple PGP traits and Cd tolerance. Interestingly, soil HM-contamination significantly increased the percentage of Cd tolerance isolates of Agrobacterium and Epicoccum, but significantly decreased the ration of Agrobacterium with the siderophore production ability. However, the other PGP traits of isolates from site H and N showed no significant difference. Therefore, it was suggested that D. ambrosioides might improve its HM tolerance and accumulation through harboring more HM-resistant endophytes rather than PGP endophytes, but to prove this, more work need to be conducted in the future.

Heavy metals immobilization and bioavailability in multi-metal contaminated soil under ryegrass cultivation as affected by ZnO and MnO2 nanoparticle-modified biochar.

Pollution by heavy metals (HMs) has become a global problem for agriculture and the environment. In this study, the effects of pristine biochar and biochar modified with manganese dioxide (BC@MnO2) and zinc oxide (BC@ZnO) nanoparticles on the immobilization and bioavailability of Pb, Cd, Zn, and Ni in soil under ryegrass (Lolium perenne L.) cultivation were investigated. The results of SEM-EDX, FTIR, and XRD showed that ZnO and MnO2 nanoparticles were successfully loaded onto biochar. The results showed that BC, BC@MnO2 and BC@ZnO treatments significantly increased shoots and roots dry weight of ryegrass compared to the control. The maximum dry weight of root and shoot (1.365 g pot-1 and 4.163 g pot-1, respectively) was reached at 1% BC@MnO2. The HMs uptake by ryegrass roots and shoots decreased significantly after addition of amendments. The lowest Pb, Cd, Zn and Ni uptake in the plant shoot (13.176, 24.92, 32.407, and 53.88 µg pot-1, respectively) was obtained in the 1% BC@MnO2 treatment. Modified biochar was more successful in reducing HMs uptake by ryegrass and improving plant growth than pristine biochar and can therefore be used as an efficient and cost effective amendment for the remediation of HMs contaminated soils. The lowest HMs translocation (TF) and bioconcentration factors were related to the 1% BC@MnO2 treatment. Therefore, BC@MnO2 was the most successful treatment for HMs immobilization in soil. Also, a comparison of the TF values of plant showed that ryegrass had a good ability to accumulate all studied HMs in its roots, and it is a suitable plant for HMs phytostabilization.

Modified diatomite for soil remediation and its implications for heavy metal absorption in Calendula officinalis.

BACKGROUND: Among different adsorbents, natural and inorganic compounds such as diatomite are important and advantageous in terms of high efficiency and cost-effectiveness, and function in stabilizing heavy metals in the environment. Calendula officinalis, a plant known as a high accumulator of heavy metals, was cultivated in soil treated with varying concentrations of modified diatomite to demonstrate the efficiency of modified diatomite in stabilizating of heavy metals in soils, RESULTS: The modification of diatomite aimed to enhance Calendula officinalis adsorptive properties, particularly towards heavy metals such as lead (Pb), Zinc (Zn), Chromium (Cr), Nickle (Ni), and Copper (Cu), common contaminants in industrial soils. The experimental design included both control and treated soil samples, with assessments at regular intervals. Modified diatomite significantly decreased the bioaccumulation of heavy metals in contaminated soils except Zn, evidenced by decreased DTPA extractable heavy metals in soil and also heavy metal concentrations in plant tissues. Using 10% modified diatomite decreased 91% Pb and Cu, 78% Cr, and 79% Ni concentration of plants compared to the control treatment. The highest concentration of Zn in plant tissue was observed in 2.5% modified diatomite treatment. Remarkably, the application of modified diatomite also appeared to improve the nutrient profile of the soil, leading to enhanced uptake of key nutrients like phosphorus (P) 1.18%, and potassium (K) 79.6% in shoots and 82.3% in roots in Calendula officinalis. Consequently, treated plants exhibited improved growth characteristics, including shoots and roots height of 16.98% and 12.8% respectively, and shoots fresh and dry weight of 48.5% and 50.2% respectively., compared to those in untreated, contaminated soil. CONCLUSION: The findings suggest promising implications for using such amendments in ecological restoration and sustainable agriculture, particularly in areas impacted by industrial pollution.

Improving plant adaptation to soil antimony contamination: the synergistic contribution of arbuscular mycorrhizal fungus and olive mill waste.

BACKGROUND: This study aimed to investigate the alterations in biochemical and physiological responses of oat plants exposed to antimony (Sb) contamination in soil. Specifically, we evaluated the effectiveness of an arbuscular mycorrhizal fungus (AMF) and olive mill waste (OMW) in mitigating the effects of Sb contamination. The soil was treated with a commercial strain of AMF (Rhizophagus irregularis) and OMW (4% w/w) under two different levels of Sb (0 and 1500 mg kg-1 soil). RESULTS: The combined treatment (OMW + AMF) enhanced the photosynthetic rate (+ 40%) and chlorophyll a (+ 91%) and chlorophyll b (+ 50%) content under Sb condition, which in turn induced more biomass production (+ 67-78%) compared to the contaminated control plants. More photosynthesis in OMW + AMF-treated plants gives a route for phenylalanine amino acid synthesis (+ 69%), which is used as a precursor for the biosynthesis of secondary metabolites, including flavonoids (+ 110%), polyphenols (+ 26%), and anthocyanins (+ 63%) compared to control plants. More activation of phenylalanine ammonia-lyase (+ 38%) and chalcone synthase (+ 26%) enzymes in OMW + AMF-treated plants under Sb stress indicated the activation of phenylpropanoid pathways in antioxidant metabolites biosynthesis. There was also improved shifting of antioxidant enzyme activities in the ASC/GSH and catalytic pathways in plants in response to OMW + AMF and Sb contamination, remarkably reducing oxidative damage markers. CONCLUSIONS: While individual applications of OMW and AMF also demonstrated some degree of plant tolerance induction, the combined presence of AMF with OMW supplementation significantly enhanced plant biomass production and adaptability to oxidative stress induced by soil Sb contamination.

Enhanced remediation of chlorpyrifos-contaminated soil by immobilized strain Bacillus H27.

Chlorpyrifos is a pesticide widely used in agricultural production with a relatively long residual half-life in soil. Addressing the problem of residual chlorpyrifos is of universal concern. In this study, rice hull biochar was used as an immobilized carrier to prepare the immobilized strain H27 for the remediation of chlorpyrifos-contamination soil. Soil microorganisms after remediation were investigated by ecotoxicological methods. The immobilized strain H27 had the highest removal rate of chlorpyrifos when 10% bacterial solution was added to the liquid medium containing 0.075-0.109 mm diameter biochar cultured for 22 hr. This study on the removal of chlorpyrifos by immobilized strain H27 showed that the initial concentration of chlorpyrifos in solution was 25 mg/L, and the removal rate reached 97.4% after 7 days of culture. In the soil, the removal rate of the immobilized bacteria group increased throughout the experiment, which was significantly higher than that of the free bacteria and biochar treatment groups. The Biolog-ECO test, T-RFLP and RT-RCR were used to study the effects of the soil microbial community and nitrogen cycling functional genes during chlorpyrifos degradation. It was found that ICP group had the highest diversity index among the four treatment groups. The microflora of segment containing 114 bp was the dominant bacterial community, and the dominant microflora of the immobilized bacteria group was more evenly distributed. The influence of each treatment group on ammonia-oxidizing bacteria (AOB) was greater than on ammonia-oxidizing archaea (AOA). This study offers a sound scientific basis for the practical application of immobilized bacteria to reduce residual soil pesticides.

Effects of Graphene Oxide on Endophytic Bacteria Population Characteristics in Plants from Soils Contaminated by Polycyclic Aromatic Hydrocarbons.

Environmental pollution stands as one of the significant global challenges we face today. Polycyclic aromatic hydrocarbons (PAHs), a class of stubborn organic pollutants, have long been a focal point of bioremediation research. This study aims to explore the impact and mechanisms of graphene oxide (GO) on the phytoremediation effectiveness of PAHs. The results underscore the significant efficacy of GO in accelerating the degradation of PAHs. Additionally, the introduction of GO altered the diversity and community structure of endophytic bacteria within the roots, particularly those genera with potential for PAH degradation. Through LEfSe analysis and correlation studies, we identified specific symbiotic bacteria, such as Mycobacterium, Microbacterium, Flavobacterium, Sphingomonas, Devosia, Bacillus, and Streptomyces, which coexist and interact under the influence of GO, synergistically degrading PAHs. These bacteria may serve as key biological markers in the PAH degradation process. These findings provide new theoretical and practical foundations for the application of nanomaterials in plant-based remediation of polluted soils and showcase the immense potential of plant-microbe interactions in environmental restoration.

Novel enzymes for biodegradation of polycyclic aromatic hydrocarbons identified by metagenomics and functional analysis in short-term soil microcosm experiments.

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic substances. On soils contaminated with PAHs, crop cultivation, animal husbandry and even the survival of microflora in the soil are greatly perturbed, depending on the degree of contamination. Most microorganisms cannot tolerate PAH-contaminated soils, however, some microbial strains can adapt to these harsh conditions and survive on contaminated soils. Analysis of the metagenomes of contaminated environmental samples may lead to discovery of PAH-degrading enzymes suitable for green biotechnology methodologies ranging from biocatalysis to pollution control. In the present study, our goal was to apply a metagenomic data search to identify efficient novel enzymes in remediation of PAH-contaminated soils. The metagenomic hits were further analyzed using a set of bioinformatics tools to select protein sequences predicted to encode well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one peroxidase) were cloned and used in soil remediation microcosms experiments. The experimental design of the present study aimed at evaluating the effectiveness of the novel enzymes on short-term PAH degradation in the soil microcosmos model. The novel enzymes were found to be efficient for degradation of naphthalene and phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading potential of the novel enzymes for anthracene and pyrene. We conclude that metagenome mining paired with bioinformatic predictions, structural modelling and functional assays constitutes a powerful approach towards novel enzymes for soil remediation.

The fluoride exporter (CsFEX) regulates fluoride uptake/accumulation in Camellia sinensis under different pH.

Fluoride (F) can be absorbed from the environment and hyperaccumulate in leaves of Camellia sinensis without exhibiting any toxic symptoms. Fluoride exporter in C. sinensis (CsFEX) could transport F to extracellular environment to alleviate F accumulation and F toxicity, but its functional mechanism remains unclear. Here, combining with pH condition of C. sinensis growth, the characteristics of CsFEX and mechanism of F detoxification were further explored. The results showed that F accumulation was influenced by various pH, and pH 4.5 and 6.5 had a greater impact on the F accumulation of C. sinensis. Through Non-invasive Micro-test Technology (NMT) detection, it was found that F uptake/accumulation of C. sinensis and Arabidopsis thaliana might be affected by pH through changing the transmembrane electrochemical proton gradient of roots. Furthermore, diverse expression patterns of CsFEX were induced by F treatment under different pH, which was basically up-regulated in response to high F accumulation, indicating that CsFEX was likely to participate in the process of F accumulation in C. sinensis and this process might be regulated by pH. Additionally, CsFEX functioned in the mitigation of F sensitivity and accumulation strengthened by lower pH in Escherichia coli and A. thaliana. Moreover, the changes of H+ flux and potential gradient caused by F were relieved as well in transgenic lines, also suggesting that CsFEX might play an important role in the process of F accumulation. Above all, F uptake/accumulation were alleviated in E. coli and A. thaliana by CsFEX through exporting F-, especially at lower pH, implying that CsFEX might regulate F accumulation in C. sinensis.

R3 strain and Fe-Mn modified biochar reduce Cd absorption capacity of roots and available Cd content of soil by affecting rice rhizosphere and endosphere key flora.

Microorganisms have a significant role in regulating the absorption and transportation of Cd in the soil-plant system. However, the mechanism by which key microbial taxa play a part in response to the absorption and transportation of Cd in rice under Cd stress requires further exploration. In this study, the cadmium-tolerant endophytic bacterium Herbaspirillum sp. R3 (R3) and Fe-Mn-modified biochar (Fe-Mn) were, respectively, applied to cadmium-contaminated rice paddies to investigate the effects of key bacterial taxa in the soil-rice system on the absorption and transportation of Cd in rice under different treatments. The results showed that both R3 and Fe-Mn treatments considerably decreased the content of cadmium in roots, stems and leaves of rice at the peak tillering stage by 17.24-49.28% in comparison to the control (CK). The cadmium content reduction effect of R3 treatment is better than that of Fe-Mn treatment. Further analysis revealed that the key bacterial taxa in rice roots under R3 treatment were Sideroxydans and Actinobacteria, and that their abundance showed a substantial positive correlation and a significant negative correlation with the capacity of rice roots to assimilate Cd from the surroundings, respectively. The significant increase in soil pH under Fe-Mn treatment, significant reduction in the relative abundances of Acidobacteria, Verrucomicrobia, Subdivision3 genera incertae sedis, Sideroxydans, Geobacter, Gp1, and Gp3, and the significant increase in the relative abundance of Thiobacillus among the soil bacterial taxa may be the main reasons for the decrease in available Cd content of the soil. In addition, both the R3 and Fe-Mn treatments showed some growth-promoting effects on rice, which may be related to their promotion of transformations of soil available nutrients. This paper describes the possible microbial mechanisms by which strain R3 and Fe-Mn biochar reduce Cd uptake in rice, providing a theoretical basis for the remediation of Cd contamination in rice and soil by utilizing key microbial taxa.

Cadmium phytoremediation potential of Houttuynia cordata: Insights from growth, uptake, and rhizosphere mechanisms.

Cadmium (Cd) pollutes 7.0 % of China's land area. This study examined the potential of Houttuynia cordata for Cd phytoremediation because of its ability to accumulate Cd in its growth matrix. H. cordata were planted in plastic pots filled with paddy field soils having low (LCd), medium (MCd), and high (HCd) Cd levels of 0.19, 0.69, and 2.91 mg/kg, respectively. After six months of growth, harvested plant parts were evaluated for Cd uptake and tolerance mechanisms. Metabolomics and metagenomics approaches were employed to investigate the soil rhizosphere mechanism. Results showed that the average plant biomass increased as soil Cd increased. The biomass Cd contents surpassed the allowable Cd limits for food (≤ 0.2 mg/kg) and medicinal uses (≤ 0.3 mg/kg). Cd contents were higher in H. cordata roots (30.59-86.27 mg/kg) than in other plant parts (0.63-2.90 mg/kg), with significantly increasing values as Cd soil level increased. Phenolic acids, lipids, amino acids and derivatives, organic acids, and alkaloids comprised the majority (69 in MCd vs HCd and 73 % in LCd vs HCd) of the shared upregulated metabolites. In addition, 13 metabolites specific to H. cordata root exudates were significantly increased. The top two principal metabolic pathways were arginine and proline metabolism, and beta-alanine metabolism. H. cordata increased the abundance of Firmicutes and Glomeromycota across all three Cd levels, and also stimulated the growth of Patescibacteria, Rozellomycota, and Claroideoglomus in HCd. Accordingly, H. cordata demonstrated potential for remediation of Cd-contaminated soils, and safety measures for its production and food use must be highly considered.

Industrial hemp (Cannabis sativa L.) can utilize and remediate soil strongly contaminated with Cu, As, Cd, and Pb by phytoattenuation.

Industrial hemp (Cannabis sativa L.) has great application potential in heavy metal-polluted soils owing to its safe non-food utilization. However, the fate of heavy metals in different varieties of hemp planted in strongly contaminated natural soils remains unknown. Here, we investigated the growth, heavy metal uptake, distribution, and transfer of nine hemp varieties in soils strongly contaminated with Cu, As, Cd, and Pb. Hemp variety and metal type were the main factors affecting the growth and heavy metal uptake in hemp. The nine hemp varieties grew well in the contaminated soils; however, differences existed among the varieties. The biomass of Z3 reached 5669.1 kg hm-1, whereas that of Yunma No. 1 was only 51.8 % of Z3. The plant height, stalk diameter, and stalk bark thickness of Z3 were greater than those of the other varieties, reaching 168 cm, 9.2 mm, and 0.56 mm, respectively. Permanova's analysis revealed that the total effects of Cu, As, Cd, and Pb on the growth of the nine hemp varieties reached 60 %, with leaf As having the greatest effect, reaching 16 %. , Even in strongly contaminated soils, the nine varieties showed poor Cu, As, Cd, and Pb uptake. Most of the Cu, As, Cd, and Pb were retained in the root, reaching 57.7-72.4, 47.6-64.7, 76.0-92.9, and 70.0-87.8 %, respectively. Overall, the Cu, As, Cd, and Pb uptake of Wanma No.1 was the highest among the nine varieties, whereas that of Guangxi Bama was the lowest. These results indicate that hemp is a viable alternative for phytoattenuation in soils contaminated with heavy metals because of its ability to tolerate and accumulate Cu, As, Cd, and Pb in its roots, and Guangxi Bama is superior to the other varieties considering the safe utilization of hemp products.

Responses of soil and rhizosphere microbial communities to Cd-hyperaccumulating willows and Cd contamination.

BACKGROUND: The pollution of soil by heavy metals, particularly Cd, is constitutes a critical international environmental concern. Willow species are renowned for their efficacy in the phytoremediation of heavy metals owing to their high Cd absorption rate and rapid growth. However, the mechanisms underlying microbial regulation for high- and low-accumulating willow species remain poorly understood. Therefore, we investigated the responses of soil and rhizosphere microbial communities to high- and low-Cd-accumulating willows and Cd contamination. We analyzed soil properties were analyzed in bulk soil (SM) and rhizosphere soil (RM) planted with high-accumulating (H) and low-accumulating (L) willow species. RESULTS: Rhizosphere soil for different willow species had more NH4+ than that of bulk soil, and RM-H soil had more than RM-L had. The available phosphorus content was greater in hyper-accumulated species than it was in lower-accumulated species, especially in RM-H. Genome sequencing of bacterial and fungal communities showed that RM-L exhibited the highest bacterial diversity, whereas RM-H displayed the greatest richness than the other groups. SM-L exhibited the highest diversity and richness of fungal communities. Ralstonia emerged as the predominant bacterium in RM-H, whereas Basidiomycota and Cercozoa were the most enriched fungi in SM-H. Annotation of the N and C metabolism pathways revealed differential patterns: expression levels of NRT2, NarB, nirA, nirD, nrfA, and nosZ were highest in RM-H, demonstrating the effects of NO3-and N on the high accumulation of Cd in RM-H. The annotated genes associated with C metabolism indicated a preference for the tricarboxylic pathway in RM-H, whereas the hydroxypropionate-hydroxybutyrate cycle was implicated in C sequestration in SM-L. CONCLUSIONS: These contribute to elucidation of the mechanism underlying high Cd accumulation in willows, particularly in respect of the roles of microbes and N and C utilization. This will provide valuable insights for repairing polluted soil using N and employing organic acids to improve heavy metal remediation efficiency.

Physiological and transcriptomic analyses reveal the cadmium tolerance mechanism of Miscanthus lutarioriparia.

Miscanthus lutarioriparia is a promising energy crop that is used for abandoned mine soil phytoremediation because of its high biomass yield and strong tolerance to heavy metals. However, the biological mechanism of heavy metal resistance is limited, especially for applications in the soil restoration of mining areas. Here, through the investigation of soil cadmium(Cd) in different mining areas and soil potted under Cd stress, the adsorption capacity of Miscanthus lutarioriparia was analyzed. The physiological and transcriptional effects of Cd stress on M. lutarioriparia leaves and roots under hydroponic conditions were analyzed. The results showed that M. lutarioriparia could reduce the Cd content in mining soil by 29.82%. Moreover, different Cd varieties have different Cd adsorption capacities in soils with higher Cd concentration. The highest cadmium concentrations in the aboveground and belowground parts of the plants were 185.65 mg/kg and 186.8 mg/kg, respectively. The total chlorophyll content, superoxide dismutase and catalase activities all showed a trend of increasing first and then decreasing. In total, 24,372 differentially expressed genes were obtained, including 7735 unique to leaves, 7725 unique to roots, and 8912 unique to leaves and roots, which showed differences in gene expression between leaves and roots. These genes were predominantly involved in plant hormone signal transduction, glutathione metabolism, flavonoid biosynthesis, ABC transporters, photosynthesis and the metal ion transport pathway. In addition, the number of upregulated genes was greater than the number of downregulated genes at different stress intervals, which indicated that M. lutarioriparia adapted to Cd stress mainly through positive regulation. These results lay a solid foundation for breeding excellent Cd resistant M. lutarioriparia and other plants. The results also have an important theoretical significance for further understanding the detoxification mechanism of Cd stress and the remediation of heavy metal pollution in mining soil.

Soil-dwelling grub larvae of Protaetia brevitarsis biodegrade polystyrene: Responses of gut microbiome and host metabolism.

Plastic pollution poses a significant threat to terrestrial ecosystems, yet the potential for soil fauna to contribute to plastic biodegradation remains largely unexplored. In this study, we reveal that soil-dwelling grubs, Protaetia brevitarsis larvae, can effectively biodegrade polystyrene (PS) plastics. Over a period of 4 weeks, these grubs achieved a remarkable 61.5 % reduction in PS foam mass. This biodegradation was confirmed by the depolymerization of ingested PS, formation of oxidative functional groups, noticeable chemical modifications, and an increase of δ13C of residual PS in frass. Additionally, antibiotic treatment to suppress gut microbes led to variations in the biodegradation process. PS ingestion induced a significant shift in the gut microbiome, promoting the growth of degradation-related bacteria such as Promicromonosporaceae, Bacillaceae, and Paenibacillaceae. Furthermore, the digestion of plastic triggered extensive metabolomic reprogramming of grubs' intestines, enhancing redox capabilities and facilitating PS biodegradation. These results indicate that responsive adaptation of both the gut microbiome and the host's intestinal metabolism contributes to PS degradation. Collectively, these findings demonstrate P. brevitarsis larvae's capability to alleviate soil plastic pollution, and highlight the potential of researching soil fauna further for sustainable plastic waste management solutions.

Effects of nitrogen forms on Cd uptake and tolerance in wheat seedlings.

Hydroponic experiment was conducted to explore the effects of two nitrogen (N) levels with five nitrate nitrogen (NO3--N) and ammonium nitrogen (NH4+-N) ratios on the growth status and Cd migration patterns of wheat seedlings under Cd5 and Cd30 level. Results showed that higher Cd were detrimental to the growth, absorption of K and Ca, expression of genes mediating NO3--N and NH4+-N transport, which also increased the content of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in shoots and roots of wheat seedlings. Higher N treatment alleviated the inhibitory effects of Cd stress on the biomass, root development, photosynthesis and increased the tolerance index of wheat seedlings. The ratio of NO3--N and NH4+-N was the main factor driving Cd accumulation in wheat seedlings, the combined application of NH4+-N and NO3--N was more conducive for the growth, nitrogen assimilation and Cd tolerance to the Cd stressed wheat seedlings. Increased NO3--N application rates significantly up-regulated the expression levels of TaNPF2.12, TaNRT2.2, increased NH4+-N application rates significantly up-regulated the expression levels of TaAMT1.1. The high proportion of NO3--N promoted the absorption of K, Ca and Cd in the shoots and roots of wheat seedlings, while NH4+-N was the opposite. Under low Cd conditions, the NO3--N to NH4+-N ratio of 1:1 was more conducive to the growth of wheat seedlings, under high Cd stress, the optimal of NO3--N to NH4+-N was 1:2 for inhibiting the accumulation of Cd in wheat seedlings. The results indicated that increasing NH4+-N ratio appropriately could inhibit wheat Cd uptake by increasing NH4+, K+ and Ca2+ for K and Ca channels, and promote wheat growth by promoting N assimilation process.

Biochar and peat amendments affect nitrogen retention, microbial capacity and nitrogen cycling microbial communities in a metal and polycyclic aromatic hydrocarbon contaminated urban soil.

Soil contaminants may restrict soil functions. A promising soil remediation method is amendment with biochar, which has the potential to both adsorb contaminants and improve soil health. However, effects of biochar amendment on soil-plant nitrogen (N) dynamics and N cycling microbial guilds in contaminated soils are still poorly understood. Here, a metal- and polycyclic aromatic hydrocarbon (PAH) contaminated soil was amended with either biochar (0, 3, 6 % w/w) and/or peat (0, 1.5, 3 % w/w) in a full-factorial design and sown with perennial ryegrass in an outdoor field trial. After three months, N and the stable isotopic ratio δ15N was measured in soil, roots and leaves, along with microbial responses. Aboveground grass biomass decreased by 30 % and leaf N content by 20 % with biochar, while peat alone had no effect. Peat in particular, but also biochar, stimulated the abundance of microorganisms (measured as 16S rRNA gene copy number) and basal respiration. Microbial substrate utilization (MicroResp™) was altered differentially, as peat increased respiration of all carbon sources, while for biochar, respiration of carboxylic acids increased, sugars decreased, and was unaffected for amino acids. Biochar increased the abundance of ammonia oxidizing archaea, while peat stimulated ammonia oxidizing bacteria, Nitrobacter-type nitrite oxidizers and comB-type complete ammonia oxidizers. Biochar and peat also increased nitrous oxide reducing communities (nosZI and nosZII), while peat alone or combined with biochar also increased abundance of nirK-type denitrifiers. However, biochar and peat lowered leaf δ15N by 2-4 ‰, indicating that processes causing gaseous N losses, like denitrification and ammonia volatilization, were reduced compared to the untreated contaminated soil, probably an effect of biotic N immobilization. Overall, this study shows that in addition to contaminant stabilization, amendment with biochar and peat can increase N retention while improving microbial capacity to perform important soil functions.