Microbial communities in the rhizosphere of different willow genotypes affect phytoremediation potential in Cd contaminated soil

Enhanced mobilization of soil heavy metals by the enantioselective herbicide R-napropamide compared to its S-isomer: Analyses of abiotic and biotic drivers

Chiral herbicides applied to agricultural soils are typically mildly to moderately contaminated with heavy metals (HMs), necessitating a thorough investigation into their effects on soil HMs availability. This study evaluated the effect of the chiral herbicide napropamide (NAP) on HMs bioavailability in different soil types, including weakly alkaline clay in Northeast China, neutral sandy loam in Zhejiang, and weakly acidic clay loam in Sichuan, China. The results demonstrate significant differences in the availability of HMs (Cd, Pb, Zn, and Ni) in the soil following enantiomer treatments, with variation ranges of 4.57-45.67 %, 5.03-96.21 %, 2.92-52.30 %, and 10.57-29.79 %, respectively. Overall, R-NAP enhanced the bioavailability of HMs more effectively than S-NAP, specifically by significantly activating available iron 3.33-191.97 % and markedly affecting soil pH and cation exchange capacity. Additionally, R-NAP influenced biotic processes by enriching dominant microbial communities, such as Chitinophaga, Niabella, and Promicromonospora, and by constructing more stable microbial networks. Notably, bioavailable Fe plays a dual regulatory role, affecting both the abiotic and biotic processes affected by soil NAP. In summary, although R-NAP is commonly used in agriculture, it poses a greater risk of HMs contamination in crops, highlighting the need for careful application and management. This study provides a fundamental theoretical basis for the judicious use of chiral herbicides in agricultural soils with mild-to-moderate HMs contamination.

Uncovering the mechanisms of how corn steep liquor and microbial communities minimize cadmium translocation in Chinese cabbage

Corn steep liquor-assisted microbial remediation has been proposed as a promising strategy to remediate cadmium (Cd)-contaminated soil. In this study, we determined Bacillus subtilis (K2) with a high cadmium (Cd) accumulation ability and Cd resistance. However, studies on this strategy used in the Cd uptake of Chinese cabbage are lacking, and the effect of the combined incorporation of corn steep liquor and K2 on the functions and microbial interactions of soil microbiomes is unclear. Here, we study the Cd uptake and transportation in Chinese cabbage by the combination of K2 and corn steep liquor (K2 + C7) in a Cd-contaminated soil and corresponding microbial regulation mechanisms. Results showed that compared to inoculant K2 treatment alone, a reduction of Cd concentration in the shoots by 14.4% and the dry weight biomass of the shoots and the roots in Chinese cabbage increased by 21.6% and 30.8%, respectively, under K2 + C7 treatment. Meanwhile, hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels were decreased by enhancing POD and SOD activity, thereby reversing Cd-induced oxidative damage. Importantly, inoculation of K2 would decrease the diversity of the microbial community while enhancing the abundance of dominant species. These findings provide a promising strategy for reducing the Cd accumulation in Chinese cabbage and recovering soil ecological functions.

Thallium content in vegetables and derivation of threshold for safe food production in soil: A meta-analysis

Soil thallium (Tl) pollution is a serious environmental problem, and vegetables are the primary pathway for human exposure to Tl. Therefore, it is important to investigate the characteristics of soil Tl uptake by vegetables. In this study, the meta-analysis approach was first applied to explore the relationship between Tl content in vegetables and soil environment, as well as key factors influencing soil physical-chemical properties, and to derive soil thresholds for Tl. The results indicated that various types of vegetables have different capabilities for Tl accumulation. Vegetables from contaminated areas showed high Tl accumulation, and the geomean Tl content in different types of vegetables was in the following order: leafy > root-stalk > solanaceous vegetables. Taro and kale had significantly higher capability to accumulate soil Tl among the 35 species studied, with Tl bioconcentration factor values of 0.060 and 0.133, respectively. Pearson correlation analysis and meta-analysis revealed that the Tl content in vegetables was significantly correlated with soil pH and Tl content in soil. The linear predictive model for Tl accumulation in vegetables based on soil Tl content described the data well, and the fitting coefficient R2 increased with soil pH value. According to potential dietary toxicity, the derived soil Tl thresholds for all, leafy and root-stalk vegetables increased with an increase in soil pH, and were in the range of 1.46-6.72, 1.74-5.26 and 0.92-6.06 mg/kg, respectively. The soil Tl thresholds for kale, lettuce and carrot were in the range of 0.24-4.89, 2.94-3.32 and 3.77-14.43 mg/kg, respectively. Ingestion of kale, beet, sweet potato, potato, taro, pepper, turnip, Chinese cabbage, eggplant and carrot poses potential health risks. The study provides scientific guidance for vegetable production in Tl-contaminated areas and can help with the selection of vegetable species suitable for avoiding the absorption of Tl from contaminated soil.

Responses of microbial communities in rhizocompartments of king grass to phytoremediation of cadmium-contaminated soil

King grass has been recognized as a potential phytoremediation plant species due to its high biomass and resistance to heavy metals (HMs). However, the possible impacts of cadmium (Cd) contamination on rhizocompartments' microbial activities in association with king grass have not been extensively explored. The utilization of 16S rRNA gene and ITS sequencing was carried out to examine alterations in the bacterial and fungal communities in the rhizosphere and rhizoplane of king grass in response to low and high Cd stress. Results demonstrated that both bacterial and fungal communities' diversity and richness were negatively impacted by Cd stress, regardless of its concentration. However, evenness did not exhibit any significant response to either of the concentrations. Additionally, nonmetric multidimensional scaling (NMDS) ordination demonstrated a significant difference (p < 0.001) in microbial communities under different treatments. The abundance of bacterial taxa such as Steroibacter, Nitrospira, Pseudoxanthomonas, Cellvirio, Phenylobacterium, Mycobacterium, Pirellula and Aquicella was adversely affected under Cd stress while Flavobacterium, Gemmata, Thiobacillus and Gemmatimonas showed no prominent response, indicating their resistance to Cd stress. Like that, certain fungal taxa for instance, Cladosporium, Cercophora, Acremonium, Mortierella, Aspergillus, Penicillium, Glomus and Sebacina were also highly reduced by low and high Cd stress. In contrast, Fusarium, Thanatephorus, Botrytis and Curvularia did not show any response to Cd stress. The identified taxa may have a crucial role in the growth of king grass under heavy metal contamination, making them promising candidates for developing bioinoculants to encourage plant performance and phytoremediation capability in HM-contaminated soils.

Natural enrichment of Cd and Tl in the bark of trees from a rural watershed devoid of point sources of metal contamination

To help understand the bioaccumulation of Cd and Tl in beaver tissue, we examined the enrichment of these metals in vegetation available to the animals. Bark was collected from 40 species of trees and shrubs, along with a complete soil weathering profile, within a small watershed devoid of trace metal contamination. Weathering resulted in a 5x enrichment of Cd in the soils relative to the underlying sediments, and a 6x Tl depletion: while Cd was lost from calcite and accumulates in the organic matter and oxyhydroxide fractions, Tl occurred only in the residual fraction. Soil processes alone, however, cannot explain the anomalous concentrations and enrichments of Cd in willow and poplar which contain up to 8.5 mg/kg Cd. The concentrations of Cd and Tl in the dissolved fraction (<0.45 μm) of the Wye River are similar (1.2 ± 0.4 and 1.6 ± 0.1 ng/L, respectively), and are taken to estimate their bioavailability in soil solutions. Normalizing the Cd/metal ratios in bark to the corresponding ratios in water yields the Stream Enrichment Factor: this novel approach shows that all plant species are enriched in Cd relative to Ni; 33 relative to Cu, 13 relative to Zn, and 7 relative to Mn. Thus, many plants preferentially accumulate Cd, especially willow and poplar, over these essential micronutrients. Clearly, the enrichment of Cd over Tl in bark is not a reflection of differences in bioavailability, but rather on the preferential uptake of Cd by the plants. The profound natural bioaccumulation of Cd in the bark of willow and poplar, the two favourite foods of the beaver, has ramifications for the use of these aquatic mammals as biomonitors of environmental contamination, as well as for the direct and indirect consumption of bark for traditional food and medicine.

Soil microbial community compositions and metabolite profiles of Achnatherum inebrians affect phytoremediation potential in Cd contaminated soil

Cadmium (Cd) contamination poses serious risks to soil ecosystems and human health. Herein, the effect of two drunken horse grasses (Achnatherum inebrians) including endophytes Epichloë gansuensis infected (E+ ) and uninfected (E-) on the phytoremediation of Cd-contaminated soils were analyzed by coupling high-throughput sequencing and soil metabolomics. The results showed that the high-risk soil Cd decreased and the medium- and low-risk Cd fraction increased to varying degrees after planting E+ and E- plants in the soil. Meanwhile, total Cd content decreased by 19.7 % and 35.1 % in E+ and E- A. inebrians-planted soils, respectively. Principal coordinate analysis revealed a significant impact of E+ and E- plants on the soil microbial community. Most stress-tolerant and gram-positive functional bacterial taxa were enriched to stabilize Cd(II) in E+ planted soil. Several beneficial fungal groups related to saprotroph and symbiotroph were enriched to absorb Cd(II) in E- soil. Soil metabolomic analysis showed that the introduction of A. inebrians could weaken the threat of CdCl2 to soil microbe metabolism and improve soil quality, which in turn promoted plant growth and improved phytoremediation efficiency in Cd-contaminated soil. In conclusion, A. inebrians plants alleviate soil Cd pollution by regulating soil microbial metabolism and microbial community structure. These results provide valuable information for an in-depth understanding of the phytoremediation mechanisms of A. inebrians.

Phytoextraction of per- and polyfluoroalkyl substances (PFAS) and the influence of supplements on the performance of short-rotation crops

Per- and polyfluoroalkyl substances (PFAS) are anthropogenic compounds threatening water quality and food safety worldwide. Phytoremediation is a nature-based, cost-effective, and scalable solution with high potential for treating PFAS-contaminated sites. However, there is a large knowledge gap regarding choice of plant species and methods to enhance performance. This study assessed the PFAS phytoextraction potential of sunflower (Helianthus annuus), mustard (Brassica juncea), and industrial hemp (Cannabis sativa) in a greenhouse experiment, using inorganic fertilizer and a microbial mixture as supplements. PFAS concentrations were measured using UPLC-MS/MS, and bioconcentration factors for different plant tissues and removal efficiency were determined. Perfluoroalkyl carboxylic acid (PFCA) accumulation was 0.4-360 times higher than that of perfluoroalkyl sulfonic acid (PFSA) homologues of similar perfluorocarbon chain length. Inorganic fertilizer significantly (p < 0.001) reduced PFAS concentration in all plant tissues, whereas the microbial mixture tested did not affect PFAS concentration. PFAS uptake ranged from 0.2 to 33% per crop cycle. Overall, the potential number of crop cycles required for removal of 90% of individual PFAS ranged from six (PFPeA) to 232 (PFOA) using sunflower, 15 (PFPeA) to 466 (PFOS) using mustard and nine (PFPeA) to 420 (PFOS) using Hemp. In this study, the percentage of PFAS removal by plants was determined, and an estimation of the time required for PFAS phytoextraction was determined for the first time. This information is important for practical phytoremediation applications.

The fate of sulfonamides in microenvironments of rape and hot pepper rhizosphere soil system

Sulfonamides (SAs) in agricultural soils can be degraded in rhizosphere, but can also be taken up by vegetables, which thereby poses human health and ecological risks. A glasshouse experiment was conducted using multi-interlayer rhizoboxes to investigate the fate of three SAs in rape and hot pepper rhizosphere soil systems to examine the relationship between the accumulation and their physicochemical processes. SAs mainly entered pepper shoots in which the accumulation ranged from 0.40 to 30.64 mg kg-1, while SAs were found at high levels in rape roots ranged from 3.01 to 16.62 mg kg-1. The BCFpepper shoot exhibited a strong positive linear relationship with log Dow, while such relationship was not observed between other bioconcentration factors (BCFs) and log Dow. Other than lipophilicity, the dissociation of SAs may also influence the uptake and translocation process. Larger TF and positive correlation with log Dow indicate preferential translocation of pepper SAs. There was a significant (p < 0.05) dissipation gradient of SAs observed away from the vegetable roots. In addition, pepper could uptake more SAs under solo exposure, while rape accumulated more SAs under combined exposure. When SAs applied in mixture, competition between SAs might occur to influence the translocation and dissipation patterns of SAs.

Climatic CO2 level-driven changes in the bioavailability, accumulation, and health risks of Cd and Pb in paddy soil-rice systems

Rising atmospheric carbon dioxide (CO₂) and soil heavy metal pollution, which affects safe rice production and soil ecosystem stability, have caused widespread concern. In this study, we evaluated the effects of elevated CO₂ on Cd and Pb accumulation in rice plants (Oryza sativa L.), Cd and Pb bioavailability, and soil bacterial communities in Cd-Pb co-contaminated paddy soils via rice pot experiments. We showed that elevated CO₂ accelerates the accumulation of Cd and Pb in rice grains by 48.4-75.4% and 20.5-39.1%, respectively. Elevated CO₂ levels decreased soil pH value by 0.2 units, which increased Cd and Pb bioavailability in soil but inhibited iron plaque formation on rice roots, ultimately promoting Cd and Pb uptake. 16S rRNA sequencing analysis revealed that elevated CO₂ increased the relative abundance of certain soil bacteria (e.g., Acidobacteria, Alphaproteobacteria, Holophagae, and Burkholderiaceae). A health risk assessment showed that elevated CO₂ markedly increased the total carcinogenic risk values for children, adult males, and adult females by 75.3% (P < 0.05), 65.6% (P < 0.05), and 71.1% (P < 0.05), respectively. These results demonstrate the serious performance of elevated CO₂ levels in accelerating the bioavailability and accumulation of Cd and Pb in paddy soil-rice ecosystems, with particular risks for future safe rice production.

Responses of Fungal Assembly and Co-Occurrence Network of Rhizosphere Soil to Amaranthus palmeri Invasion in Northern China

The interaction between invasive plants and soil microbial communities is critical for plant establishment. However, little is known about the assembly and co-occurrence patterns of fungal communities in the rhizosphere soil of Amaranthus palmeri. The soil fungal communities and co-occurrence networks were investigated in 22 invaded patches and 22 native patches using high-throughput Illumina sequencing. Despite having little effect on alpha diversity, plant invasion significantly altered the composition of the soil fungal community (ANOSIM, p < 0.05). Fungal taxa associated with plant invasion were identified using linear discriminant analysis effect size (LEfSe). In the rhizosphere soil of A. palmeri, Basidiomycota was significantly enriched, while Ascomycota and Glomeromycota were significantly reduced when compared to native plants. At the genus level, the invasion of A. palmeri dramatically increased the abundance of beneficial fungi and potential antagonists such as Dioszegia, Tilletiopsis, Colacogloea, and Chaetomium, while it significantly decreased the abundance of pathogenic fungi such as Alternaria and Phaeosphaeria. Plant invasion reduced the average degree and average path length, and increased the modularity value, resulting in a less complex but more effective and stable network. Our findings improved the knowledge of the soil fungal communities, network co-occurrence patterns, and keystone taxa in A. palmeri-invaded ecosystems.

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.

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress

Introduction

Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear.

Methods

This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress.

Results and Discussion

Compared to the control (treated with ddH₂O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.

The effects of biochar aging on rhizosphere microbial communities in cadmium-contaminated acid soil

Biochars are widely used in the remediation of Cd-contaminated soils. However, changes in the bacterial communities in the rhizosphere contaminated with Cd in response to biochar aging are poorly studied. Addressing this gap in knowledge is important to improving micro-ecological services on healthy growth of plants with mitigation strategies against Cd contamination. An aging experiment (270 days) was conducted with biochars derived from poultry litter and sugar-gum wood added to a Cd-contaminated acid soil. Bacterial communities in the rhizosphere of Brassica rapa and bulk soils were investigated after 1, 90 and 270 days of biochar aging. There was no significant difference (P > 0.05) in bacterial Shannon and Simpson indices between the control and biochar treatments. However, compared to the no-Cd control, the addition of Cd decreased the relative abundances of Firmicutes, Chloroflexi and Acidobacteriota but increased those of Actinobacteriota and Proteobacteria. Poultry-litter biochar had the largest effect on bacterial community composition, especially in the rhizosphere. Aging of poultry-litter biochar increased the abundance of Armatimonadota over time more than the sugar-gum-wood biochar, which was attributed to a lower pH and higher bioavailability of Cd in the sugar-gum-wood biochar treatment. The addition of poultry-litter biochar to the contaminated soil mitigated the bioaccumulation of Cd by increasing soil pH and restoring soil bacterial ecology in contaminated acid soils over time.

Physiological and rhizospheric response characteristics to cadmium of a newly identified cadmium accumulator Coreopsis grandiflora Hogg. (Asteraceae)

Screening for superior cadmium (Cd) phytoremediation resources and uncovering the mechanisms of plant response to Cd are important for effective phytoremediation of Cd-polluted soils. In this study, the characteristics of Coreopsis grandiflora related to Cd tolerance and accumulation were analyzed to evaluate its Cd phytoremediation potential. The results revealed that C. grandiflora can tolerate up to 20 mg kg^-1 of Cd in the soil. This species showed relatively high shoot bioconcentration factors (1.09-1.85) and translocation factors (0.46-0.97) when grown in soils spiked with 5-45 mg kg^-1 Cd, suggesting that C. grandiflora is a Cd accumulator and can potentially be used for Cd phytoextraction. Physiological analysis indicated that antioxidant enzymes (i.e., superoxide dismutase, peroxidase, and catalase) and various free amino acids (e.g., proline, histidine, and methionine) participate in Cd detoxification in C. grandiflora grown in soil spiked with 20 mg kg^-1 of Cd (Cd20). The overall microbial richness and diversity remained similar between the control (Cd0) and Cd20 soils. However, the abundance of multiple rhizospheric microbial taxa was altered in the Cd20 soil compared with that in the Cd0 soil. Interestingly, many plant growth-promoting microorganisms (e.g., Nocardioides, Flavisolibacter, Rhizobium, Achromobacter, and Penicillium) enriched in the Cd20 soil likely contributed to the growth and vitality of C. grandiflora under Cd stress. Among these, some microorganisms (e.g., Rhizobium, Achromobacter, and Penicillium) likely affected Cd uptake by C. grandiflora. These abundant plant growth-promoting microorganisms potentially interacted with soil pH and the concentrations of Cd and AK in soil. Notably, potassium-solubilizing microbes (e.g., Rhizobium and Penicillium) may effectively solubilize potassium to assist Cd uptake by C. grandiflora. This study provides a new plant resource for Cd phytoextraction and improves our understanding of rhizosphere-associated mechanisms of plant adaptation to Cd-contaminated soil.

Response of microbial community structure to chromium contamination in Panax ginseng-growing soil

Chromium (Cr) contamination in soil poses a serious security risk for the development of medicine and food with ginseng as the raw material. Microbiome are critical players in the functioning and service of soil ecosystems, but their feedback to Cr-contaminated ginseng growth is still poorly understood. To study this hypothesis, we evaluated the effects of microbiome and different Cr exposure on the soil microbial community using Illumina HiSeq high-throughput sequencing. Our results indicated that 2467 OTUs and 1785 OTUs were obtained in 16S and ITS1 based on 97% sequence similarity, respectively. Bacterial and fungal diversity were affected significantly in Cr-contaminated soil. Besides, Cr contamination significantly changed the composition of the soil bacterial and fungal communities, and some biomarkers were identified in the different classification level of the different Cr-contaminated treatments using LEfSe. Finally, a heatmap of Spearman's rank correlation coefficients and canonical discriminant analysis (CDA) indicated that Chloroflexi, Gemmatimonadetes, Acidobacteria, Verrucomicobia, and Parcubacteria in phylum level and Acidimicrobiia, Gemmatimonadetes, and Deltaproteobacteria in class level were positively correlated with AK, AP, and NO₃^--N (p < 0.05 or p < 0.01), but negatively correlated with total Cr and available Cr (p < 0.05 or p < 0.01). Similarly, in the fungal community, Tubaria, Mortierellaceae, and Rhizophagus in the phylum level and Glomeromycetes, Agaricomycetes, and Exobasidiomycetes in the class level were positively correlated with AK, AP, and NO₃^--N (p < 0.05 or p < 0.01), but negatively correlated with total Cr and available Cr (p < 0.05 or p < 0.01). Our findings provide new insight into the effects of Cr contamination on the microbial communities in ginseng-growing soil.

Combined Plant Growth-Promoting Bacteria Inoculants Were More Beneficial than Single Agents for Plant Growth and Cd Phytoextraction of Brassica juncea L. during Field Application

Single or combined plant growth-promoting bacteria (PGPB) strains were widely applied as microbial agents in cadmium (Cd) phytoextraction since they could promote plant growth and facilitate Cd uptake. However, the distinct functional effects between single and combined inoculants have not yet been elucidated. In this study, a field experiment was conducted with single, double and triple inoculants to clarify their divergent impacts on plant growth, Cd uptake and accumulation at different growth stages of Brassica juncea L. by three different PGPB strains (Cupriavidus SaCR1, Burkholdria SaMR10 and Sphingomonas SaMR12). The results show that SaCR1 + SaMR10 + SaMR12 combined inoculants were more effective for growth promotion at the bud stage, flowering stage, and mature stage. Single/combined PGPB agents of SaMR12 and SaMR10 were more efficient for Cd uptake promotion. In addition, SaMR10 + SaMR12 combined the inoculants greatly facilitated Cd uptake and accumulation in shoots, and enhanced the straw Cd extraction rates by 156%. Therefore, it is concluded that the application of PGPB inoculants elevated Cd phytoextraction efficiency, and the combined inoculants were more conductive than single inoculants. These results enriched the existing understanding of PGPB agents and provided technical support for the further exploration of PGPB interacting mechanisms strains on plant growth and Cd phytoextraction, which helped establish an efficient plant–microbe combined phytoremediation system and augment the phytoextraction efficiency in Cd-contaminated farmlands.

Synergistic effects of Cd-loving Bacillus sp. N3 and iron oxides on immobilizing Cd and reducing wheat uptake of Cd

Iron oxides and microorganisms are important soil components that profoundly affect the transformation and bioavailability of heavy metals in soils. Here, batch and pot experiments were conducted to investigate the immobilization mechanisms of Cd by Cd-loving Bacillus sp. N3 and ferrihydrite (Fh) as well as their impacts on Cd uptake by wheat and bacterial community composition in wheat rhizospheric soil. The results showed that the combination of strain N3 with Fh could immobilize more Cd compared to strain N3 and Fh, respectively. Furthermore, strain N3 facilitated Cd retention on Fh, which synergistically reduced the concentration of DTPA extracted Cd in the soil and decreased Cd content (57.1%) in wheat grains. Moreover, inoculation with strain N3 increased the complexity of the co-occurrence network of the bacterial community in rhizospheric soil, and the abundance of beneficial bacteria with multipel functions including heavy metal immobilization, dissimilatory iron reduction, and plant growth promotion. Overall, this study demonstrated the enrichment of strain N3 and iron oxides, together with increased soil pH, synergistically immobilized soil Cd, which strongly suggested inoculation with Cd-loving strains could be a promising approach to immobilize Cd and reduce wheat uptake of Cd, particular for soils rich in iron oxides.

A Stronger Rhizosphere Impact on the Fungal Communities Compared to the Bacterial Communities in Pecan Plantations

Understanding microbial communities associated with bulk and rhizosphere soils will benefit the maintenance of forest health and productivity and the sustainable development of forest ecosystems. Based on MiSeq sequencing, we explored the differences between the bulk soil and the rhizosphere soil on bacterial and fungal communities of pecan plantation. Results suggested that rhizosphere-associated fungal rather than bacterial community structures differed from bulk soil, and rhizosphere soil had lower fungal diversity than bulk soil. Actinobacteria and Cantharellales were the bacterial and fungal biomarkers of the rhizosphere soil of pecan plantation, respectively. In addition, Pleosporales, which are mainly involved in saprophylaxis and plant pathogenic processes, was identified as one of the most important fungal biomarkers for the bulk soil, and the FunGuild predicted a higher relative abundance of pathogenic fungi in bulk soil compared to rhizosphere soil. The pH, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N), and total carbon (TC) contents drove microbial community structure and composition. The bacterial network was simpler in the rhizosphere soil than in the bulk soil. However, fungi showed the opposite network pattern. Keystone species in bacterial and fungal networks were mostly involved in nutrient cycling and the C cycling, and were found to be enriched in the rhizosphere soil. Overall, in terms of bacterial and fungal communities, the rhizosphere soil behaves more healthily than the bulk soil and has a higher potential for nutrient cycling.

Microbial Interventions in Bioremediation of Heavy Metal Contaminants in Agroecosystem

Soil naturally comprises heavy metals but due to the rapid industrialization and anthropogenic events such as uncontrolled use of agrochemicals their concentration is heightened up to a large extent across the world. Heavy metals are non-biodegradable and persistent in nature thereby disrupting the environment and causing huge health threats to humans. Exploiting microorganisms for the removal of heavy metal is a promising approach to combat these adverse consequences. The microbial remediation is very crucial to prevent the leaching of heavy metal or mobilization into the ecosystem, as well as to make heavy metal extraction simpler. In this scenario, technological breakthroughs in microbes-based heavy metals have pushed bioremediation as a promising alternative to standard approaches. So, to counteract the deleterious effects of these toxic metals, some microorganisms have evolved different mechanisms of detoxification. This review aims to scrutinize the routes that are responsible for the heavy metal(loid)s contamination of agricultural land, provides a vital assessment of microorganism bioremediation capability. We have summarized various processes of heavy metal bioremediation, such as biosorption, bioleaching, biomineralization, biotransformation, and intracellular accumulation, as well as the use of genetically modified microbes and immobilized microbial cells for heavy metal removal.

Microbial metabolic limitation of rhizosphere under heavy metal stress: Evidence from soil ecoenzymatic stoichiometry

Slow nutrient turnover and destructed soil function were the main factors causing low efficiency in phytoremediation of heavy metal (HM)-contaminated soil. Soil ecoenzymatic stoichiometry can reflect the ability of soil microorganisms to acquire energy and nutrients, and drive nutrient cycling and carbon (C) decomposition in HM-contaminated soil. Therefore, for the first time, we used the enzymatic stoichiometry modeling to examine the microbial nutrient limitation in rhizospheric and bulk soil of different plants (Medicago sativa, Halogeton arachnoideus and Agropyron cristatum) near the Baiyin Copper Mine. Results showed that the main pollutants in this area were Cu, Zn, Cd, and Pb, while Cd and Zn have the greatest contribution according to the analysis of pollution load index (PLI). The activities of soil C-, nitrogen (N)-, and phosphorus (P)-acquiring enzymes in the rhizosphere of plants were significantly greater than that in bulk soil. Moreover, microbial C and P limitations were observed in all plant treatments, while the lower limitation was generally in the rhizosphere compared to bulk soil. The HM stress significantly increased microbial C limitation and decreased microbial P limitation, especially in the rhizospheric soil. The partial least squares path modeling (PLS-PM) further indicated that HM concentration has the greatest effects on microbial P limitation (-0.64). In addition, the highest enzyme activities and the lowest P limitation were observed in the rhizospheric and bulk soil of M. sativa, thereby implying that soil microbial communities under the remediation of M. sativa were steadier and more efficient in terms of their metabolism. These findings are important for the elucidation of the nutrient cycling and microbial metabolism of rhizosphere under phytoremediation, and provide guidance for the restoration of HM-contaminated soil.

Root-associated microbiota drive phytoremediation strategies to lead of Sonchus Asper (L.) Hill as revealed by intercropping-induced modifications of the rhizosphere microbiome

Intercropping or assistant endophytes promote phytoremediation capacities of hyperaccumulators and enhance their tolerance to heavy metal (HM) stress. Findings from a previous study showed that intercropping the hyperaccumulator Sonchus asper (L.) Hill grown in HM-contaminated soils with maize improved the remediating properties and indicated an excluder-to-hyperaccumulator switched mode of action towards lead. In the current study, RNA-Seq analysis was conducted on Sonchus roots grown under intercropping or monoculture systems to explore the molecular events underlying this shift in lead sequestering strategy. The findings showed that intercropping only slightly affects S. asper transcriptome but significantly affects expression of root-associated microbial genomes. Further, intercropping triggers significant reshaping of endophytic communities associated with a 'root-to-shoot' transition of lead sequestration and improved phytoremediation capacities of S. asper. These findings indicate that accumulator activities of a weed are partially attributed to the root-associated microbiota, and a complex network of plant-microbe-plant interactions shapes the phytoremediation potential of S. asper. Analysis showed that intercropping may significantly change the structure of root-associated communities resulting in novel remediation properties, thus providing a basis for improving phytoremediation practices to restore contaminated soils.

Insight into how fertilization strategies increase quality of grape (Kyoho) and shift microbial community

Organic and bioorganic fertilizers were increasingly used for agricultural soil. However, little is known on what kind of organic fertilizer application strategies can promote grape production well and how appropriate fertilization strategies improve soil properties and shift microbial community. This study investigated the improvement in soil physicochemical properties as well as their relations with microbial community structure and grape quality under different fertilization strategies. Our results found that (bio)organic fertilizer (CF1, CF2, and BF) especially combined application of organic and bioorganic fertilization (CBF) had smaller effects on electrical conductivity (EC) and pH, while it improved soil nutrients including N, P, K, and organic matter (OM) well, thereby promoting the grape quality comparing to the group without any fertilizer (CK) and with chemical fertilizer (NPK). Especially, the concentrations of Cr, Hg, Zn, and Cu were reduced by 13.63%, 12.50%, 12.52%, and 11.75% in CBF, respectively. Additionally, CF1, CF2, and BF, especially CBF, optimized the communities' composition and increased the abundance of some plant probiotics such as Solirubrobacter and Lysobacter. Nevertheless, excessive application of organic fertilizer derived from livestock manure could cause the accumulation of heavy metals such as Zn and Cu in soil and leaves, which could further influence the grape quality. Additionally, the structure of microbial communities was also changed possibly because some bacterial genera showed distinct adaptability to the stress of heavy metals or the utilization capacity of N, P, K, and OM. Our results demonstrated that combined application of organic and bioorganic fertilization showed a great influence on soil physicochemical properties, whose positive changes could further optimize microbial communities and facilitate the promotion of grape quality.

Effects of cadmium contamination on bacterial and fungal communities in Panax ginseng-growing soil

Background

Cadmium (Cd) contamination in soil poses a serious safety risk for the development of medicine and food with ginseng as the raw material. Microorganisms are key players in the functioning and service of soil ecosystems, but the effects of Cd-contaminated ginseng growth on these microorganisms is still poorly understood. To study this hypothesis, we evaluated the effects of microorganisms and Cd (0, 0.25, 0.5, 1.0, 2.0, 5.0, and 10.0 mg kg^-1 of Cd) exposure on the soil microbial community using Illumina HiSeq high-throughput sequencing.

Results

Our results indicated that Cd-contaminated soil affected the soil microbial diversity and composition, and bacterial diversity was affected more than fungal diversity in Cd-contaminated soil, especially according to Shannon indices. The abundance of the soil microbial community decreased and the composition changed according to the relative abundances at the phylum level, including those of Saccharibacteria and Gemmatimonadetes in bacteria and Mortierellomycota in fungi. The LEfSe algorithm was used to identify active biomarkers, and 45 differentially abundant bacterial taxonomic clades and 16 differentially abundant fungal taxonomic clades were identified with LDA scores higher than 4.0. Finally, a heatmap of Spearman's rank correlation coefficients and canonical discriminant analysis (CDA) indicated that some key biomarkers, Arenimonas, Xanthomonadales, Nitrosomonadaceae, Methylophilales, Caulobacterales, Aeromicrobium, Chitinophagaceae, Acidimicrobiales, Nocardioidaceae, Propionibacteriales, Frankiales, and Gemmatimonadaceae, were positively correlated with the total and available Cd (p<0.05) but negatively correlated with AK, AP, and pH (p<0.05) in the bacterial community. Similarly, in the fungal community, Tubaria, Mortierellaceae, and Rhizophagus were positively correlated with the total and available Cd but negatively correlated with AK, AP, TK, and pH.

Conclusion

Cd contamination significantly affected microbial diversity and composition in ginseng-growing soil. Our findings provide new insight into the effects of Cd contamination on the microbial communities in ginseng-growing soil.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02488-z.

Recent Developments in Microbe-Plant-Based Bioremediation for Tackling Heavy Metal-Polluted Soils

Soil contamination with heavy metals (HMs) is a serious concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Rapid industrialization and activities such as mining, manufacturing, and construction are generating a huge quantity of toxic waste which causes environmental hazards. There are various traditional physicochemical techniques such as electro-remediation, immobilization, stabilization, and chemical reduction to clean the contaminants from the soil. However, these methods require high energy, trained manpower, and hazardous chemicals make these techniques costly and non-environment friendly. Bioremediation, which includes microorganism-based, plant-based, microorganism-plant associated, and other innovative methods, is employed to restore the contaminated soils. This review covers some new aspects and dimensions of bioremediation of heavy metal-polluted soils. The bioremediation potential of bacteria and fungi individually and in association with plants has been reviewed and critically examined. It is reported that microbes such as Pseudomonas spp., Bacillus spp., and Aspergillus spp., have high metal tolerance, and bioremediation potential up to 98% both individually and when associated with plants such as Trifolium repens, Helianthus annuus, and Vallisneria denseserrulata. The mechanism of microbe's detoxification of metals depends upon various aspects which include the internal structure, cell surface properties of microorganisms, and the surrounding environmental conditions have been covered. Further, factors affecting the bioremediation efficiency and their possible solution, along with challenges and future prospects, are also discussed.

A Mini-Review on the Co-growth and Interactions Among Microorganisms (Fungi and Bacteria) From Rhizosphere of Metal-Hyperaccumulators

The co-growth and synergistic interactions among fungi and bacteria from the rhizosphere of plants able to hyper accumulate potentially toxic metals (PTMs) are largely unexplored. Fungi and bacteria contribute in an essential way to soil biogeochemical cycles mediating the nutrition, growth development, and health of associated plants at the rhizosphere level. Microbial consortia improve the formation of soil aggregates and soil fertility, producing organic acids and siderophores that increase solubility, mobilization, and consequently the accumulation of nutrients and metals from the rhizosphere. These microorganism consortia can both mitigate the soil conditions promoting plant colonization and increase the performance of hyperaccumulator plants. Indeed, microfungi and bacteria from metalliferous soils or contaminated matrices are commonly metal-tolerant and can play a key role for plants in the phytoextraction or phytostabilization of metals. However, few works deepen the effects of the inoculation of microfungal and bacterial consortia in the rhizosphere of metallophytes and their synergistic activity. This mini-review aimed to collect and report the data regarding the role of microbial consortia and their potentialities known to date. Moreover, our new data had shown an active fungal-bacteria consortium in the rhizosphere of the hyperaccumulator plant Alyssoides utriculata.