Changes induced by heavy metals in the plant-associated microbiome of Miscanthus x giganteus

Integrative study of transcriptome and microbiome to reveal the response of Rhododendron decorum to cadmium stress

The anomalies of cadmium (Cd) in karst region pose a severe threat to plant growth and development. In this study, the responses of Rhododendron decorum to Cd stress were investigated at physiological, molecular, and endophytic microbial levels, and the potential correlation among these responses was assessed. The Cd stress impeded R. decorum growth and led to an increase in malondialdehyde (MDA) and hydrogen peroxide (H2O2) levels, as well as enhanced superoxide dismutase (SOD) and catalase (CAT) activities. Meanwhile, Cd stress increased the Cd (up to 80 times compared to the control), sodium (Na), aluminum (Al), and zinc (Zn) contents, while decreased the magnesium (Mg) and manganese (Mn) contents in R. decorum leaves. Transcriptome suggested that Cd significantly regulated the pathways including "protein repair", "hormone-mediated signaling pathway", and "ATP-binding cassette (ABC) transporters". Additionally, q-PCR analysis showed that Cd stress significantly up-regulated the expressions of ABCB19-like and pleiotropic drug resistance, while down-regulated the expressions of indole-3-acetic acid-amido synthetase and cytokinin dehydrogenase. The Cd stress influenced the composition of endophytic microbial communities in R. decorum leaves and enhanced the interspecific bacterial associations. Furthermore, the bacterial genera Achromobacter, Aureimonas and fungal genus Vishniacozyma exhibited a high degree of connectivity with other nodes in networks constructed by the metal element contents, differentially expressed genes (DEGs), and microbial communities, respectively. These findings provide a comprehensive insight into the response of R. decorum to Cd-induced stress, which might facilitate the breeding of the Cd-tolerant R. decorum.

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.

Aragonite crystallization in a sulfate-rich hypersaline wetland under dry Mediterranean climate (Laguna Honda, eastern Guadalquivir basin, S Spain)

This research investigates the influence of water composition, the presence of seasonal algal mats, detrital inputs and the activity of microorganisms on the crystallization of aragonite in the sediments deposited in the hypersaline Laguna Honda wetland (S of Spain). The high alkaline and hypersaline waters (pH > 9.2 and C.E. > 70 mS/cm) of the wetland lake are rich in SO42- (>24,000 mg/l), Cl- (>21,000 mg/l), Na+ (>11,000 mg/l) Mg2+ (>8400 mg/l) and Ca2+ (>1000 mg/l), and are supersaturated for dolomite, calcite and aragonite. Sediments have lower pH values than column waters, oscillating from 8.54 in the low Eh (up to -80.9 mV) central deep sediments and 6.33 in the shallower higher Eh (around -13.6 mV) shore sediments. Erosion of the surrounding olive groves soils produced detrital silicates rich sediments with concretions of carbonate or sulfate. Aragonite (up to 19 %) and pyrite (up to 13 %) are mainly concentrated in the organic matter rich samples from the upper part of the sediment cores, whereas gypsum is preferably concentrated in low organic matter content samples. Mineral crusts containing a MgAl silicate phase, epsomite, halite and gypsum are precipitated on the floating algal mats covering the wetland waters. Floating algal mats deposit increased the organic matter content of the upper sediments which promoted the presence of fermentative microorganisms, sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) communities and variations of Eh that influence the authigenesis of carbonate and S-bearing minerals. Replacement of poorly crystalline MgSi phases infilling algal cells by aragonite was favored in the organic matter rich sediments with low Eh values and important SRB communities that promoted sulfate bioreduction processes to form pyrite. Aragonite precipitation was favored by the increase of carbonate and bicarbonate concentration produced by the SRB oxidation of organic matter, the CO2 degassing by high summer temperatures and the CO2 uptake by photosynthesis of the algal mats.

Enhancing La(III) biosorption and biomineralization with Micromonospora saelicesensis: Involvement of phosphorus and formation of monazite nano-minerals

The release of rare earth elements (REEs) from mining wastes and their applications has significant environmental implications, necessitating the development of effective prevention and reclamation strategies. The mobility of REEs in groundwater due to microorganisms has garnered considerable attention. In this study, a La(III) resistant actinobacterium, Micromonospora saelicesensis KLBMP 9669, was isolated from REE enrichment soil in GuiZhou, China, and evaluated for its ability to adsorb and biomineralize La(III). The findings demonstrated that M. saelicesensis KLBMP 9669 immobilized La(III) through the physical and chemical interactions, with immobilization being influenced by the initial La(III) concentration, biomass, and pH. The adsorption kinetics followed a pseudo-second-order rate model, and the adsorption isotherm conformed to the Langmuir model. La(III) adsorption capacity of this strain was 90 mg/g, and removal rate was 94 %. Scanning electron microscope (SEM) coupled with energy dispersive X-ray spectrometer (EDS) analysis revealed the coexistence of La(III) with C, N, O, and P. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) investigations further indicated that carboxyl, amino, carbonyl, and phosphate groups on the mycelial surface may participate in lanthanum adsorption. Transmission electron microscopy (TEM) revealed that La(III) accumulation throughout the M. saelicesensis KLBMP 9669, with some granular deposits on the mycelial surface. Selected area electron diffraction (SAED) confirmed the presence of LaPO4 crystals on the M. saelicesensis KLBMP 9669 biomass after a prolonged period of La(III) accumulation. This post-sorption nano-crystallization on the M. saelicesensis KLBMP 9669 mycelial surface is expected to play a crucial role in limiting the bioimmobilization of REEs in geological repositories.

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.

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb

IMPORTANCE

Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro-generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants.

How does metal soil pollution change the plant mycobiome?

Microorganisms play a key role in plant adaptation to the environment. The aim of this study was to evaluate the effect of toxic metals present in the soil on the biodiversity of plant-related, endophytic mycobiota. The mycobiome of plants and soil from a Zn-Pb heap and a metal-free ruderal area were compared via Illumina sequencing of the ITS1 rDNA. The biodiversity of plants and fungi inhabiting mine dump substrate was lower than that of the metal free site. In the endosphere of Arabidopsis arenosa from the mine dump the number of endophytic fungal taxa was comparable to that in the reference population, but the community structure significantly differed. Agaricomycetes was the most notably limited class of fungi. The results of plant mycobiota evaluation from the field study were verified in terms of the role of toxic metals in plant endophytic fungi community assembly in a reconstruction experiment. The results presented in this study indicate that metal toxicity affects the structure of the plant mycobiota not by changing the pool of microorganisms available in the soil from which the fungal symbionts are recruited but most likely by altering plant and fungi behaviour and the organisms' preferences towards associating in symbiotic relationships.

Combination of Biochar and Trichoderma harzianum Can Improve the Phytoremediation Efficiency of Brassica juncea and the Rhizosphere Micro-Ecology in Cadmium and Arsenic Contaminated Soil

Phytoremediation is an environment-friendly method for toxic elements remediation. The aim of this study was to improve the phytoremediation efficiency of Brassica juncea and the rhizosphere soil micro-ecology in cadmium (Cd) and arsenic (As) contaminated soil. A field experiment was conducted with six treatments, including a control treatment (CK), two treatments with two contents of Trichoderma harzianum (T1: 4.5 g m-2; T2: 9 g m-2), one biochar treatment (B: 750 g m-2), and two combined treatments of T1B and T2B. The results showed Trichoderma harzianum promoted the total chlorophyll and translocation factor of Brassica juncea, while biochar promoted plant biomass compared to CK. T2B treatment showed the best results, which significantly increased Cd accumulation by 187.49-308.92%, and As accumulation by 125.74-221.43%. As a result, the soil's total Cd content was reduced by 19.04% to 49.64% and total As contents by 38.76% to 53.77%. The combined amendment increased the contents of soil available potassium, phosphorus, nitrogen, and organic matter. Meanwhile, both the activity of glutathione and peroxidase enzymes in plants, together with urease and sucrase enzymes in soil, were increased. Firmicutes (dominant bacterial phylum) and Ascomycota (dominant fungal phylum) showed positive and close correlation with soil nutrients and plant potentially toxic elements contents. This study demonstrated that phytoremediation assisted by biochar and Trichoderma harzianum is an effective method of soil remediation and provides a new strategy for enhancing plant remediation efficiency.

Effect of Heavy-Metal-Resistant PGPR Inoculants on Growth, Rhizosphere Microbiome and Remediation Potential of Miscanthus × giganteus in Zinc-Contaminated Soil

Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the host plant grown in control and zinc-contaminated (1650 mg/kg) soil in a 4-month pot experiment. The diversity and taxonomic structure of the rhizosphere microbiomes, assessed with metagenomic analysis of rhizosphere samples for the 16S rRNA gene, were studied. Principal coordinate analysis showed differences in the formation of the microbiomes, which was affected by zinc rather than by the inoculants. Bacterial taxa affected by zinc and the inoculants, and the taxa potentially involved in the promotion of plant growth as well as in assisted phytoremediation, were identified. Both inoculants promoted miscanthus growth, but only Chitinophaga sp. Zn19 contributed to significant Zn accumulation in the aboveground part of the plant. In this study, the positive effect of miscanthus inoculation with Mycolicibacterium spp. and Chitinophaga spp. was demonstrated for the first time. On the basis of our data, the bacterial strains studied may be recommended to improve the efficiency of M. × giganteus phytoremediation of zinc-contaminated soil.

Combined forage grass-microbial for remediation of strontium-contaminated soil

Enrichment plants were screened from six forage grasses in this study to establish a complete combined forage grass-microbial remediation system of strontium-contaminated soil, and microbial groups were added to the screened dominant forage grasses. The occurrence states of strontium in forage grasses were explored by the BCR sequential extraction method. The results showed that the annual removal rate of Sudan grass (Sorghum sudanense (Piper) Stapf.) reached 23.05% in soil with a strontium concentration of 500 mg·kg^-1. Three dominant microbial groups: E, G and H, have shown good facilitation effects in co-remediation with Sudan grass and Gaodan grass (Sorghum bicolor × sudanense), respectively. When compared to the control, the strontium accumulation of forage grasses in kg of soil with microbial groups was increased by 0.5-4 fold. The optimal forage grass-microbial combination can theoretically repair contaminated soil in three years. The microbial group E was found to promote the transfer of the exchangeable state and the reducible state of strontium to the overground part of the forage grass. Metagenomic sequencing results showed that the addition of microbial groups increased Bacillus spp. in rhizosphere soil, enhanced the disease resistance and tolerance of forage grasses, and improved the remediation ability of forage grass-microbial combinations.

The root-associated Fusarium isolated based on fungal community analysis improves phytoremediation efficiency of Ricinus communis L. in multi metal-contaminated soils

Phytoremediation is a widely accepted bioremediation method of treating heavy metal contaminated soils. Nevertheless, the remediation efficiency in multi-metal contaminated soils is still unsatisfactory attributable to susceptibility to different metals. To isolate root-associated fungi for improving phytoremediation efficiency in multi-metal contaminated soils, the fungal flora in root endosphere, rhizoplane, rhizosphere of Ricinus communis L. in heavy metal contaminated soils and non-heavy metal contaminated soils were compared by ITS amplicon sequencing, and then the critical fungal strains were isolated and inoculated into host plants to improve phytoremediation efficiency in Cd, Pb, and Zn-contaminated soils. The fungal ITS amplicon sequencing analysis indicated that the fungal community in root endosphere was more susceptible to heavy metals than those in rhizoplane and rhizosphere soils and Fusarium dominated the endophytic fungal community of R. communis L. roots under heavy metal stress. Three endophytic strains (Fusarium sp. F2, Fusarium sp. F8, and Fusarium sp. F14) isolated from Ricinus communis L. roots showed high resistances to multi-metals and possessed growth-promoting characteristics. Biomass and metal extraction amount of R. communis L. with Fusarium sp. F2, Fusarium sp. F8, and Fusarium sp. F14 inoculation in Cd-, Pb- and Zn-contaminated soils were significantly higher than those without the inoculation. The results suggested that fungal community analysis-guided isolation could be employed to obtain desired root-associated fungi for enhancing phytoremediation of multi-metal contaminated soils.

Potential application of novel cadmium-tolerant bacteria in bioremediation of Cd-contaminated soil

With the increase in cadmium (Cd) release into the environment, it is necessary to find appropriate solutions to reduce soil Cd pollution. Microorganisms are a green and effective means for the remediation of Cd-contaminated soil. In this study, in a Cd-contaminated farmland, we screened and identified novel Cd-resistant strains, Paenarthrobactor nitroguajacolicus, Lysinibacillus fusiformis, Bacillus licheniformis, and Methyllobacium brachiatum, with minimum inhibitory concentrations of 100, 100, 50, and 50 mg/L, respectively, and added them each to pots containing Cd-contaminated rape plants to explore their remediation ability. The results showed that treatment with each of the four strains significantly increased the abundance of Nitrospirae, Firmicutes, Verrucomicrobia, and Patescibacterium in the rhizosphere soil of the plants. This led to changes in soil physical and chemical indices; pH; and available phosphorus, urease, and catalase activities, which were significantly negatively correlated with bioavailable Cd, reducing 28.74-58.82 % Cd enrichment to plants and 23.72-43.79 % Cd transport within plants, and reducing 5.52-10.68 % available cadmium in soil, effectively reducing the biotoxicity of Cd. Thus, this study suggests microbial remediation as a reliable option, forming a basis for the remediation of Cd-contaminated soil.

Effect of bioaugmentation on tetracyclines influenced chicken manure composting and antibiotics resistance

Antibiotic residue in husbandry waste has become a serious concern. In this study, contaminated chicken manure composting was conducted to reveal the bioaugmentation effect on tetracyclines residue and antibiotics resistance genes (ARGs). The bioaugmented composting removed most of the antibiotics in 7 days. Under bioaugmentation, 96.88 % of tetracycline and 92.31 % of oxytetracycline were removed, 6.32 % and 20.93 % higher than the control (P < 0.05). The high-temperature period was the most effective phase for eliminating antibiotics. The treatment showed a long high-temperature period (7 days), while no high-temperature period was in control. After composting, the treatment showed 13.87 % higher TN (26.51 g/kg) and 13.42 % higher NO₃^--N (2.45 g/kg) than control (23.28 and 2.16 g/kg, respectively) but 12.72 % lower C/N, indicating fast decomposition and less nutrient loss. Exogenous microorganisms from bioaugmentation significantly reshaped the microbial community structure and facilitated the enrichment of genera such as Truepera and Fermentimonas, whose abundance increased by 71.10 % and 75.37 % than the control, respectively. Remarkably, ARGs, including tetC, tetG, and tetW, were enhanced by 198.77 %, 846.77 %, and 62.63 % compared with the control, while the integron gene (intl1) was elevated by 700.26 %, indicating horizontal gene transfer of ARGs. Eventually, bioaugmentation was efficient in regulating microbial metabolism, relieving antibiotic stress, and eliminating antibiotics in composting. However, the ability to remove ARGs should be further investigated. Such an approach should be further considered for treating pollutants-influenced organic waste to eliminate environmental concerns.

Differences in Physiological Metabolism and Antioxidant System of Different Ecotypes of Miscanthus floridulus under Cu Stress

To reveal the similarities and differences in the resistance mechanisms of different ecotypes to Cu stress, a pot experiment was used to systematically compare the physiological responses of non-mining ecotype Miscanthus floridulus (collected from Boluo County, Huizhou City) and mining ecotype Miscanthus floridulus (collected from Dabaoshan mining area) under different Cu concentrations. The results showed that chlorophyll a, chlorophyll b and total chlorophyll in the leaves of the two ecotypes of M. floridulus were negatively correlated with Cu stress concentration (p < 0.01), but the extent of decrease for the ecotypes in the mining area was lower than that for the ecotypes in the non-mining area. The values of chlorophyll a/b for both ecotypes increased with increasing Cu treatment concentration, indicating that Cu is more harmful to chlorophyll b than to chlorophyll a for M. floridulus. Cu stress can lead to the accumulation of malondialdehyde (MDA) in the leaves of M. floridulus with the amount of MDA accumulation observed being greater in the non-mining ecotype than in the mining ecotype (p < 0.05). The content of antioxidant substances (ascorbic acid and reduced glutathione) in the mining ecotype M. floridulus was significantly higher than that in the non-mining ecotype. The activity of SOD in the leaves of non-mining ecotypes was inhibited by Cu stress and the activity of POD was increased by Cu stress. However, the increase in POD in the mining ecotypes was greater than that in the non-mining ecotypes and the activities of the two enzymes in the mining ecotypes were significantly higher than those in the non-mining ecotypes at the highest concentration of Cu. Cu had different effects on PPO activity in the leaves of the two ecotypes of M. floridulus. The plant leaves of the non-mining ecotype at 400 and 800 mg·kg−1 were significantly fewer than those of the control group (p < 0.05), which were 87.1% and 65.2% of the control group, respectively. The PPO activity in the plant leaves of the mining ecotype was higher than that in the leaves of the non-mining ecotype and was significantly higher at 400 and 800 mg·kg−1 than that of the control group (p < 0.05), at 226.5% and 268.1% of the control group, respectively. These results indicate that the mining ecotype M. floridulus is more resistant to copper stress, that resistant ecotypes have been formed, and that small-molecule antioxidant substances play an important role in increasing resistance levels.

The Difference of Lead Accumulation and Transport in Different Ecotypes of Miscanthus floridulus

Miscanthus floridulus is a plant with a high biomass and heavy metal tolerance, which is a good candidate for phytoremediation. Pot experiments were conducted to compare the growth response, Pb enrichment ability, and the effect on Pb speciation of two ecotypes of M. floridulus from the Dabaoshan Mining Area and the non-mining area of Boluo County, Huizhou, in soils with different Pb contents. The results showed that two ecotypes of M. floridulus had different growth responses to Pb concentrations in soil. Under a low concentration of Pb (100 mg·kg−1) treatment, the aboveground biomass of the non-mining area plant ecotype was significantly affected, while the plants with the mining area ecotype were not significantly affected. When the concentration of Pb increased, the aboveground biomass of the non-mining ecotype was 30.2–41.1% of the control, while that of the mining ecotype was 57.8–65.0% of the control. The root biomass of the non-mining ecotype decreased with the increase of treatment concentration, accounting for 57.8–64.2% of the control, while that of the mining ecotype increased significantly, accounting for 119.5–138.6% of the control. The Pb content in the shoots and roots of the mining ecotype M. floridulus increased rapidly with the increase of the Pb treatment concentration in the soil, and the increase in speed was obviously faster than that of the non-mining ecotype. The total amount of Pb accumulated in the roots of the ecotype from the mining area was much greater than that of the ecotype from the non-mining area, and increased significantly with the increase of Pb concentration in the soil (p < 0.05). With the aggravation of Pb stress, the transfer coefficient and tolerance index of the two ecotypes decreased by different degrees. The transfer coefficient and tolerance index of the mining ecotype were significantly higher than those of the non-mining ecotype. Pearson correlation analysis showed that root biomass was positively correlated with shoot biomass, and shoot biomass was negatively correlated with Pb content in both root and shoot, indicating that Pb accumulation in root and shoot was toxic to plants and inhibited the growth of M. floridulus. The mining ecotypes showed stronger tolerance to and enrichment of Pb.

Phosphate mining activities affect crop rhizosphere fungal communities

Phosphate mining releases heavy metals into the surrounding environment. In this study, the effects of phosphate mining on rhizosphere soil fungi in surrounding crops, including Lactuca sativa var. angustata, Glycine max (L.) Merr., and Triticum aestivum L., were assessed. Phosphate mining significantly reduced the crop rhizosphere fungal diversity (P < 0.05). The relative abundances of Fusarium and Epicoccum increased in mining rhizosphere soil compared with the baseline. Beta diversity analysis indicated that phosphate mining led to the differentiation of fungal community structure in plant rhizospheres. Guild analysis indicated that different plant rhizosphere fungi developed various guilds in response to phosphate mining stress. Nine fungi were isolated from soil samples, with solubilization index values ranging from 1.1 to 2.5. Two efficient phosphate solubilizers, Epicoccum nigrum and Fusarium verticillioides, were enriched in phosphate mining rhizosphere soil samples. The dissolution kinetics of inorganic phosphorus and alkaline phosphatase activity assay showed strong phosphorus dissolution ability of the isolated fungi. Penicillium aculeatum, Trichoderma harzianum, Chaetomium globosum, and F. verticillioides showed strong tolerance to multiple heavy metals. This study furthers our understanding of how rhizosphere fungal ecology is affected by phosphate mining and provides important resources for the remediation of phosphate mining soil pollution.

A scoping review of bryophyte microbiota: diverse microbial communities in small plant packages

Plant health depends not only on the condition of the plant itself but also on its diverse community of microbes, or microbiota. Just like the better-studied angiosperms, bryophytes (mosses, liverworts, and hornworts) harbor diverse communities of bacteria, archaea, fungi, and other microbial eukaryotes. Bryophytes are increasingly recognized as important model systems for understanding plant evolution, development, physiology, and symbiotic interactions. Much of the work on bryophyte microbiota in the past focused on specific symbiont types for each bryophyte group, but more recent studies are taking a broader view acknowledging the coexistence of diverse microbial communities in bryophytes. Therefore, this review integrates studies of bryophyte microbes from both perspectives to provide a holistic view of the existing research for each bryophyte group and on key themes. The systematic search also reveals the taxonomic and geographic biases in this field, including a severe under-representation of the tropics, very few studies on viruses or eukaryotic microbes beyond fungi, and a focus on mycorrhizal fungi studies in liverworts. Such gaps may have led to errors in conclusions about evolutionary patterns in symbiosis. This analysis points to a wealth of future research directions that promise to reveal how the distinct life cycles and physiology of bryophytes interact with their microbiota.

Influence of Miscanthus Rhizome Pyrolysis Operating Conditions on Products Properties

Waste from the Miscanthus production cycle may be a promising source of material for the pyrolysis and biochar production. The biochar can be used to enrich the soil on which the crop grows, thus increasing productivity. A sample of Miscanthus rhizomes was used as a raw material in a series of experiments in order to find the most suitable conditions for the preparation of biochar. Miscanthus biochar was prepared in a laboratory unit using four different temperatures (i.e., 400, 500, 600 and 700 °C). All pyrolysis products were subsequently evaluated in terms of their quality and product yields were determined. For a temperature of 600 °C and a residence time of 2 h, the appropriate properties of biochar were achieved and the process was still economical. The biochar contained a minimal number of polycyclic aromatic hydrocarbons and a high percentage of carbon. Surface area was measured to be 217 m2/g. The aqueous extract of biochar was alkaline.

Improved phytoremediation of heavy metal contaminated soils by Miscanthus floridulus under a varied rhizosphere ecological characteristic

Miscanthus floridulus is a plant with high biomass and heavy metal tolerance, which is a good candidate for phytoremediation. It is essential to explore how to improve its remediation ability, especially the rhizosphere ecological characteristics which are significant for phytoremediation efficiency. Therefore, the heavy metals accumulation of M. floridulus, rhizosphere soil physicochemical properties, enzyme activities, and bacterial community of different distances from the tailing were measured, focusing on the relationship between phytoremediation ability and rhizosphere ecological characteristics. The results show that the stronger the phytoremediation ability is, the better is the soil environment, and the higher the coverage with plants. Soil rhizosphere environment and the phytoremediation ability are shaped by heavy metals. Rhizosphere microecology may regulate phytoremediation by improving soil nutrients and enzyme activities, alleviating heavy metal toxicity, changing rhizosphere microbial community structure, increasing beneficial microbial abundance, promoting heavy metals accumulation by plants. This study not only clarified the relationship between rhizosphere ecological factors, but also elucidated the phytoremediation regulatory mechanism. Some of microbial taxa might developed as biological bioinoculants, providing the possibility to promote the growth of plants with ecological restoration ability and improve the phytoremediation efficiency.

Effects of perfluoroalkyl substances on root and rhizosphere bacteria: Phytotoxicity, phyto-microbial remediation, risk assessment

BACKGROUND

Per- and polyfluoroalkyl substances (PFAS) is easily sink into soil, affecting plants growth and microenvironment. However, the impacts of PFAS-related risk assessment on root and rhizosphere microbiomes are still poorly understood.

OBJECTIVE

Researched on Arabidopsis thaliana and Nicotiana benthamiana growing in contaminated with perfluorooctanoic acid (PFOA), hexafluoropropylene oxide-dimer acid (HFPO-DA) and their mixtures.

RESULTS

(i) Bioaccumulation of PFAS in roots was positively correlated with carbon chain length, contamination levels and exposure time, the phytotoxicity was as follows: HFPO-DA < (PFOA + HFPO-DA) < PFOA; (ii) Both short-term and long-term accumulation of PFAS would affect the changes in root antioxidant system and physiological metabolism; (iii) Single or mixed contamination of PFAS had unique influences on rhizosphere microbial diversity, community composition and interspecies interaction, and mixture was more complex. More importantly, the performance of Sphingomonadaceae and Rhizobiaceae microbial communities could contribute to the practice of phyto-microbial soil remediation.

FUTURE DIRECTION

Pay more attention on novel pollution pathway in cultivation, exposure levels for different plants (especially crops), as well as more exact and scientific risk assessments. Establish a new PFAS grouping strategy and ecotoxicity life cycle assessment framework.

Enhanced effects of walnut green husk solution on the phytoextraction of soil Cd and Zn and corresponding microbial responses

Walnut green husk (WGH) is a common agricultural waste, but it may be conducive to phytoremediation of heavy metals owing to its abundant phenolic hydroxyl, carboxyl, and other functional groups. In this study, WGH solution was used as an enhancer in the phytoextraction process via Sedum plumbizincicola, a hyperaccumulator of Zn and Cd. Microbial responses in the soil and plants were seamlessly analyzed to determine the underlying mechanisms of heavy metal extraction in this process. The results showed that the addition of 0.05 g/mL WGH solution increased the accumulation of Cd (by 153%) and Zn (by 220%) in plants as well as the availabilities of Cd (by 29.46%) and Zn (by 9.71%) in the soil, which can be attributed to an increase in the relative abundance of plant growth-promoting rhizobacteria that benefit phytoextraction. Furthermore, co-occurrence network analysis indicated the keystone taxa in the microbial community. Particularly, one of the keystone taxa, Pseudomonas, was also identified as distinct taxon in soil, and it was dominant among the endophytic bacteria. These results indicated that Pseudomonas, a taxon responded to WGH solution, may play a key role in enhanced phytoextraction in both soil and plant root. These results help to a better understanding of the microbial mechanisms for heavy metal accumulation in hyperaccumulator.

Unveiling Endophytic Bacterial Community Structures of Different Rice Cultivars Grown in a Cadmium-Contaminated Paddy Field

Endophytic bacteria play potentially important roles in the processes of plant adaptation to the environment. Understanding the composition and dynamics of endophytic bacterial communities under heavy metal (HM) stress can reveal their impacts on host development and stress tolerance. In this study, we investigated root endophytic bacterial communities of different rice cultivars grown in a cadmium (Cd)-contaminated paddy field. These rice cultivars are classified into low (RBQ, 728B, and NX1B) and high (BB and S95B) levels of Cd-accumulating capacity. Our metagenomic analysis targeting 16S rRNA gene sequence data reveals that Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes, and Spirochaetes are predominant root endophytic bacterial phyla of the five rice cultivars that we studied. Principal coordinate analysis shows that the developmental stage of rice governs a larger source of variation in the bacterial communities compared to that of any specific rice cultivar or of the root Cd content. Endophytic bacterial communities during the reproductive stage of rice form a more highly interconnected network and exhibit higher operational taxonomic unit numbers, diversities, and abundance than those during the vegetative stage. Forty-five genera are significantly correlated with Cd content in rice root, notably including positive-correlating Geobacter and Haliangium; and negative-correlating Pseudomonas and Streptacidiphilus. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis shows that functional pathways, such as biosynthesis of siderophore and type II polyketide products, are significantly enhanced during the reproductive stage compared to those during the vegetative stage under Cd stress. The isolated endophytic bacteria from the Cd-contaminated rice roots display high Cd resistance and multiple traits that may promote plant growth, suggesting their potential application in alleviating HM stress on plants. This study describes in detail for the first time the assemblage of the bacterial endophytomes of rice roots under Cd stress and may provide insights into the interactions among endophytes, plants, and HM contamination.

Responses of rhizosphere bacterial communities, their functions and their network interactions to Cd stress under phytostabilization by Miscanthus spp

Miscanthus has good tolerance to heavy metals (HMs) and has received increasing attention in studies of HM-contaminated soil remediation. In this study, four Miscanthus cultivars (M. lutarioriparius Xiangnadi NO4, M. sinensis Xiangmang NO1, M. lutarioriparius × M. sinensis hybrid Xiangzamang NO1, and M. floridulus Wujiemang NO1) that grow in China were studied. Their tolerance and enrichment abilities in soils containing 50 mg kg^-1 cadmium (Cd) and the structure and function of their rhizosphere bacterial communities during the remediation process were analyzed. The results exhibiting a tolerance index (TI) higher than 75 in roots and the aboveground parts (TI > 60, indicating highly tolerant plants) indicated that all four Miscanthus cultivars were tolerant to high Cd concentrations. Moreover, Cd was mainly enriched in roots, the translocation ability from roots to aboveground parts was weak, and the four cultivars exhibited phytostabilization ability in Cd-contaminated soils. High-throughput sequencing (HTS) analysis showed that the Miscanthus rhizosphere bacterial community comprised 33 phyla and 446 genera, including plant growth-promoting rhizobacteria (PGPRs), such as Bacillus, Sphingomonas, and Mesorhizobium. The addition of Cd affected the Miscanthus rhizosphere bacterial community and reduced community diversity. Phylogenetic molecular ecological networks (pMENs) indicated that Cd addition reduced interactions between Miscanthus rhizosphere bacteria and thereby led to a simpler network structure, increased the number of negative-correlation links, enhanced the competition between rhizosphere bacterial species, reduced the number of key bacteria, and changed the composition of those bacteria. PICRUSt functional predictive analysis indicated that Cd stress reduced soil bacterial functions in the Miscanthus rhizosphere. The results of this study provide a basis for the remediation of Cd-contaminated soils by Miscanthus and provide a reference for the subsequent regulation of Miscanthus remediation efficiency by PGPRs or key bacteria.

Impact of cigarette butts on bacterial community structure in soil

Cigarette butts contribute significantly to global pollution present on the planet. The filters found in cigarette butts contain a microplastic, cellulose acetate, as well as toxic metals and metalloids which are responsible for pollution in the environment. Although cigarette butt litter is prevalent in many soils, research on the effects of these cigarette butts is limited. In this study, we used Automated Ribosomal Intergenic Spacer Analysis (ARISA) to generate DNA fingerprints of bacterial communities in soil before and after the addition of cigarette butt leachate treatments. An ICP-MS analysis of the biodegradable and non-biodegradable cigarette butts revealed the presence of various elements: Al, As, B, Ba, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Sb, Se, Sn, Sr, V, and Zn. The analysis also specified which metals were present at the highest concentrations in the biodegradable and non-biodegradable cigarette butts, and these were, respectively, Al (1,31 g/kg and 2,35 g/kg), Fe (2,03 g/kg and 1,11 g/kg), and Zn (3,18 mg/kg and 15,70 mg/kg). Our results show that biodegradable cigarette butts had a significant effect on bacterial community composition (beta diversity), unlike the non-biodegradable butts. This effect can be attributed to higher concentrations of certain metals and metalloids in the leachate of biodegradable cigarette butts compared to the non-biodegradable ones. Our findings suggest that biodegradable and non-biodegradable cigarette butts can significantly affect bacterial communities in soil as a result of the leaching of significant quantities of certain elements into the surrounding soils.

Amynthas corticis genome reveals molecular mechanisms behind global distribution

Earthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

Effects of Zinc Pollution and Compost Amendment on the Root Microbiome of a Metal Tolerant Poplar Clone

Until recently, many phytoremediation studies were focused solely on a plants ability to reclaim heavy metal (HM) polluted soil through a range of different processes, such as phytoextraction and phytostabilization. However, the interaction between plants and their own rhizosphere microbiome represents a new research frontier for phytoremediation. Our hypothesis is that rhizomicrobiome might play a key role in plant wellness and in the response to external stimuli; therefore, this study aimed to shed light the rhizomicrobiome dynamics after an organic amendment (e.g., compost) and/or HM pollution (e.g., Zn), and its relation with plant reclamation ability. To reach this goal we set up a greenhouse experiment cultivating in pot an elite black poplar clone (N12) selected in the past for its excellent ability to reclaim heavy metals. N12 saplings were grown on a soil amended with compost and/or spiked with high Zn doses. At the end of the experiment, we observed that the compost amendment strongly increased the foliar size but did not affect significantly the Zn accumulation in plant. Furthermore, the rhizomicrobiome communities (bacteria and fungi), investigated through NGS, highlighted how α diversity increased in all treatments compared to the untreated N12 saplings. Soil compost amendment, as well as Zn pollution, strongly modified the bacterial rhizomicrobiome structure. Conversely, the variation of the fungal rhizomicrobiome was only marginally affected by soil Zn addition, and only partially impaired by compost. Nevertheless, substantial alterations of the fungal community were due to both compost and Zn. Together, our experimental results revealed that organic amendment increased the bacterial resistance to external stimuli whilst, in the case of fungi, the amendment made the fungi microbiome more susceptible. Finally, the greater microbiome biodiversity does not imply, in this case, a better plant wellness or phytoremediation ability, although the microbiome plays a role in the external stimuli response supporting plant life.

Azolla filiculoides L. as a source of metal-tolerant microorganisms

The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95–105 versus 36–44). In these treatments the share of subdominant Actinobacteria (0.4–0.8%), Firmicutes (0.5–0.9%) and Bacteroidetes (0.2–0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.

Agricultural Selection of Wheat Has Been Shaped by Plant-Microbe Interactions

The influence of wheat (modern wheat, both bread and pasta, their wild ancestors and synthetic hybrids) on the microbiota of their roots and surrounding soil is characterized. We isolated lines of bread wheat by hybridizing diploid (Aegilops tauschii) with tetraploid Triticum durum and crossed it with a modern cultivar of Triticum aestivum. The newly created, synthetic hybrid wheat, which recapitulate the breeding history of wheat through artificial selection, is found to support a microbiome enriched in beneficial Glomeromycetes fungi, but also in, potentially detrimental, Nematoda. We hypothesize that during wheat domestication this plant-microbe interaction diminished, suggesting an evolutionary tradeoff; sacrificing advantageous nutrient acquisition through fungal interactions to minimize interaction with pathogenic fungi. Increased plant selection for Glomeromycetes and Nematoda is correlated with the D genome derived from A. tauschii. Despite differences in their soil microbiota communities, overall wheat plants consistently show a low ratio of eukaryotes to prokaryotes. We propose that this is a mechanism for protection against soil-borne fungal disease and appears to be deeply rooted in the wheat genome. We suggest that the influence of plants on the composition of their associated microbiota is an integral factor, hitherto overlooked, but intrinsic to selection during wheat domestication.