Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake

To investigate the impact of Poa alpigena Lindm on rhizosphere and bulk soil microorganisms in Haixin Mountain, Qinghai Lake, this study employed metagenomics technology to analyze the microbial communities of the samples. Results showed that 65 phyla, 139 classes, 278 orders, 596 families, 2376 genera, and 5545 species of soil microorganisms were identified from rhizosphere and bulk soil samples. Additionally, a microbial gene library specific to Poa alpigena Lindm was established for Qinghai Lake. Through α-diversity analysis, the richness and diversity of bulk microorganisms both significantly had a higher value than that in rhizosphere soil. The indicator microorganisms of rhizosphere and bulk soil at class level were Actinobacteria and Alphaproteobacteria, respectively. KEGG pathway analysis indicated that Carotenoid biosynthesis, Starch and sucrose metabolism, Bacterial chemotaxis, MAPK signaling pathway, Terpenoid backbone biosynthesis, and vancomycin resistance were the key differential metabolic pathways of rhizosphere soil microorganisms; in contrast, in bulk soil, the key differential metabolic were Benzoate degradation, Glycolysis gluconeogenesis, Aminobenzoate degradation, ABC transporters, Glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, Degradation of aromatic compounds, Methane metabolism, Pyruvate metabolism and Microbial metabolism diverse environments. Our results indicated that Poa alpigena Lindm rhizosphere soil possessed selectivity for microorganisms in Qinghai Lake Haixin Mountain, and the rhizosphere soil also provided a suitable survival environment for microorganisms.

OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake

Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress. The quantification of nifH gene expression demonstrated a significant enhancement in nitrogen-fixing capabilities in the roots of RC transgenetic rice. Synthetic microbial communities (SynCom) consisting of six nitrogen-fixing bacterial strains were observed to be enriched in the roots of RC, leading to a substantial improvement in rice growth and nitrogen uptake in nitrogen-deficient soils. Forty and twenty-three metabolites exhibiting differential abundance were identified in the roots and rhizosphere soils of RC transgenic rice compared to wild-type (WT) rice. These findings suggest that OSCIPK2 plays a role in restructuring the microbial community in the roots through the regulation of metabolite synthesis and secretion. Further experiments involving the exogenous addition of citric acid revealed that an optimal concentration of this compound facilitated the growth of nitrogen-fixing bacteria and substantially augmented their population in the soil, highlighting the importance of citric acid in promoting nitrogen fixation under conditions of low nitrogen availability. These findings suggest that OsCIPK2 plays a role in enhancing nitrogen uptake by rice plants from the soil by influencing the assembly of root microbial communities, thereby offering valuable insights for enhancing nitrogen utilization in rice cultivation.

nov., isolated from the rhizosphere soil of plant in temperate semi-arid steppe

A bacterial strain PJ23T was isolated from the rhizosphere soil of Elymus dahuricus Turcz. sampled from a temperate semi-arid steppe in the northern of Inner Mongolia Autonomous Region, China. The strain is Gram-stain-negative, aerobic, light-pink, short rod-shaped, and non-spore-forming. Cell growth could be observed at 4-29℃ (optimal at 24℃), pH 6.0-8.6 (optimal at 8.0) and in the presence of 0-5.0% (w/v) NaCl (optimal at 2.5%). The major cellular fatty acids of strain PJ23T were Summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) (39.42%) and C16:0 (9.60%). The polar lipids were phosphatidylcholine, two unidentified glycolipids, one unidentified aminophospholipid, and two other unidentified polar lipids. The major respiratory quinone was ubiquinone-10. Phylogeny analysis based on 16S rRNA gene sequences retrieved from the genomes showed that, the strain was closely related to the species Terrihabitans soli IZ6T and Flaviflagellibacter deserti SYSU D60017T, with the sequence similarities of 96.79% and 96.15%, respectively. The G + C content was 65.23 mol% calculated on draft genome sequencing. Between the strains PJ23T and Terrihabitans soli IZ6T, the average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) was 73.39%,71.12% and 15.7%, these values were lower than the proposed and generally accepted species boundaries of ANI, AAI and dDDH, respectively. Based on phenotypic, chemotaxonomic, and phylogenetic characteristics, strain PJ23T represents a novel species of Terrihabitans, for which the name Terrihabitans rhizophilus sp. nov. is proposed. The type strain is PJ23T (= KCTC 92977 T = CGMCC 1.61577 T).

Selenium and Bacillus proteolyticus SES increased Cu-Cd-Cr uptake by ryegrass: highlighting the significance of key taxa and soil enzyme activity

Many studies have focused their attention on strategies to improve soil phytoremediation efficiency. In this study, a pot experiment was carried out to investigate whether Se and Bacillus proteolyticus SES promote Cu-Cd-Cr uptake by ryegrass. To explore the effect mechanism of Se and Bacillus proteolyticus SES, rhizosphere soil physiochemical properties and rhizosphere soil bacterial properties were determined further. The findings showed that Se and Bacillus proteolyticus SES reduced 23.04% Cu, 36.85% Cd, and 9.85% Cr from the rhizosphere soil of ryegrass. Further analysis revealed that soil pH, organic matter, soil enzyme activities, and soil microbial properties were changed with Se and Bacillus proteolyticus SES application. Notably, rhizosphere key taxa (Bacteroidetes, Actinobacteria, Firmicutes, Patescibacteria, Verrucomicrobia, Chloroflexi, etc.) were significantly enriched in rhizosphere soil of ryegrass, and those taxa abundance were positively correlated with soil heavy metal contents (P < 0.01). Our study also demonstrated that in terms of explaining variations of soil Cu-Cd-Cr content under Se and Bacillus proteolyticus SES treatment, soil enzyme activities (catalase and acid phosphatase) and soil microbe properties showed 42.5% and 12.2% contributions value, respectively. Overall, our study provided solid evidence again that Se and Bacillus proteolyticus SES facilitated phytoextraction of soil Cu-Cd-Cr, and elucidated the effect of soil key microorganism and chemical factor.

Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana

The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.

Biochar application alters soil metabolites and nitrogen cycle-related microorganisms in a soybean continuous cropping system

Biochar application is a promising practice to enhance soil fertility. However, it is unclear how field-aged biochar affects the soil metabolites and microbial communities in soybean fields. Here, the rhizosphere soil performance after amending with biochar addition rates at 0 (CK), 20 (B20), 40 (B40), and 60 t ha-1 (B60) was examined via a five-year in-situ field experiment based on a soybean continuous cropping system. Untargeted metabolomics and metagenomics analysis techniques were applied to study the regulatory mechanism of biochar on soybean growth from metabolomics and N cycle microbiology perspectives. We found that the contents of soil total N (TN), available N (Ava N), NH4+-N, and NO3--N were significantly increased with biochar addition amounts by 20.0-65.7 %, 3.6-10.7 %, 29.5-57.1 %, and 24.4-46.7 %, respectively. The B20, B40, and B60 triggered 259 (236 were up-regulated and 23 were down-regulated), 236 (220 were up-regulated and 16 were down-regulated), and 299 (264 were up-regulated and 35 were down-regulated) differential metabolites, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and topology analysis demonstrated that differential metabolites were highly enriched in seven metabolic pathways such as Oxidative phosphorylation and Benzoxazinoid biosynthesis. Moreover, ten differential metabolites were up-regulated in all three treatments with biochar. Biochar treatments decreased the Nitrospira abundance in soybean rhizosphere soil while increasing Bradyrhizobium abundance significantly in B60. Mantel test revealed that as the biochar addition rate grows, the correlation between Nitrospira and soil properties other than NO3--N became stronger. In conclusion, the co-application of biochar with fertilizers is a feasible and effective way to improve soil N supply, even though biochar has undergone field aging. This work offers new insights into the variations in soil metabolites and microbial communities associated with N metabolism processes under biochar addition in soybean continuous cropping soils.

Effects of continuous monoculture on rhizosphere soil nutrients, growth, physiological characteristics, hormone metabolome of Casuarina equisetifolia and their interaction analysis

Continuous planting is unavoidable in agricultural production, but continuous planting affects plant growth and physiological characteristics. In this study, we analyzed rhizosphere soil nutrients, physiological characteristics, hormone metabolome changes and their interactions of Casuarina equisetifolia (C. equisetifolia) with the increase of continuous planting number. The results found that C. equisetifolia root was significantly inhibited, the plant height was dwarfed and the biomass was significantly reduced as continuous planting number increased. Secondly, continuous planting caused a decrease in the rhizosphere soil nutrient transformation capacity, and a significant decrease in the total soil nutrient and available nutrient content. Analysis of physiological indexes showed that continuous planting resulted in a decrease in nitrogen, phosphorus, and potassium content, a decrease in the activity of physiological indexes of resistance, and a decrease in photosynthetic capacity of C. equisetifolia leaves. Hormone metabolome analysis showed that continuous planting critically affected the accumulation of five characteristic hormones in C. equisetifolia leaves, in which salicylic acid 2-O-β-glucoside (SAG), 2-oxindole-3-acetic acid (OxIAA), trans-zeatin-O-glucoside (tZOG) and gibberellin A3 (GA3) content decreased significantly while abscisic acid (ABA) content increased significantly. In conclusion, continuous planting lowered the rhizosphere soil nutrient transformation capacity of C. equisetifolia, lowered the soil available nutrient content, inhibited their root growth, and hindered the nutrient uptake and transportation by the root, thus led to the decrease of the nutrient accumulation capacity in the leaves of C. equisetifolia, and the decrease of SAG, OxIAA, and tZOG, GA3 synthesis ability decreased, ABA accumulated in large quantities, C. equisetifolia resistance and photosynthesis ability decreased, and their growth was impeded. This study provides insights for the effective management of continuous planting in the cultivation of C. equisetifolia.

Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China

Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.

Effects of polystyrene microplastics on the agronomic traits and rhizosphere soil microbial community of highland barley

This study investigated the influence of polystyrene microplastics (MPs) with two different particle sizes (<1 mm, 1-5 mm) and three concentrations (1 g/m2, 10 g/m2, 50 g/m2), as well as added degrading bacteria, on the agronomic traits of highland barley and the bacterial communities in the rhizosphere soil. Results revealed that the small particle size treatment had a significant effect on reducing the 1000-grain weight of highland barley, while the large particle size treatment had an effect on reducing the spike length, width, and awn length (P < 0.05). Additionally, the MP treatment was found to significantly reduce the rhizosphere soil bacterial diversity and richness, including the Shannon, Chao1, observed species, and dominance indices (P < 0.05). Interestingly, the inoculation treatment also reduced microbial diversity, though the microbial diversity after treatment was similar to that of the control community structure, indicating its regulating effect on the soil microbial community. The abundance of Domibacillus, Pedosphaeraceae, and Enterococcus decreased due to the MP treatment, whereas Achromobacter, Massilia, Ralstonia, and Nitrosospira increased (P < 0.05). Furthermore, functional prediction indicated that MP treatment resulted in the enrichment of microbial functions, such as an AraC-type DNA-binding domain, etc. The microbial communities exposed to different sizes and concentrations of MPs had their own unique functions in response to the effects of the MPs. This study provided novel insights into the effects of different particle sizes and concentrations of MPs on the rhizosphere microbial community and agronomic traits of highland barley. It could be used to improve the understanding of the impact of MPs on the rhizosphere soil microecology and enhance bioremediation of MPs.

Metagenomic profiling of tomato rhizosphere delineates the diverse nature of uncultured microbes as influenced by Bacillus velezensis VB7 and Trichoderma koningiopsis TK towards the suppression of root-knot nematode under field conditions

The plant-parasitic Root Knot Nematodes (Meloidogyne spp.,) play a pivotal role to devastate vegetable crops across the globe. Considering the significance of plant-microbe interaction in the suppression of Root Knot Nematode, we investigated the diversity of microbiome associated with bioagents-treated and nematode-infected rhizosphere soil samples through metagenomics approach. The wide variety of organisms spread across different ecosystems showed the highest average abundance within each taxonomic level. In the rhizosphere, Proteobacteria, Firmicutes, and Actinobacteria were the dominant bacterial taxa, while Ascomycota, Basidiomycota, and Mucoromycota were prevalent among the fungal taxa. Regardless of the specific treatments, bacterial genera like Bacillus, Sphingomonas, and Pseudomonas were consistently found in high abundance. Shannon diversity index vividly ensured that, bacterial communities were maximum in B. velezensis VB7-treated soil (1.4-2.4), followed by Root Knot Nematode-associated soils (1.3-2.2), whereas richness was higher with Trichoderma konigiopsis TK drenched soils (1.3-2.0). The predominant occurrence of fungal genera such as Aspergillus Epicoccum, Choanephora, Alternaria and Thanatephorus habituate rhizosphere soils. Shannon index expressed the abundant richness of fungal species in treated samples (1.04-0.90). Further, refraction and species diversity curve also depicted a significant increase with maximum diversity of fungal species in B. velezensis VB7-treated soil than T. koningiopsis and nematode-infested soil. In field trial, bioagents-treated tomato plant (60% reduction of Meloidogyne incognita infection) had reduced gall index along with enhanced plant growth and increased fruit yield in comparison with the untreated plant. Hence, B. velezensis VB7 and T. koingiopsis can be well explored as an antinemic bioagents against RKN.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03851-1.

Migration of polycyclic aromatic hydrocarbons in the rhizosphere micro-interface of soil-ryegrass (Lolium perenne L.) system

The unclear multi-media and multi-interface processes of polycyclic aromatic hydrocarbons (PAHs) in environments have drawn great concern. Here, 16 controlled PAHs were selected to reveal the differences in the bioavailability and migration of congeners in soil-ryegrass exposure system. The presence of ryegrass in the exposure groups (with newly introduced PAHs) resulted in a decrease in PAHs dissipation (31.3 %) from soil compared to the unplanted groups (43.2 %). The presence of ryegrass inhibited the soil-air exchange process, which has not been widely reported. PAH congeners with less benzene rings (molecular weight < B[a]A) had consistent bioavailability before and after long-term aging, the competition between adsorption/absorption to plants and soil was not strong (RCFs < 3.5), and their migration in the rhizosphere rapidly reached equilibrium. PAH congeners with more benzene rings (molecular weight ≥ B[a]A) adsorbed to soil particles and significantly decreased their bioavailability after long-term aging. Their concentrations in the rhizosphere were stable and lower than bulk soil, revealing their slow equilibrium process in soil. In addition, PAHs with larger molecular weight and KOW showed less migration at the rhizosphere micro-interface. The migration behavior of congeners with close KOW depended on their molecular structure. Congeners with non-symmetric K-region or L-region showed greater migration ability in the rhizosphere. These findings revealed the fate of PAHs, especially different PAH congeners, in the rhizosphere interfaces for the first time, and explored the molecular mechanisms that affect their rhizosphere behaviors, improving the understanding and knowledge of PAHs in the microenvironment, providing new data on evaluating and controlling the environmental risks of PAHs.

Isolation and in-vitro characterization of extracellular phytase producing bacterial isolates for potential application in poultry feed

BACKGROUND

Phytase catalyses the breakdown of complex organic forms of phosphorous into simpler forms by sequential hydrolysis of phosphate ester bonds to liberate the inorganic phosphate. Supplementation of feeds with bacterial phytase therefore could enhance the bioavailability of phosphorus and micronutrients. Hence, the aim of this study was to isolate and characterize phytase producing bacteria from rhizosphere soil, fresh poultry excreta, and cattle shed to evaluate their potential in improving poultry feeds. Phytase producing bacteria were isolated using wheat bran extract medium.

RESULTS

A total of 169 bacterial isolates were purified and screened for phytase activity. Out of these, 36 were confirmed as positive for phytase enzyme activity. The bacterial isolates were identified by cultural, morphological, and biochemical features. The isolates were also identified by using 16 S rRNA gene sequencing. The bacterial isolates (RS1, RS8, RS10 and RS15) were provided with gene bank database accession numbers of MZ407562, MZ407563, MZ407564 and MZ407565 respectively. All isolates increased phytase production when cultured in wheat bran extract medium (pH 6) supplemented with 1% (wt/v) galactose and 1% (wt/v) ammonium sulphate incubated at 50oC for 72 h. Proximate composition analysis after supplementation of phytase showed that phytase supplementation improved bioavailability of phosphorus, calcium, potassium and sodium in poultry feed.

CONCLUSIONS

Overall, this study showed that the nutritional value of poultry feed can be improved using microbial phytase enzyme which reduces the cost of supplementation with inorganic phosphate.

Life-cycle selenium accumulation and its correlations with the rhizobacteria and endophytes in the hyperaccumulating plant Cardamine hupingshanensis

Cardamine hupingshanensis (C. hupingshanensis) is known for its ability to hyperaccumulate selenium (Se). However, the roles of the rhizobacteria or endophytes in Se hyperaccumulation have not been explored in C. hupingshanensis. Here, in-situ-like pot experiments were conducted to investigate the characteristics of Se accumulation throughout C. hupingshanensis growth stages and its correlations with rhizobacteria and endophytes under varying soil Se levels. Results showed that Se levels in roots, stems and leaves increased from the seedling to bolting stage, but remained relatively stable during the flowering and maturity. Leaves exhibited the highest Se levels (736.48 ± 6.51 mg/kg DW), followed by stems (575.39 ± 27.05 mg/kg DW), and lowest in roots (306.62 ± 65.45 mg/kg DW) under high-Se stress. The Se translocation factors from soils to C. hupingshanensis roots was significantly higher (p < 0.05) in low-Se soils compared to medium- and high-Se soils. Rhizobacterial diversity showed significant positive correlations (p < 0.05) with both total and bioavailable soil Se contents. The levels of soil Se and growth stages of C. hupingshanensis were found to have significant effects (p < 0.03) on the compositions of rhizosphere bacteria and C. hupingshanensis endophytes. Low-abundance bacteria (< 5%), including Gemmatimonadetes, Latescibacteria and Nitrospirae, were identified to potentially increase the bioavailable Se levels in the rhizosphere. The Se accumulation significantly decreased (p < 0.05) in C. hupingshanensis grown in sterilized low- (32.4%), medium- (17%) and high-Se (42%) soils. Endophytes in C. hupingshanensis, such as Firmicutes and Proteobacteria, were likely recruited from the rhizobacteria, as evidenced by the isolated bacterial strains, and played an important role in Se hyperaccumulation, particularly during the flowering stage. This study provides new insights into potential mechanism underlying Se hyperaccumulation in C. hupingshanensis.

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

BACKGROUND

Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes.

RESULTS

Our results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla.

CONCLUSIONS

We provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity. Video Abstract.

Effects of a compound Trichoderma agent on Coptis chinensis growth, nutrients, enzyme activity, and microbial community of rhizosphere soil

Background

Root rot diseases are prevalent in many Coptis chinensis Franch. production areas, perhaps partially due to the overuse of synthetic fertilizers. Synthetic fertilizers can also lead to soil degradation. Trichoderma is widely used in biofertilizers and biopesticides. This study applied a combination of four Trichoderma species (compound Trichoderma agent, CTA) to C. chinensis and evaluated its effects on growth, as well as rhizosphere soil nutrients, enzyme activities, and microbial community structure. The purpose of this study was to estimate the potential of using CTA as a biofertilizer for C. chinensis, and determine if it could, at least partially, replace synthetic fertilizers to control root rot disease and maintain soil fertility.

Method

CTA, compound fertilizer and sterile water were applied to C. chinensis plants. After 60 days, the soluble sugar, soluble protein, chlorophyll of leaves, and individual weight of each plant were measured. The rhizosphere soil nutrient content, enzymatic activity, and the microbial community were also determined. The results were analyzed to evaluate the effect of CTA on C. chinensis growth and soil fertility.

Results

CTA increased the soluble protein, chlorophyll, and individual weight of C. chinensis plants while compound fertilizer decreased chlorophyll. CTA increased the activities of urease and catalase in rhizosphere soil, whereas the compound fertilizer decreased urease, catalase, and alkaline phosphatase activities. CTA elevated soil pH, while compound fertilizer reduced it. CTA had no significant effects on soil nutrients and organic matter. CTA decreased the fungal number and alpha-diversity of fungi and bacteria, and both the fungal and bacterial communities were significantly different from the other two. CTA increased B/F value, which improved the rhizosphere microbial community. Both CTA and the compound fertilizer significantly altered the soil microbial community. The relative abundance of Ascomycota was higher and Basidiomycota was lower after CTA treatment than after the other two treatments, indicating that the soil treated with CTA was healthier than that of the other two treatments. CTA decreased harmful Ilyonectria mors-panacis and Corynebacterium sp. And increased beneficial Ralstonia picketti. Trichoderma spp. could exist in C. chinensis rhizosphere soil for a long time. The functional prediction results demonstrated that CTA reduced some rhizosphere phytopathogenic fungi. Correlation analysis showed that CTA elevated rhizosphere pH and enzyme activities. In summary, synthetic fertilizers damaged soil fertility, and the overuse of them might be responsible for root rot disease, while CTA could promote C. chinensis growth, improve soil and decrease the incidence and severity of C. chinensis root rot disease. Therefore, as a biofertilizer, CTA can, at least partially, replace synthetic fertilizers in C. chinensis production. Combining it with organic fertilizer will increase the potential of Trichoderma.

Cover Crop Amendments and Lettuce Plant Growth Stages Alter Rhizobacterial Properties and Roles in Plant Performance

Lettuce plants respond differently to cover crop amendments by altering their biomass and nitrogen uptake (Nup) at different plant growth stages. Nonetheless, plant-microbe interactions involved in the alterations are scarcely studied. This study elucidated how the properties of the soil microbial community inhabiting the rhizosphere associated with lettuce (Lactuca sativa L. var. crispa "Red fire") change during plant growth stages. Lettuce plants were cultivated in control soil and soil with rye, hairy vetch (HV), and rye plus HV (rye + HV) cover crop amendments. Rhizosphere soil samples were collected at the mid-growth and mature stages of plant development. DNA was extracted from the soil, and the 16S rRNA region was amplified using polymerase chain reaction to analyze bacterial genes and community structures and functions. Cover crop amendments and plant growth stages increased or decreased the relative abundances of bacterial taxa at the genus level. Plant maturity decreased 16S rRNA gene expression and the number of bacterial operational taxonomic units in all treatments. The unique, core, and shared taxa with low relative abundances may be associated with improved lettuce Nup and lettuce shoot and root biomass at each plant growth stage under different cover crop amendments based on multivariate analysis between plant indicators and bacterial genera groups. This study revealed the importance of bacterial groups with low relative abundance in plant-microbe interactions; such bacteria may promote the cover crop application for high lettuce productivity.

Temporal transformation of indium speciation in rice paddy soils and spatial distribution of indium in rice rhizosphere

Indium is a potentially toxic element that could enter human food chains, including soil-rice systems. The submerged environment in rice paddy soil results in temporal and spatial variations in the chemical properties of the rice rhizosphere and bulk soils, expected to cause changes in indium's chemical speciation and consequently affect its bioavailability. Therefore, this study aimed to investigate indium speciation and fractionation in soils at different periods of rice growth under continuous submergence using X-ray absorption spectroscopy and a sequential extraction method. The predominant indium species were identified as indium-associated Fe hydroxide, and indium hydroxide and phosphate precipitates. The reductive dissolution of indium-associated Fe hydroxides led to the release of indium into the soil solution under continuous submergence of soils, and the released indium concentration decreased with time due to re-sorption and re-precipitation. Meanwhile, indium hydroxide was found to be the predominant species in rice rhizosphere using μ-X-ray absorption spectroscopy. The relative depletion of indium-associated Fe hydroxides in the rice rhizosphere was attributed to the low mobility of indium from bulk soil to rice rhizosphere and the root uptake of indium associated with Fe hydroxide around rice roots. Consequently, indium uptake by rice roots was lower during the reproductive and grain-ripening stage of rice growth. Understanding the behavior of indium will help develop a strategy to minimize uptake into crops in indium-contaminated paddy soils.

Shifts of active microbial community structure and functions in constructed wetlands responded to continuous decreasing temperature in winter

Important functions of constructed wetland related to biogeochemical processes are mediated by soil microbes and low-temperature damage is the main limiting factor for microbes in winter. However, the response thresholds for active microbial community and enzyme activities to continuous decreases in temperature remain unclear. In this study, total 90 soil samples were collected every week over a 6-week period to track the dynamics of four enzymes involved in cycles of C, N, P and active bacterial community as field soil temperature decreased continuously from 6.62 °C to 0.55 °C. Enzyme activity changed suddenly when the temperature decreased to 4.83 °C, the nitrite reductase activity reduced by 36.2%, while alkaline phosphatase activity is increased by 396%. The cellulase and urease were only marginally influenced by cold stress. Decreased nitrite reductase activities corresponded with loss of nir-type denitrifiers important for nitrite reduction. For cold stress, N-related bacteria were sensitive species. Whereas increased alkaline phosphatase activity may be due to the fact that P-related bacteria were opportunistic species. Key functional taxa connected with degradation of cellulose promoted species coexistence and microbial network stability. The lower and upper temperature thresholds for community change were 4.85 °C and 6.30 °C, respectively. Collectively, these results revealed that microbial taxa involved in C, N and P cycling respond differently to continuous decreases in temperature and higher than 4.85 °C is an ideal environment to prevent loss of microbial diversity and functions in winter, providing a scientific reference for the targeted isolation and cultivation of key microbial taxa in rhizosphere soil and adjusting temperature range to improve the purification capacity of wetlands during low temperature periods.

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

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

Selenium and Bacillus proteolyticus SES synergistically enhanced ryegrass to remediate Cu-Cd-Cr contaminated soil

Heavy metal compound contaminated soil is an ecological threat, and soil containing copper (Cu), cadmium (Cd) and chromium (Cr) simultaneously is widely distributed. The application of phytoremediation in heavy metal combined contamination is still limited. In this study, to explore whether and how exogenous selenium (Se) and Bacillus proteolyticus SES enhance the remediation of combined Cu-Cd-Cr contaminated soil by ryegrass, pot experiments were carried out. Se alone or in combination with B. proteolyticus SES treatment increased the removal rates of heavy metals in the rhizosphere soil by 17.38%-157.25% relative to the control, while Se + B. proteolyticus SES treatment played a greater role in improving the heavy metals tolerance of ryegrass and increasing the activity of soil acid phosphatase. Moreover, Se and B. proteolyticus SES favored the preferential recruitment of specific taxa with the capacity of plant growth promotion and heavy metals resistance to the rhizosphere. The rhizosphere soil of Se treatment was specifically enriched with Lysobacter, Rhodanobacter, Micrococcales, Paenarthrobacter, and Adhaeribacter, while from class Bacilli to genus Bacillus enriched extensively and specifically in the rhizosphere of B. proteolyticus SES + Se treatment. Furthermore, five functional beneficial rhizosphere microbes including: Microbacterium sp., Pseudomonas extremaustralis, Bacillus amyloliquefaciens, Priestia megaterium, and Bacillus subtilis were isolated from the two treatments with the best remediation effect and synthetic communities (SynComs) were constructed. SynComs inoculation experiment further demonstrated the role of specific beneficial microbes in regulating the bioavailability of heavy metals. Results revealed that Se supplementation efficiently facilitated the phytoextraction of combined Cu-Cd-Cr contaminated soil, and B. proteolyticus SES inoculation showed the synergistical enhancement effect in the presence of Se.

Reprogramming of microbial community in barley root endosphere and rhizosphere soil by polystyrene plastics with different particle sizes

Polystyrene plastics is an emerging pollutant affecting plant performance and soil functioning. However, little information is available on the effects of microplastics and nanoplastics on plant root endophytic and rhizospheric soil microbial communities. Here, barley plants were grown in microplastics/nanoplastics -treated soil and the diversity, composition and function of bacteria and fungi in the root and rhizosphere soil were examined. At the seedling stage, greater changes of root endophytes were found compared with rhizosphere microorganisms under the plastic treatments. Nanoplastics decreased the richness and diversity of the fungal community, while microplastics increased the diversity of the root endophytic bacterial community. The network of the bacterial community under nanoplastics showed higher vulnerability while lower complexity than that under the control. However, the bacterial community under microplastics had a relatively higher resistance than the control. For the rhizosphere microbial community, no significant effect of plastics was found on the α-diversity index at the seedling stage. In addition, the nanoplastics resulted in higher sensitivity in the relative abundance and function of rhizosphere soil microbes than root endophytic microbes at the mature stage. Treatments of polystyrene plastics with different particle sizes reprogramed the rhizosphere and root endophytic microbial communities. Different effects of microplastics and nanoplastics were found on the diversity, composition, network structure and function of bacteria and fungi, which might be due to the variation in particle sizes. These results lay a foundation for learning the effects of polystyrene plastics with different particle sizes on the microorganisms in rhizosphere soil and plant roots, which may have important implications for the adaptation of plant-microbial holobiont in polystyrene plastics-polluted soils.

Assessment of the rhizosphere fungi and bacteria recruited by sugarcane during smut invasion

Whip smut is one of the most serious and widely spread sugarcane diseases. Plant-associated microbes play various roles in conferring advantages to the host plant. Understanding the microbes associated with sugarcane roots will help develop strategies for the biocontrol of smut. Therefore, the present study explored microbe-mediated sugarcane response to smut invasion via 16S rRNA and ITS metabarcoding survey of the rhizosphere soils of resistant and susceptible sugarcane varieties. The bacterial and fungal diversity in the rhizosphere soils differed between the resistant and susceptible varieties. The bacterial genera Sphingomonas, Microcoleus_Es-Yyy1400, Marmoricola, Reyranella, Promicromonospora, Iamia, Phenylobacterium, Aridibacter, Actinophytocola, and Edaphobacter and one fungal genus Cyphellophora were found associated with smut resistance in sugarcane. Detailed analysis revealed that the majority of bacteria were beneficial, including the actinomycete Marmoricola and Iamia and Reyranella with denitrification activity. Analysis of bacterial network interaction showed that three major groups interacted during smut invasion. Meanwhile, seven of these genera appeared to interact and promote each other's growth. Finally, functional annotation based on the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database predicted that the abundant bacteria are dominated by oxygenic photoautotrophy, photoautotrophy, and phototrophy functions, which may be related to smut resistance in sugarcane. The present study thus provides new insights into the dynamics of the sugarcane rhizosphere microbial community during smut invasion.

Mycorrhizal diversity and community composition in co-occurring Cypripedium species

Orchids commonly rely on mycorrhizal fungi to obtain the necessary resources for seed germination and growth. Whereas most photosynthetic orchids typically associate with so-called rhizoctonia fungi to complete their life cycle, there is increasing evidence that other fungi may be involved as well and that the mycorrhizal communities associated with orchids may be more diverse. Coexisting orchid species also tend to associate with different fungi to reduce competition for similar resources and to increase long-term population viability. However, few studies have related the mycorrhizal communities in the rhizosphere to communities found in the roots of closely related coexisting orchid species. In this study, we used high-throughput sequencing to investigate the diversity and community composition of orchid mycorrhizal fungi in the roots and the rhizosphere of four Cypripedium species growing in forests in Northeast China. The results showed that the investigated Cypripedium species associated with a wide variety of fungi including members of Tulasnellaceae, Psathyrellaceae, and Herpotrichiellaceae, whereas members of Russulaceae, Cortinariaceae, Thelephoraceae, and Herpotrichiellaceae showed high abundance in rhizosphere soils. The diversity of fungi detected in the rhizosphere soil was much higher than that in the roots. The observed variation in fungal communities in Cypripedium roots was not related to forest site or orchid species. On the other hand, variation in mycorrhizal communities of rhizosphere soil was significantly related to sampling site. These results indicate that orchid mycorrhizal communities in the rhizosphere display considerable variation among sites and that orchids use only a subset of the locally available fungi. Future studies focusing on the fine-scale spatial distribution of orchid mycorrhizal fungi and more detailed assessments of local environmental conditions will provide novel insights into the mechanisms explaining variation of fungal communities in both orchid roots and the rhizosphere.

nov., a potential novel plant growth promoting bacterium isolated from rhizosphere soil of citrus

A novel potential plant growth promoting bacterium, designated OPS13-3^T, was isolated from rhizosphere soil of citrus in Aotou Town of Guangzhou, Guangdong Province, PR China. It showed high ability to dissolve insoluble inorganic phosphate and organic phosphorus and to produce 3-indoleacetic acid (IAA) and siderophore. Cells of the novel strain were Gram-stain-negative, rod-shaped, aerobic and motile with polar flagellum. It shared the highest 16S rRNA gene similarity with Pseudomonas mucoides CCUG 74874^T (98.7%) and P. bijieensis LMG 31948^T (98.7%). Phylogenetic analyses based the 16S rRNA gene and genome sequences revealed that strain OPS13-3^T belonged to the genus Pseudomonas, and was most closely related to P. mediterranea ICMP 14184^T and P. corrugate ICMP 5819^T. The average nucleotide identity (ANI) and DNA-DNA hybridization (dDDH) values between the novel strain and closely relatives with high 16S rRNA gene similarities were 80.8‒87.5% and 24.7‒34.6%, respectively, which were much below the threshold values for species delimitation. The major fatty acids included C_16:0, C_10:0 3-OH and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c). It took ubiquinone 9 as the predominant respiratory quinone and the polar lipids contained phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), three unidentified phospholipids, an unidentified aminophospholipid and an unidentified lipid. Based on the phylogenetic, phenotypic and chemotaxonomic analyses and genome comparison, strain OPS13-3^T should be considered as a novel species of the genus Pseudomonas, for which the name Pseudomonas citri sp. nov. is proposed (type strain OPS13-3^T = GDMCC 1.3118^T = JCM 35385^T).

Harnessing bacterial strain from rhizosphere to develop indigenous PGPR consortium for enhancing lobia (Vigna unguiculata) production

The rhizosphere microbes play a key role in plant nutrition and health. However, the interaction of beneficial microbes and Vigna unguiculata (lobia) production remains poorly understood. Thus, we aimed to isolate and characterize the soil microbes from the rhizosphere and develop novel microbial consortia for enhancing lobia production. Fifty bacterial strains were isolated from the rhizosphere soil samples of lobia. Finally, five effective strains (e.g., Pseudomonas sp. IESDJP-V1 and Pseudomonas sp. IESDJP-V2, Serratia marcescens IESDJP-V3, Bacillus cereus IESDJP-V4, Ochrobactrum sp. IESDJP-V5) were identified and molecularly characterized by 16 S rDNA gene amplification. All selected strains showed positive plant growth promoting (PGP) properties in broth culture. Based on morphological, biochemical, and plant growth promoting activities, five effective isolated strains and two collected strains (Azospirillum brasilense MTCC-4037 and Paenibacillus polymyxa BHUPSB17) were selected. The pot trials were conducted with seed inoculations of lobia (Vigna unguiculata) var. Kashi Kanchan with thirty treatments and three replications. The treatment combination T3 (Pseudomonas sp. IESDJP-V2), T14 (Pseudomonas sp. IESDJP-V2 + A. brasilense), T26 (Pseudomonas sp. IESDJP-V1+ B. cereus IESDJP-V4 + P. polymyxa) and T27 (IESDJP-V1+ IESDJP-V5+ A. brasilense) were recorded for enhancing plant growth attributes, yield, nutritional content like protein, total sugar, flavonoid and soil properties as compared to control and others. The effective treatments T3 (Pseudomonas sp.), T14 (Pseudomonas sp. IESDJP-V2 + A. brasilense), T26 (Pseudomonas sp. IESDJP-V1+ B. cereus IESDJP-V4 + P. polymyxa) and T27 (IESDJP-V1+ IESDJP-V5+ A. brasilense) recorded as potential PGPR consortium for lobia production. The treatment of single (Pseudomonas sp.), duel (IESDJP-V2 + A. brasilense) and triple combination (IESDJP-V1+ IESDJP-V4 + P. polymyxa) and (IESDJP-V1+ IESDJP-V5+ A. brasilense) can be further used for developing effective indigenous consortium for lobia production under sustainable farming practices. These PGPR bio-inoculant will be cost-effective, environment-friendly and socially acceptable.

Cultivar-specific response of rhizosphere bacterial community to uptake of cadmium and mineral elements in rice (Oryza sativa L.)

Toxic metal-contaminated farmland from Cadmium (Cd) can enhance the accumulation of Cd and impair the absorption of mineral elements in brown rice. Although several studies have been conducted on Cd exposure on rice, little has been reported on the relationship between Cd and mineral elements in brown rice and the regulatory mechanism of rhizosphere microorganisms during element uptake. Thus, a field study was undertaken to screen japonica rice cultivars with low Cd and high mineral elements levels, analyze the quantitative relationship between Cd and seven mineral elements, and investigate the cultivar-specific response of rice rhizosphere bacterial communities to differences in Cd and mineral uptake in japonica rice. Results showed that Huaidao-9 and Xudao-7 had low Cd absorption and high amounts of mineral nutrient elements (Fe, Zn, Mg, and Ca, LCHM group), whereas Zhongdao-1 and Xinkedao-31 showed opposite accumulation characteristics (HCLM group). Stepwise regression analysis showed that zinc, iron, and potassium are the key minerals that affect Cd accumulation in japonica rice and zinc was the most important factor, accounting for 68.99 %. The accumulation of Cd and mineral elements is potentially associated with rhizosphere soil bacteria. Taxa enriched in the LCHM rhizosphere (phyla Acidobacteriota and MBNT15) indicated the high nutrient characteristics of the soil and reduced activity of Cd in soil. The HCLM rhizosphere was highly colonized by metal-activating bacteria (Actinobacteria), lignin-degrading bacteria (Actinobacteria and Chlorofexi), and bacteria scavenging nutrients and trace elements (Anaerolinea and Ketobacter). Moreover, the differences in the uptake of Cd and mineral elements affected predicted functions of microbial communities, including sulfur oxidation and sulfur derivative formation, human or plant pathogen, and functions related to the iron oxidation and nitrate reduction. The results indicate a potential association of Cd and mineral elements uptake and accumulation with rhizosphere bacteria in rice, thus providing theoretical basis and a new perspective on the maintenance of rice security and high quality simultaneously.

Molecular analysis of microbial nitrogen transformation and removal potential in the plant rhizosphere of artificial tidal wetlands across salinity gradients

This study explored the microbial nitrogen transformation and removal potential in the plant rhizosphere of seven artificial tidal wetlands under different salinity gradients (0-30‰). Molecular biological and stable isotopic analyses revealed the existence of simultaneous anammox (anaerobic ammonium oxidation), nitrification, DNRA (dissimilatory nitrate reduction to ammonium) and denitrification processes, contributing to nitrogen loss in rhizosphere soil. The microbial abundances were 2.87 × 10³-9.12 × 10⁸ (nitrogen functional genes) and 1.24 × 10⁸-8.43 × 10⁹ copies/g (16S rRNA gene), and the relative abundances of dissimilatory nitrate reduction and nitrification genera ranged from 6.75% to 24.41% and from 0.77% to 1.81%, respectively. The bacterial 16S rRNA high-throughput sequencing indicated that Bacillus, Zobellella and Paracoccus had obvious effects on nitrogen removal by heterotrophic nitrifying/aerobic denitrifying process (HN-AD), and autotrophic nitrification (Nitrosomonas, Nitrospira and Nitrospina), conventional denitrification (Bradyrhizobium, Burkholderia and Flavobacterium), anammox (Candidatus Brocadia and Candidatus Scalindua) and DNRA (Clostridium, Desulfovibrio and Photobacterium) organisms co-existed with HN-AD bacteria. The potential activities of DNRA, nitrification, anammox and denitrification were 1.23-9.23, 400.03-755.91, 3.12-35.24 and 30.51-300.04 nmolN₂·g^-1·d^-1, respectively. The denitrification process contributed to 73.59-88.65% of NO_x^- reduction, compared to 0.71-13.20% and 8.20-15.42% via DNRA and anammox, as 83.83-90.74% of N₂ production was conducted by denitrification, with the rest through anammox. Meanwhile, the nitrification pathway accounted for 95.28-99.23% of NH₄⁺ oxidation, with the rest completed by anammox bacteria. Collectively, these findings improved our understanding on global nitrogen cycles, and provided a new idea for the removal of contaminants in saline water treatment.

Effects of composting pig manure at different mature stages on ARGs in different types of soil-vegetable systems

Aerobic composting is considered as an economically as well as environmentally friendly technology that prevents the diffusion of ARGs and ARBs from manure to farmland soil, on which many studies have been conducted. However, the transmission route and potential ecological risks of ARGs in soil-vegetable systems after application of manure at different maturity stages remain unclear. Therefore, through a pot experiment, this study analyzed the effects of manure composted from livestock excrement on ARGs and microbial community in different soil-vegetable systems, taking leafy plants (Shanghai green) and tuber plants (carrot) as examples. It was noted that the highly matured manure could reduce the ARGs contamination in soil and crops, and the ARGs in soil tended to accumulate in the direction of plant roots. The edible part of crops often had a more serious ecological risk of ARGs, and the potential pathogenic bacteria and ARGs could harm human health through exposure and dietary routes. In summary, this study provides new evidence for the transmission of ARGs in soil-vegetable systems with different mature stages of manure and highlights the potential safety risks of the transfer of antibiotic resistance from manure to soil and ultimately to the human food chain.

Exploring the Risk Thresholds of Soil Heavy Metals in Carbonate and Non-carbonate Rock Areas: The Case of Qianjiang District in Chongqing, China

To determine whether the national soil heavy metal standards (GB 15618-2018) are applicable to some carbonate and non-carbonate zones in Southwest China, rice and rhizosphere soil samples were collected in Chongqing and analyzed for heavy metal contents, pH, and other chemical parameters. In addition, regression analysis was also used to predict the risk threshold of soil heavy metals. The Cd risk screening value in GB 15618-2018 was strict for alkaline soils (pH > 7.5) as compared to those revealed in carbonate and non-carbonate areas, while the calculated pollution threshold for Cd in acidic soils (pH ≤ 5.5) in the non-carbonate area was lower than that in GB 15618-2018. Therefore, to improve the applicability of the evaluation results, a soil-crop system evaluation is recommended.

Diversity analysis of leaf endophytic fungi and rhizosphere soil fungi of Korean Epimedium at different growth stages

BACKGROUND

Rhizosphere fungi and endophytic fungi play key roles in plant growth and development; however, their role in the growth of Epimedium koreanum Nakai at different stages remains unclear. Here, we used the Illumina MiSeq system, a high-throughput sequencing technology, to study the endophytic fungi and rhizosphere microbiome of Korean Epimedium.

RESULTS

Epimedium koreanum Nakai rhizosphere soil and leaves had highly diverse fungal communities during the growth process. The relative abundance of soil fungi in the rhizosphere stage was higher than that of leaf endophytic fungi in the early growth stage, but the overall abundance was basically equal. Sebacina is a significantly divergent fungal genera, and Sebacina sp. are present among leaf fungi species in the rhizosphere soil of Epimedium koreanum Nakai. Sebacina sp. can move to each other in rhizosphere soil fungi and leaf endophytes. VIF (variance inflation factor) analysis showed that soluble salt, whole nitrogen, alkaline lysis nitrogen, whole phosphorus, total potassium, and fast-acting potassium are useful environmental factors for rhizosphere soil and leaf endophytic fungi: potassium, total nitrogen, whole phosphorus, and three environmental factors were significantly and positively associated with the relative abundance of Sebacina sp.

CONCLUSIONS

(1) This study is the first to clarify the species diversity of fungi in Epimedium koreanum Nakai leaf and rhizosphere soil. (2) Different fungal communities of rhizosphere soil fungi and leaf endophytic fungi at different growth stages of Epimedium koreanum Nakai were examined. (3) Sebacina sp. can move to each other between rhizosphere soil fungi and leaf endophytic fungi. (4) Nitrogen, phosphorus and potassium elements in the environment have a significant positive effect on the relative abundance of Sebacina sp.

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.

Role of the rhizosphere of a flooding-tolerant herb in promoting mercury methylation in water-level fluctuation zones

The water-level fluctuation zone (WLFZ) has been considered as a hotspot for mercury (Hg) methylation. Flooding-tolerant herbs are gradually acclimated to this water-land ecotone, tending to form substantial root systems for improving erosion resistance. Accompanying rhizosphere microzone plays crucial but unclear roles in methylmercury (MeHg) formation in the WLFZ. Thus, we conducted this study in the WLFZ of the Three Gorges Reservoir, to explore effects of the rhizosphere of a dominant flooding-tolerant herb (bermudagrass) on MeHg production. The elevated Hg and MeHg in rhizosphere soils suggest that the rhizosphere environment provides favorable conditions for Hg accumulation and methylation. The increased bioavailable Hg and microbial activity in the rhizosphere probably serve as important factors driving MeHg formation in the presence of bermudagrass. Simultaneously, the rhizosphere environments changed the richness, diversity, and distribution of hgcA-containing microorganisms. Here, a typical iron-reducing bacterium (Geobacteraceae) has been screened, however, the majority of hgcA genes detected in rhizosphere, near-, and non-rhizosphere soils of the WLFZ were unclassified. Collectively, these results provide new insights into the elevated MeHg production as related to microbial processes in the rhizosphere of perennial herbs in the WLFZ, with general implications for Hg cycling in other ecosystems with water-level fluctuations.

Microplastic particles alter wheat rhizosphere soil microbial community composition and function

The wide existence of microplastics (MPs) in the terrestrial systems is proved by -many studies, and their presence could potentially change the soil chem-physical properties and processes. Various types of microplastics may have different behaviors, inducing distinct effects on the soil ecosystems. However, the knowledge of microplastic impacts on rhizosphere soil bacterial community structure is limited. In our study, three types of microplastics, i.e., polyethylene (PE), polyvinylchloride (PVC) and polystyrene (PS), with the same particle size (200 µm) and concentration (2%) were used to investigate their influences on the rhizosphere soil bacterial communities. Results revealed that the alpha diversities (richness, evenness and diversity) of microbiota in the rhizosphere soil were variously decreased by the microplastics, especially the PE MPs. The relative abundance of some various phyla and genera related to pollution degradation was miscellaneously increased, indicating that the MPs with different characterizations may have miscellaneous biodegradation pathways. Moreover, the PICRUSt2 analysis demonstrated that PS decreased most functional category levels and led to a decrease of bacterial genus number, however, PE and PVC improved metabolic pathways and xenobiotics biodegradation and metabolism. Our findings offer important knowledge of how the microplastics with different characterizations influence rhizosphere soil bacterial communities and their related function.

Distribution and transfer of antibiotic resistance genes in different soil-plant systems

The extensive application of farm manure that is contaminated with pharmaceutical antibiotics not only causes substantial soil pollution but additionally leads to the input of antibiotic resistance genes (ARGs) into the soil. These ARGs would proliferate and affect human health via the food chain. The effects of cultivated crops and wild plants on ARGs in rhizosphere soil are unclear. Therefore, we chose potted plants of cultivated crops (pakchoi, lettuce, corn) and wild plants (barnyard grass, crabgrass, dog tail), and set up test groups, i.e., treatment group, antibiotic-contaminated soil; control group, no antibiotic-contaminated soil; and a blank group without plants. The aim was to explore differences in the distribution and transfer of ARGs in the soil-plant system between cultivated crops and wild plants and at the same time to explore the influence of bacterial community evolution on ARGs in the rhizosphere soil of cultivated crops and wild plants. We concluded that under the pressure of antibiotic selection, ARGs can be transferred to the root endophytes of plants through the soil and further to the phyllosphere of plants, and cultivated crops such as pakchoi and wild plants barnyard grass have a strong ability to transport ARGs. Regardless of cultivated crops or wild plants, the abundance of ARGs in rhizosphere soil can be substantially reduced by 66.53 ~ 85.35%. Redundancy analysis and network analysis indicated that bacterial community succession is the main mechanism affecting changes of ARGs in rhizosphere soil. The reduction of Firmicutes due to the plant was the main factor responsible for the reduction of the abundance of ARGs in rhizosphere soil. The tetA, tetG, tetX, sul2, and qnrS genes are highly related to some potential pathogens, and the health risks they bring are a red flag that deserves attention.

Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity

Rotational strip intercropping (RSI) of cereals and legumes has been developed and widely carried out to alleviate continuous cropping obstacles, to control erosion and to improve field use efficiency. In this study, a four-year fixed-field experiment was carried out in northeast China with three treatments: continuous cropping of maize, continuous cropping of peanuts and rotational strip intercropping of maize and peanut. The results show that crop rotation improved the main-stem height, branch number, lateral branch length, and yield and quality of peanuts; the yield was the highest in 2018, when it was increased by 39.5%. RSI improved the contents of total N, available N, total P, available P, total K and available K; the content of available N was the highest in 2018, with an increase of 70%. Rhizosphere soil urease and catalase activities were significantly increased and were the highest in 2017, reaching 183.13% and 91.21%, respectively. According to a high-throughput sequencing analysis, the rhizosphere soil bacterial richness and specific OTUs decreased in peanut rhizosphere soil, while the fungal increased. There were differences in the bacterial and fungal community structures; specifically, the abundance of Acidobacteria and Planctomycetes increased among bacteria and the abundance of beneficial microorganisms such as Ascomycota increased among fungi. In conclusion, rotational strip intercropping of maize and peanut increased the yield and quality of peanuts and conducive to alleviating the obstacles facing the continuous cropping of peanuts. Among then, soil physicochemical properties, enzyme activity and microbial diversity were significantly affected the yield of peanut.

Characterization of the belowground microbial community and co-occurrence networks of tobacco plants infected with bacterial wilt disease

Characterizing the microbial communities associated with soil-borne disease incidence is a key approach in understanding the potential role of microbes in protecting crops from pathogens. In this study, we compared the soil properties and microbial composition of the rhizosphere soil and roots of healthy and bacterial wilt-infected tobacco plants to assess their potential influence on plant health. Our results revealed that the relative abundance of pathogens was higher in diseased plants than in healthy plants. Moreover, compared with healthy plants, there was a significantly higher microbial alpha diversity in the roots and rhizosphere soil of diseased plants. In addition, we detected a lower abundance of certain plant microbiota, including species in the genera Penicillium, Trichoderma, and Burkholderia in the rhizosphere of diseased plants, which were found to be significantly negatively associated with the relative abundance of Ralstonia. Indeed, compared with healthy plants, the co-occurrence networks of diseased plants included a larger number of associations linked to plant health. Furthermore, structural equation modeling revealed that these specific microbes were correlated with disease suppression, thereby implying that they may play important roles in maintaining plant health. In conclusion, our findings provide important insights into the relationships between soil-borne disease incidence and changes in the belowground microbial community. These findings will serve as a basis for further research investigating the use of specific plant-associated genera to inhibit soil-borne diseases.

nov., isolated from the citrus rhizosphere soil

Two Gram-staining positive strains, FJAT-49825^T and FJAT-50051^T were isolated from a citrus rhizosphere soil sample. Strains FJAT-49825^T and FJAT-50051^T showed the highest 16S rRNA gene sequence similarity with the type strain of Neobacillus cucumis (98.4-98.5%). The 16S rRNA gene sequence similarity between strains FJAT-49825^T and FJAT-50051^T was 99.8%. Strain FJAT-49825^T optimally grew at 35 °C, pH 6.0 in the absence of NaCl while strain FJAT-50051^T grew at 40 °C, pH 7.0 and in presence of 2% NaCl (w/v). Both strains contained meso-2,6-diaminopimelic acid as the cell-wall diamino acid. The respiratory quinone of strains FJAT-49825^T and FJAT-50051^T was MK-7. The polar lipids of strain FJAT-49825^T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipid and unidentified lipid whereas strain FJAT-50051^T polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipid and unidentified lipid. The major fatty acids (> 10%) in both strains were iso-C_15:0 and anteiso-C_15:0. The genomic DNA G + C content of strains FJAT-49825^T and FJAT-50051^T were 40.8 and 41.1%, respectively. The average nucleotide identity and digital DNA-DNA hybridization value between strains FJAT-49825^T and FJAT-50051^T and with other members of the genus Neobacillus were lower than the cut-off value (95-96/70%) for interspecies identity. Based on the results, strains FJAT-49825^T and FJAT-50051^T represent two novel species of the genus Neobacillus, for which the names Neobacillus rhizophilus sp. nov. and Neobacillus citreus sp. nov. are proposed. The type strains are FJAT-49825^T (= GDMCC 1.2592^T = JCM 34834^T) and FJAT-50051^T (= GDMCC 1.2593^T = JCM 34835^T).

Temporal and spatial differentiation characteristics of soil arsenic during the remediation process of Pteris vittata L. and Citrus reticulata Blanco intercropping

The intercropping of hyperaccumulators and fruit trees has great application prospects owing to its environmental and economic benefits. However, the variation tendency and spatial distribution characteristics of pollutants in soil are unclear. A 19-month pot positioning experiment was conducted to clarify the spatio-temporal characteristics of arsenic (As) during Pteris vittata L.-Citrus reticulata Blanco intercropping process. The results showed that: (1) In the early stage, the solubilization of soil As by P. vittata was dominant. At 3 months, the water-soluble As in P. vittata rhizosphere soil increased by 19.4-55.4% compared with the initial state. In the later stage, the As extraction from soil by P. vittata was dominant. At 19 months, the water-soluble As in P. vittata rhizosphere soil decreased by 24.6-71.2% compared with the initial state. The water-soluble As in C. reticulata rhizosphere soil in intercropping, under the role of P. vittata, reached 1.75-2.35 times that of monoculture at 7 months, and was not significantly different from that of monoculture at 19 months. (2) The spatial distribution characteristics of soil As, affected by As-hyperaccumulation of P. vittata, showed that the As variability of intercropping and P. vittata monoculture was greater than that of C. reticulata monoculture. The area of P. vittata remediating soil was approximately 15 cm horizontally around its planting point and at least 25 cm vertically. (3) P. vittata-C. reticulata intercropping did not affect the phytoremediation efficiency and effectively reduced the risk of As pollution for C. reticulata. The As concentration in C. reticulata leaves of open intercropping decreased by 39.0-64.2% (early-maturity) and 25.6-59.1% (late-maturity) compared with that of monoculture, similar to that in clean soil. This study analyzed the As migration characteristics during P. vittata-C. reticulata intercropping through time and space and provides important theoretical support for the remediation and safe use of As-contaminated farmland.

Plant growth promoting rhizobacterial diversity in potato grown soil in the Gwalior region of India

There seems to be meager studies with regards to rhizo and non-rhizo microbial association with potato plant from the central India. Present study was undertaken to evaluate the microbial diversity of rhizospheric and non-rhizospheric isolates from three varieties of potato viz Kufri sindhuri, Kufri lauvkar and Kufri chipsona-3 procured from the Central Potato Research Station, Maharajpura, Gwalior. A total of 130 bacterial forms were isolated, and amongst these forty isolates were further characterized on their morphological basis, and those showing some of PGPR characteristics were identified to species level using VITEK-2 method. Various bacterial populations were found in potato rhizosphere and dominant presence was those of Bacillus subtilis, Bacillus Megaterium and Lysinibacillus sphaericus. The non-rhizospheric soil was dominant in the forms like Aeromonas salmonicida, Morxella group and Bacillus coagulans. Highest bacterial diversity was found in the rhizosphere soil of different potato cultivars than in the non-rhizospheric soil of potato.

Diversity and spatiotemporal dynamics of fungal communities in the rhizosphere soil of Lycium barbarum L.: a new insight into the mechanism of geoherb formation

Lycium barbarum L. is a well-known traditional geoherb in Ningxia, China. The fruits of L. barbarum contain several dietary constituents, and thus, they exert many beneficial effects on human health. However, a few studies have been conducted on the geoherb L. barbarum and its rhizosphere soil fungal community. In this study, we determined the physicochemical properties and fungal community structure of rhizosphere soil of L. barbarum from three regions of China, namely Ningxia (NX), Qinghai (QH), and Xinjiang (XJ), during three development stages of L. barbarum. Soil pH varied between 7.56 and 8.60 across the three regions, indicating that alkaline soil is conducive to the growth of L. barbarum. The majority of soil properties in NX, an authentic geoherb-producing area, were substantially inferior to those in XJ and QH during all three developmental stages. Total sugar, polysaccharide (LBP), and flavonoid contents were the highest in wolfberry fruits from NX. High-throughput sequencing showed that the abundance of the soil fungal population in NX was higher than that in QH and XJ during the flowering and fruiting stage and summer dormant stage. Moreover, the soil fungal diversity increased with the development of wolfberry. Ascomycota and Mortierellomycota were the predominant phyla in the rhizosphere fungal communities in all samples. Redundancy analysis showed a significant correlation of the soil-available phosphorus and LBP of wolfberry fruits with the fungal community composition. The characteristics of rhizosphere fungal communities determined in the present study provide insights into the mechanism of geoherb formation in NX wolfberry.

nov., isolated from rhizosphere soil of coastal herb Zoysia matrella within the Beibu Gulf

A bacterial isolate (BGMRC 2046^T) was isolated from the rhizosphere soil of Zoysia matrella collected from the Beibu Gulf of China. The results of a polyphasic taxonomic study revealed that this strain belongs to a member of the genus Stappia with the characteristics of Gram-stain-negative, catalase- and oxidase-positive, motile, short rod-shaped. The strain grew at 20-37 °C (optimal, 28 °C), pH 6.0-9.0 (optimal, pH 7.0), and 1-7% (w/v) optimal, NaCl (1-3%). A phylogenetic evaluation based on 16S rRNA gene sequence analysis revealed that this strain fall into the family Stappiaceae, being most closely related to Stappia indica CGMCC 1A01226^T (95.8% sequence similarity), Stappia stellulata DSM 5886^T (95.1%), and Stappia taiwanensis DSM 23284^T (94.4%). The major cellular fatty acid, respiratory quinone and polar lipids were all detected from new species (BGMRC 2046T), that shows the chemical characteristics of BGMRC 2046T. The major polar lipids were two unidentified ninhydrin positive phospholipids, four unidentified phospholipids, and one unidentified lipid. Genome sequencing revealed a genome size of 4.78 Mbp and a G + C content of 60.8%. Pairwise comparison of the genomes of the new strain BGMRC 2046^T and the three most closely related strains resulted in gANI values was lower than 75% and a digital DNA-DNA hybridization values was lower than 24%. The strain possessed genes encoding choline uptake and conversion to betaine gene clusters. The results of the polyphasic taxonomic study showed that strain BGMRC 2046^T represents a new species of the genus Stappia. The name Stappia sediminis sp. nov. is proposed for the species with the type strain BGMRC 2046^T (= KCTC52115^T = CGMCC1.17425^T).

Effect of light combination on the characteristics of dissolved organic matter and chemical forms of Cd in the rhizosphere of Arabidopsis thaliana involved in phytoremediation

Light, one of the most important natural resources for plant species, significantly influences the biomass yield and nutrient uptake capacity in plants. Light sources with different spectra combinations can impact the bioavailability, toxicity, and solubility of heavy metals in soils by altering the concentrations and fractionations of soil dissolved organic matter (DOM). A series of light irradiation treatments were performed to evaluate the influence of red, yellow, and blue lights on the characteristics of DOM in the rhizosphere soils of Arabidopsis thaliana. The results showed that monochromatic red light significantly raised the levels of DOM and proportions of hydrophilic fractionations in the rhizosphere of A. thaliana relative to the control, while monochromatic blue light had the opposite effect. Moreover, the proportions of hydrophobic acid, which can mobilize Cd effectively, also raised with increasing doses of red light, which stimulated Cd mobilization. The application of yellow light not only increased the levels of hydrophobic acid in monochromatic red light treatment but also decreased the proportion of hydrophobic fractions in monochromatic blue light treatment, partially weakening the negative impacts of pure blue light on soil Cd activation. Moreover, DOM from the combined red, yellow, and blue lights resulted in a significantly stronger Cd extraction efficiency than the other light irradiation treatments, consequently enhancing the Cd phytoextraction efficiency of A. thaliana. The findings of this study demonstrated that a suitable light combination could enhance the phytoremediation effect of A. thaliana by activating soil Cd, and this method can be extrapolated to the real field, where light irradiation can be easily applied and modulated.

Changes in microbial metabolic C- and N- limitations in the rhizosphere and bulk soils along afforestation chronosequence in desertified ecosystems

The resource acquisition strategy of soil microorganisms can be reflected by soil extracellular enzyme activity (EEA). However, there are few reports on the application of extracellular enzyme stoichiometry (EES) method to study the difference in microbial metabolic nutrient limitation between rhizosphere and bulk soil. Here, we choose the rhizosphere and bulk soils of Pinus sylvestris var. mongolica (P. sylvestris) plantations with five stand ages in the Mu Us sandy land, and analyzed the variation and differences of microbial metabolic limitation between rhizosphere and bulk soils with stand age by EES method. The results showed that the microbial metabolic C-limitation in the rhizosphere and bulk soil gradually increased with stand age. Almost all the vector angles were less than 45°, which indicated that the soil microbial metabolism was relatively limited by N rather than P. Furthermore, the microbial C- and N-limitation in rhizosphere soils were generally stronger than bulk soils. Soil physical properties (59.73%) explained most of the variations in soil EES based on the variation-partitioning analysis, followed by total nutrients (43.00%). The partial least squares path model suggested that the main driving factor for the variation of soil microbial metabolic C-limitation in the rhizosphere and bulk soils was physical properties, while the microbial N-limitation was for total nutrients. In general, the study emphasized the application of EES methods to assess the dynamic equilibrium between soil microbial resource acquisition and nutrient availability in desert ecosystems. These insights provide guidance for formulating afforestation strategies, such as nutrient management of sandy plantations.

Fumigation practice combined with organic fertilizer increase antibiotic resistance in watermelon rhizosphere soil

Chemical fumigants and organic fertilizer are commonly used in facility agriculture to control soil-borne diseases and promote soil health. However, there is a lack of evidence for the effect of non-antibiotic fumigants on the distribution of antibiotic resistance genes (ARGs) in plant rhizosphere soils. Here, the response of a wide spectrum of ARGs and mobile genetic elements (MGEs) to dazomet fumigation practice in the rhizosphere soil of watermelon was investigated along its branching, flowering and fruiting growth stages in plastic shelters using high-throughput quantitative PCR approach. Our results indicated that soil fumigation combined with organic fertilizer application significantly increased the relative abundance of ARGs and MGEs in the rhizosphere soil of watermelon plant. The positive correlations between the relative abundance of ARGs and MGEs suggested that soil fumigation might increase the horizontal gene transfer (HGT) potential of ARGs. This result was further confirmed by the enhanced associations between ARG and MGE subtypes in the networks of fumigation treatments. Moreover, bipartite associations between ARGs/MGEs and microbial communities (bacteria and fungi) revealed a higher percentage of linkage between MGEs and microbial taxa in the fumigated soils. Structural equation model analysis further suggested that the increases in antibiotic resistance after fumigation and organic fertilizer application were mainly driven by MGEs and fungal community. Together, our results provide vital evidence that dazomet fumigation process combined with organic fertilizer in plastic shelters has the great potential to promote ARGs' dissemination in the rhizosphere, and raise cautions of the acquired resistance by soil-borne fungal pathogen and the potential spreading of ARGs along soil-plant continuum.

Evaluation of maize/peanut intercropping effects on microbial assembly, root exudates and peanut nitrogen uptake

Legume/cereal intercropping has been widely studied within ecosystem function, owing to its overyield potential, predominantly by dinitrogen (N₂) fixation. In our 2-year peanut/maize intercropping field experiment, land equivalent ratio (LER) showed an average yield-increase by 41.48%. Performance index of intercropped peanut (IP) functional leaves exhibited significant improvement (2.02-fold). Moreover, IP increased dry nodule weight by 58.82% as compared to mono-cropped. Also, the ratio of nodules to aboveground biomass in IP reduced by 65.8%. In pot experiment, higher urease activity was found in rhizosphere (22.73%). The abundance of Rhizobium and niƒH gene in the rhizosphere of IP were significantly enhanced by 71.91% and 208%, respectively. To analyze root exudates, we performed hydroponic coculture, the proportion of total isoflavonoids in peanut root exudates were increased distinctly by 22.4%. Our findings certainly helped in filling one the information gaps, that how intercropping increases nitrogen fixation in rhizosphere. Lastly, it can further facilitate to understand functional significance of intercropping system for agricultural ecological sustainability and efficient resource utilization.

Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears

BACKGROUND

Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant.

RESULTS

The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani.

CONCLUSIONS

It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.

The influence of rhizosphere soil fungal diversity and complex community structure on wheat root rot disease

Wheat root rot disease due to soil-borne fungal pathogens leads to tremendous yield losses worth billions of dollars worldwide every year. It is very important to study the relationship between rhizosphere soil fungal diversity and wheat roots to understand the occurrence and development of wheat root rot disease. A significant difference in fungal diversity was observed in the rhizosphere soil of healthy and diseased wheat roots in the heading stage, but the trend was the opposite in the filling stage. The abundance of most genera with high richness decreased significantly from the heading to the filling stage in the diseased groups; the richness of approximately one-third of all genera remained unchanged, and only a few low-richness genera, such as Fusarium and Ceratobasidium, had a very significant increase from the heading to the filling stage. In the healthy groups, the abundance of most genera increased significantly from the heading to filling stage; the abundance of some genera did not change markedly, or the abundance of very few genera increased significantly. Physical and chemical soil indicators showed that low soil pH and density, increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Our results revealed that in the early stages of disease, highly diverse rhizosphere soil fungi and a complex community structure can easily cause wheat root rot disease. The existence of pathogenic fungi is a necessary condition for wheat root rot disease, but the richness of pathogenic fungi is not necessarily important. The increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Low soil pH and soil density are beneficial to the occurrence of wheat root rot disease.

nov., a bacterium isolated from rhizosphere soil of Nicotiana tabacum L

Strain W712T was isolated from rhizosphere soil of Nicotiana tabacum L. collected from Kunming, south-west China. Cells were Gram-staining negative, aerobic, motile and rod shaped. The isolate grew at 20-45 °C (optimum 30 °C), pH 6.0-8.0 (optimum pH 7.0) and in the presence of up to 3.0% (w/v) NaCl (optimum 1%, w/v). Ubiquinone-10 was the only respiratory quinone type. Polar lipids contained diphosphatidylglycerol, phosphatidylmehtylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified aminolipid. The major fatty acids were detected as summed feature 8 (C18:1 ω7c or C18:1 ω6c), summed feature 3 (C16:1 ω7c or C16:1 ω6c) and C18:1 2OH. The genomic DNA G + C content was 68.7%. The ANI values were 94.3%, 93.3% and 93.6% between Azospirillum baldaniorum Sp245T, Azospirillum brasilense ATCC 49958T, Azospirillum formosense CC-Nfb-7T and strain W712T, respectively, which were lower than the prokaryotic species delineation threshold of 95.0-96.0%. The digital DNA-DNA hybridization values between A. baldaniorum Sp245T, A. brasilense ATCC 49958T, A. formosense CC-Nfb-7T and strain W712T indicated that the candidate represents a novel genomic species. According to the phenotypic and genotypic characteristics, we propose that strain W712T warrants the assignment to a novel species, for which the name Azospirillum tabaci sp. nov. (type strain W712T = CGMCC 1.18567T = KCTC 82186T) is proposed.

Elucidating the impact of three metallic nanoagrichemicals and their bulk and ionic counterparts on the chemical properties of bulk and rhizosphere soils in rice paddies

Growing applications of nanoagrichemicals have resulted in their increasing accumulation in agricultural soils, which could modify soil properties and affect soil health. A greenhouse pot trial was conducted to determine the effects of three metallic nanoagrichemicals on several fundamental chemical properties of a rice paddy soil, including zinc oxide nanoparticles (ZnO NPs) and copper oxide nanoparticles (CuO NPs) at 100 mg/kg, and silicon oxide nanoparticles (SiO₂ NPs) at 500 mg/kg, as well as their bulk and ionic counterparts. The investigated soil amendments displayed significant and distinctive impact on the examined soil chemical properties relevant to agricultural production, including soil pH, redox potential, soil organic carbon (SOC), cation exchange capacity (CEC), and plant available As. For example, all amendments increased the bulk soil pH at day 47 to some extent, but the increase was substantially higher for SiO₃^2- (37.7%) than other amendments (5.8%-13.7%). Soil Eh was elevated markedly at day 47 after the addition of soil amendments in both the bulk soil (45.9%-74.4%) and rice rhizosphere soil (20.3%-68.9%). CuO NPs and Cu²⁺ generally exhibited greater impact on soil chemical properties than other agrichemicals. Significantly different responses to soil amendments were observed between bulk and rhizosphere soils, suggesting the essential role of plants in affecting soil properties and their responses to environmental disturbance. Overall, our results confirmed that the tested amendments could have remarkable impacts on the fundamental chemical properties of rice paddy soils.

C:N:P stoichiometry responses to 10 years of nitrogen addition differ across soil components and plant organs in a subtropical Pleioblastus amarus forest

How stoichiometry in different ecosystem components responds to long-term nitrogen (N) addition is crucial for understanding within-ecosystem biogeochemistry cycling processes in the context of global change. To explore the effects of long-term N addition on nutrient stoichiometry in soil and plant components in forest ecosystem, a 10-year N addition experiment using ammonium nitrate (NH₄NO₃) was conducted in a bamboo forest in the Rainy Zone of West China, where the background N deposition is the highest in the world. Four N treatment levels (+0, +50, +150, +300 kg N ha^-1 yr^-1) (CK, LN, MN, HN) were applied monthly since November 2007, and then, the C:N:P stoichiometry of soil, microbial biomass, and enzymes in rhizosphere soil and bulk soil, and plant organs were measured. N addition decreased the stoichiometry of C:N:P of soil, microbial biomass, and enzymes. Soil C:N:P change under N addition treatments was stronger in bulk soil, while C:N:P changes for microbial biomass and enzyme activity were significant in rhizosphere soil. N addition significantly decreased TOC in bulk soil. Changes in MBC:MBN:MBP in rhizosphere and bulk soil were mainly caused by MBN and MBP, and MBP performance was consistent with that of AP. The main variable leading to the change of enzyme C:N:P in rhizosphere soil was BG and AP, and in bulk soil was LAP + NAG activity. Plant root C:P and N:P increased with N addition, while those for leaves and twigs did not. N addition significantly reduced the pH of both rhizosphere and bulk soils. These results suggest that the stoichiometry responses of rhizosphere and bulk soils were different due to the influence of plant roots. Soil acidification, enhanced aluminum toxicity potential, decreased root biomass and enhanced microbial P limitation caused by N addition were the important mechanisms that promoted stoichiometry changes in this ecosystem. Under the chronic input of N deposition, the stoichiometry between plant and soil evolved in different directions, which may lead to the decoupling of plants from soils.