Search Results (138)

Rice cadmium (Cd) contamination is a serious threat to global food security and human health. Plant-associated microbiomes are known to affect Cd accumulation in plants. However, the response of the rice microbiome to Cd contamination and its role in modulating grain Cd accumulation remain poorly understood. In the present study, the responses of the rhizospheric fungi (RF) community and seed endophytic fungi (SEF) community to the soil physiochemical properties of rice from moderately (MC) and severely (SC1 and SC2) Cd-contaminated paddies were investigated. Moreover, the effects of soil physiochemical properties, RF community and SEF community on grain Cd accumulation were analyzed through correlation analysis. The results showed that the Cd concentration in rice grains from SC2 exceeded the food safety standard of China and was higher than that of SC1 and MC. The Cd concentration in rice grains was positively correlated with the soil-available Cd concentration, while being negatively correlated with the available nutrient elements and pH value of soil. In addition, it was found that the diversity of RF increased with the soil-available Cd concentration, while the diversity and richness of SEF decreased with the soil-available Cd concentration. Moreover, the RF community was influenced by soil physiochemical properties. The Spearman correlation analysis showed that the soil-available Cd was positively correlated with RF Sebacina, Clonostachys, Acremonium, Talaromyces and Fusarium, and most of them were related to grain Cd concentration, while unclassified SEF Pleosporales and Xylariales were associated with grain Cd concentration. These results suggested that Cd stress triggered a niche-specific response of the rice fungal microbiome. The fungi related to soil Cd availability and rice grain Cd accumulation may have a great potential application in food safety production in Cd-contaminated soil. Full article

Protected areas are essential for conserving biodiversity and sustaining ecosystems, yet their effective management requires a clear understanding of soil and water quality, which underpin ecological processes. This study evaluated 15 soil and seven water samples to assess their physico-chemical properties, focusing on heavy metal concentrations. Results showed that soils were generally neutral to alkaline, with Hashwan-2 exhibiting the highest concentrations of calcium (26.5 meq/L), magnesium (11.2 meq/L), carbonates (0.32 meq/L), bicarbonates (3.66 meq/L), and chloride (35.43 meq/L). Heavy metal analysis indicated elevated nickel (51.628 mg/kg) and chromium (76.29 mg/kg) at Albuyitlar-2, and chromium (68.015 mg/kg) at Shabak-Mateam-1 1 1, exceeding US-EPA permissible limits of 45 mg/kg for nickel and 64 mg/kg for chromium. Water samples revealed high levels of aluminum (12.681 mg/L), manganese (0.146 mg/L), and iron (7.055 mg/L), also exceeding the US-EPA thresholds of 0.2, 0.1, and 0.5 mg/L, respectively. In contrast, more toxic metals such as arsenic, cadmium, lead, and mercury remained within safe limits. These findings highlight localized concerns regarding heavy metal contamination that warrant continued monitoring to ensure ecosystem health. Full article

Continuous cropping can often deteriorate soil quality and reduce crop yield. Soil properties and microbial communities usually play a vital role in maintaining rhizosphere micro-ecosystem sustainability, which is yet to be addressed in continuous peony monoculture systems. Herein, variations in soil physiochemical properties were extensively investigated following 1, 4, and 10 years of continuous tree peony cropping, as well as microbial community diversity, composition, and predicted functions. The soil pH and contents of available Mg, Mn, Zn, and B significantly declined after 10 years of continuous monoculture, while the contents of soil organic carbon, nitrate, and available P, K, Fe, and Cu notably increased by more than 100%, implying an imbalance of soil nutrients resulting from long-term continuous cropping. High-throughput sequencing results indicated that the microbial community structure and composition were remarkably altered after either 4 or 10 years of continuous cropping, interfering with diverse microbial metabolic pathways and phenotype functions. In addition, the relative abundances of some beneficial bacteria dramatically increased, especially for Acidobacteriota and Bacillus members. Microbial selections or adaptations in response to soil nutrient changes were expected to remediate negative impacts of continuous cropping on soil quality. Findings in this study provide insights into the establishment of proper management strategies for sustaining soil quality to resist potential obstacles after long-term continuous peony cropping. Full article

Zinc (Zn) is an essential micronutrient for plant growth, serving as a co-factor in enzymatic processes and pigment biosynthesis. In horticultural crops such as lettuce, Zn fertilization is increasingly relevant for optimizing yield and nutritional quality. In this study, a greenhouse pot experiment was conducted using Lactuca sativa L. cv. Romana Verano (Ramiro Arnedo) to evaluate the effects of four Zn sources with contrasting physio-chemical properties—ZnSO₄, a synthetic chelate containing DTPA, EDTA, and HEDTA, a Zn–lignosulphonate complex, and ZnO nanoparticles—applied to soil at rates of 15, 30, 60, and 120 mg Zn·kg⁻¹. Morphometric traits, photosynthetic pigmentation, and photosystem performance were assessed to determine differences in plant response. Results showed that low to moderate Zn supply (15–60 mg Zn·kg⁻¹) maintained growth, leaf number, stem diameter, and biomass without significant changes compared to the control. In contrast, the highest dose (120 mg Zn·kg⁻¹), particularly in chelated forms, led to reductions in growth and yield exceeding 80%, reflecting supra-optimal effects. Although lignosulphonate and nanoparticles sources lowered soil Zn availability, they did not affect lettuce growth or yield, indicating their potential as safer agricultural alternatives to conventional Zn fertilizers. Photosynthetic efficiency, measured through chlorophyll fluorescence and electron transport activity, was positively modulated by adequate Zn levels but declined at excessive concentrations. These findings highlight that Zn efficiency strongly depends on its chemical form and applied dose, providing practical insights for optimizing Zn fertilization strategies in lettuce and other horticultural crops. Full article

Morchella spp. is a type of valuable and rare edible fungi cultivated in soil. Optimization of the cultivation medium for Morchella spp. is key to obtaining high-efficiency production in an ecologically friendly manner. Recently, the sustainable resource utilization of agricultural waste has gathered attention. Specifically, reusing tomato substrate, mushroom residues, and coconut shells can lower the production costs and reduce environmental pollution, demonstrating remarkable ecological and economic benefits. To determine the soil microbial communities of Morchella spp. using different culture medias and influencing factors, this study analysed the relative abundance of bacterial and fungal communities in natural soil, soil with 5% tomato substrate, soil with 5% mushroom residues, and soil with 5% coconut shells using Illumina NovaSeq high-throughput sequencing. In addition, intergroup differences, soil physiochemical properties, and product quality were also determined. Results demonstrated that agricultural waste consisting of mushroom residues, waste tomato substrate, and coconut shells can improve the efficiency of Morchella spp. cultivation. When considering yield and quality, mushroom residue achieved the highest yield (soil nutrient enrichment), followed by tomato substrate (water holding + grass carbon nutrient). All three types of agricultural waste promoted early fruiting, significantly increased polysaccharide, crude protein, and potassium content, and lowered crude fat and fibre. In regard to soil improvement, the addition of different materials optimized the soil’s physical structure (reducing volume weight and increasing water holding capacity) and chemical properties (enrichment of nitrogen, phosphorus, and potassium, regulating nitrogen and medium trace elements). For microbial regulation, the added materials significantly increased the abundance of beneficial bacteria (e.g., Actinomycetota, Gemmatimonadota and Devosia) and strengthened nitrogen’s fixation/nitration/decomposition functions. In the mushroom residue group, the abundance of Bacillaceae was positively related to yield. Moreover, it inhibited pathogenic fungi like Mortierella and Trichoderma, and lowered fungal diversity to decrease ecological competition. In summary, mushroom residues have nutrient releasing and microbial regulation advantages, while tomato substrate and coconut shells are new high-efficiency resources. These increase yield through the “physiochemical–microorganism” collaborative path. Future applications may include regulating the function of microorganisms and optimizing waste preprocessing technologies to achieve sustainability. Full article

Heavy metal (HM) contamination of soil is a worldwide problem with adverse consequences for the environment and human health. Microorganisms, as the most active fraction in soil, play a pivotal role in assessing changes in soil quality and maintaining ecological equilibrium. Accordingly, screening efficient microorganisms for remediating contaminated soils has emerged as a key research focus. This study employed high-throughput sequencing and conducted in situ field surveys to investigate the impacts of long-term HM pollution with varying severity on soil physicochemical properties, as well as the community structure and diversity of bacteria and fungi. The results showed that the major soil physiochemical properties and the bacterial and fungal β diversity significantly changed with the increase in HM pollution levels. The relative abundances of Chloroflexi, Myxococcota and Nitrospirota among bacteria, along with Chytridiomycota and Talaromyces among fungi, increased significantly with rising HM pollution levels. In low-, medium- and highly contaminated soils, the dominant bacterial species were OTU10618 (Micrococcales), OTU6447 (Chthoniobacterales), and OTU7447 (Burkholderiales), while the dominant fungal species were OTU3669 (Glomerellales), OTU397 (Olpidiales), and OTU2568 (Mortierellales). Bacterial communities were mainly affected by soil-available phosphorus, available cadmium (Cd) and available Pb, while fungal communities were predominantly influenced by soil-available phosphorus, soil organic carbon and total Pb content. These findings demonstrate that soil microorganisms in chronically HM-contaminated soils exhibit adaptive shifts, and this study thereby provides critical implications for assessing the remediation potential of diverse microbial taxa in HM-polluted soils. Full article

The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch’s postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management. Full article

The vital role of arbuscular mycorrhizal (AM) fungi in tea plant growth is well established; however, the mechanisms underlying how increasing cultivation chronosequence (CC) influences AM fungal distribution remain unclear. An investigation was conducted to investigate the temporal dynamics of AM fungal indices and soil properties across a 100-year tea CC (10-, 30-, 60-, and 100-year CC) in Xinyang Maojian tea (Camellia sinensis L.) plantations (Xinyang, Henan Province, China). Principal coordinate analysis was conducted to reveal the significant reorganization of AM fungal indices during early-to-mid stages (PCoA1: 89.2%, p < 0.05), with triphasic development. Mycorrhizal colonization (MC), hypha biomass (hypha), and spore density (SD) surged by 100% during 10–30 years; SD peaked at 60 years (164 spores g⁻¹) before declining, while glomalin-related soil protein (GRSP) accumulated significantly only at 100 years (p < 0.05). Concurrently, soil acidification (pH decreased from 6.37 to 4.84) and phosphorus depletion (AP from 119.6 mg kg⁻¹ to 32 mg kg⁻¹) intensified by 60 years, contrasting with the significant accumulations of soil organic organisms (SOM) (from 10.6 g kg⁻¹ to 36.4 g kg⁻¹), electrical conductivity (EC) (from 0.019 to 0.050 mS·cm⁻¹), and microaggregate accumulation (MAR) (from 25.8% to 40.3%) during the period. The linear regression model was performed to validate the significant effects (p < 0.05) of CC on the AM indices (MC, SD, hypha, and GRSP) and soil physiochemical characteristics (EC, moisture, and SOM). Variance partitioning attributed 97.4% of the total variation, while interactions among cultivation ages, nutrient characteristics (SOM and AP), and non-nutrient characteristics (pH, EC, moisture, and aggregates) accounted for 23.0%. To identify the driving factors of AM fungi indices, Pearson correlation and redundancy analysis (RDA) were performed, and EC (26.5%) and pH (20.9%) were identified as the paramount regulators of hyphal integrity and colonization efficiency. It was found that 60 years worked as a critical transition point for targeted interventions (e.g., organic amendments and pH buffering) to mitigate rhizosphere dysfunction and optimize mycorrhizal services in perennial monocultures. Full article

Fertilization management constitutes a critical determinant of agroecosystem productivity. Reasonable fertilization can increase the organic matter content in soil; however, the potential mechanism of how different fertilization regimes impact soil carbon sequestration is unclear. We hypothesized that the combined application of biochar and organic fertilizer would enhance soil carbon sequestration by improving soil physicochemical conditions, increasing microbial activity, and promoting the accumulation of stable forms of carbon. This study systematically investigated different regimes, including the application of chemical fertilizer alone (SCN), chemical fertilizer with biochar (SCB), chemical fertilizer with organic fertilizer (SCO), and chemical fertilizer with both biochar and organic fertilizer (SCBO), on soil physiochemical properties, enzyme activities, labile organic carbon fractions, microbial carbon fixation gene expression, and community composition. The results demonstrated that (1) the application of organic materials significantly enhanced soil nutrient levels and enzyme activities, with the best performance from SCBO; (2) the organic materials increased the labile soil organic carbon (SOC) content and the carbon pool management index, with SCO showing the highest at 69.82%; (3) SCB and SCBO improved the stability of soil carbon components by increasing the proportion of Aromatic C; and (4) the carbon fixation genes ACAT and sdhA exhibited the highest abundance in SCBO. In parallel, the relative abundance of Actinomycetota increased with the application of organic materials, reaching its peak in SCBO. Mantel testing revealed a strong correlation between microbial community composition and SOC, emphasizing the importance of SOC in microbial growth and metabolism. Moreover, the strong correlation between carbon fixation genes and aromatic carbon suggested that specific carbon forms, particularly aromatic structures, played a critical role in driving microbial carbon fixation processes. Full article

Soil microorganisms provide multifaceted benefits, including maintaining soil nutrient dynamics, improving soil structure, and instituting decomposition, all of which are important to soil health. Unpredictable weather events, including flooding from heavy rainfall, flash floods, and seawater intrusion, profoundly impact soil ecology, which is primarily challenged by flooding stress, and imbalances these microbial communities and their functions. This disturbance impairs the symbiotic exchanges between microbes and plants by limiting root exudates and habitats for microbes, as well as nutrient acquisition efficiency for plants. Therefore, this review comprehensively examines the changes in soil microbial communities that occur under flooding conditions. Flooding reduces soil oxygen (O₂) levels, limiting aerobic microbes but promoting anaerobic ones, including potential pathogens. In flooded soil, O₂ deficiency indirectly depends on the size of the soil particles and water turbidity during flooding. O₂ depletion is critical in shaping microbial community adaptation, which is linked to variations in soil pH, nutrient concentrations, and redox status, and fresh and saline water vary differently in terms of the adaptation of microorganisms. Wet soil alters soil enzyme activity, which influences microbial community composition. Notably, three-month post-flooding conditions allow microbial communities to adapt and stabilize more effectively than once-weekly flooding frequency. Based on the presence of aboveground species, fungi are found to reduce under flooding conditions, while nematode numbers, surprisingly, increase. Direct and indirect impacts between soil microbes and physio-chemical properties indicate positive or negative feedback loops that influence the soil ecosystem. Over the years, beneficial microorganisms such as plant-growth-promoting microbes (PGPMs) have been identified as important in regulating soil nutrients and microbial communities in wetland environments, thereby enhancing soil health and promoting better plant growth and development. Overall, understanding the mechanisms of belowground ecosystems under flooding conditions is essential for optimizing agricultural practices and ensuring sustainable crop production in flood-prone areas. Full article

In recent years, Cadmium (Cd) pollution in soybean farmland is severe. Therefore, this study focused on whether biochar influences soil physiochemical properties, the Cd content in soil and soybean grains, and the abundance and community structure of the czcA gene. Four doses of rice husk biochar (0, 5, 15, and 25 t·ha⁻¹) were applied under continuous cropping and crop rotation systems, and soil samples were collected after four years of one-time addition. The results indicated that biochar addition significantly increased soil available nitrogen, phosphorus, and soil organic carbon contents under continuous cropping and rotation. Biochar application significantly reduced the total Cd content of soil samples and soybean grains. Additionally, biochar application reduced czcA gene abundance in soybean soils by 14.26–37.88% and 35.96–48.71%, respectively. Correlation analysis revealed that Cd content and the abundance of the czcA gene significantly correlated with soil nutrients and pH. High-throughput sequencing revealed that the relative abundances of several Cd-resistant microorganisms were decreased by biochar addition. In addition, adding biochar significantly affected the Cd-resistant microbial community structure and diversity by influencing soil properties and Cd content. Therefore, this study has important practical significance for improving the soil environment and ensuring the quality and safety of agricultural products. Full article

In recent decades, much of China’s farmland has been transformed into forests due to the Conversion of Farmland to Forests and Grasses Project. While past research has mainly examined soil nutrients and water conservation, less attention has been given to soil microbial communities. This study examined the effects of converting farmland to forests of Pleioblastus amarus (PA), Populus deltoides (PD), or Zanthoxylum bungeanum (ZB) on the soil physiochemical properties, enzymes, and microbial communities, using abandoned land (AL) as the control, over a period of five years. The results showed that PA increased the soil organic carbon (SOC) content, although not significantly, while significantly boosting the C:N and C:P ratios and urease activity compared to the AL. PD notably reduced the amylase and cellulase activities, as well as the fungal Shannon index. Additionally, the beta diversity of both the bacterial and fungal communities in the PA stand was clearly distinct from that of the AL and the other tree species. The SOC content, total potassium content, and cellulase activity showed significant correlations with bacterial communities. Moreover, the bacterial community changes in the PD and ZB stands were mainly driven by the genera Steroidobacter, Roseisolibacter, and Serendipita, and were negatively correlated with the SOC content, C:N and C:P ratios, and cellulase activity. In contrast, the fungal community changes in the PA stand were primarily influenced by the order Capnodiales, family Capnodiaceae, genus Chaetocapnodium, and species Chaetocapnodium philippinense, which were positively correlated with the soil pH, C:N and C:P ratios, and cellulase activity. Furthermore, “Metabolism” was identified as the primary bacterial function, and converting farmland to forest altered the fungal nutritional type from Saprotroph to Pathotroph–Saprotroph–Symbiotroph, particularly in the PA stand. These findings indicate that converting farmland to forest, particularly with bamboo P. amarus, significantly impacts the bacterial and fungal communities in the soil and changes the fungal trophic type due to the carbon source and cellulase activity of this tree species. Full article

The domestication process of agaves has allowed this plant to adapt to different environmental conditions, which has led to the emergence of subspecies of the same species with altered morphological characteristics. This may lead to differences in their nutritional properties. For this reason, the aim of this study was to determine the differences in the physiochemical properties of two subspecies of Agave salmiana (crassispina and salmiana) grown in regions with different environmental characteristics. Although both regions have clay soils, some differences in cation exchange capacity (CEC) and nutrient concentration were found, which may have induced changes in leaf size in Agave during the adaptation process. Slight differences were observed in the thickness of the cuticle membrane in both agaves, but significant differences were found between the adaxial and abaxial sides. Moreover, only some macronutrients were significantly different in both agaves, so the subspecies and the development zone apparently have no influence on their composition. No significant differences were found in the color of the leaves based on the growing region of the agaves. However, the removal of the cuticle affects color perception, with significant differences observed between leaves with and without cuticles. According to the results obtained, the growing region of the Agave subspecies has a drastic effect on plant size and some nutritional traits and pigments but a lesser effect on overall coloration. The two subspecies of Agave salmiana, crassispina and salmiana, have different characteristics that enable them to adapt efficiently. Full article

Fragipans are dense subsurface soil layers that severely restrict root penetration and water movement. The presence of shallow fragipan horizons limits row crop production. We hypothesized that the roots of cover crop might improve soil physiochemical properties and biological activity, facilitating drainage and increasing effective soil depth for greater long-term soil water storage. To evaluate annual ryegrass as one component of a cover crop (CC) mix for promoting the characteristics and distribution of soil water, on-farm studies were conducted at Marion and Springerton in southern Illinois, USA. Soil samples were collected at 15 cm increments to 60 cm (Marion) and 90 cm (Springerton) depths during the fall of 2022. Both sites had low total soil carbon and nitrogen contents and acidic soil pH (≤6.4). A soil water retention curve was fitted using the van Genuchten equation. At Springerton, the CC treatment increased saturated (thetaS) and residual (thetaR) soil water contents above those of the no cover crop (NCC) at the 60–75 cm and 75–90 cm depths. Changes in volumetric soil water content were measured using a multi-depth soil water sensor for the Springerton site during late July to early August of the soybean growing phase of 2022; NCC had higher soil water than CC within the 0–15 cm depth, but CC had higher soil water than NCC at the 30–45 cm depth. These findings indicate that cover crop mix has the potential to improve soil water movement for soils with restrictive subsoil horizon, possibly through reducing the soil hydraulic gradient between the surface and restrictive subsurface soil layers. Full article

Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective. Full article