Root rot destabilizes the Sanqi rhizosphere core fungal microbiome by reducing the negative connectivity of beneficial microbes.

The stability of microbial communities, especially among core taxa, is essential for supporting plant health. However, the impacts of disease infection on the stability of rhizosphere fungal core microbiome remain largely unexplored. In this study, we delved into the effects of root rot infestation on the community structure, function, network complexity, and stability of Sanqi fungal core microbiomes, employing amplicon sequencing combined with co-occurrence network and cohesion analyses. Our investigation revealed that root rot disease led to a decrease in the α-diversity but an increase in the ß-diversity of the Sanqi fungal core microbiomes in the rhizosphere. Notably, Ilyonectria, Plectosphaerella, and Fusarium emerged as indicator species in the rhizosphere core microbiome of root rot-infected Sanqi plants, while Mortierella predominated as the dominant biomarker taxa in healthy soils. Additionally, root rot diminished the complexity and modularity of the rhizosphere networks by reducing the metrics associated with nodes, edges, degrees, and modularity. Furthermore, root rot resulted in a reduction in the proportion of negative connections in the network and the negative/positive cohesion of the entire core fungal microbiome. Particularly noteworthy was the observation that root rot infection destabilized the rhizosphere core fungal microbiome by weakening the negative connectivity associated with beneficial agents. Collectively, these results highlight the significance of the negative connectivity of beneficial agents in ensuring the stability of core microbial community.IMPORTANCERoot rot disease has been reported as the most devastating disease in the production process of artificial cultivated Sanqi ginseng, which seriously threatens the Sanqi industry. This study provides valuable insights into how root rot influences microbial relationships within the community. These findings open up opportunities for disease prevention and the promotion of plant health by regulating microbial interactions. In summary, the research sheds light on the ecological consequences of root rot on rhizosphere fungal microbiomes and offers potential strategies for managing soil-borne diseases and enhancing plant health.

The loss of microbial autotoxin degradation functions is associated with the decline of beneficial bacterial agents induced by phenolic acids.

Continuous cultivation of medicinal plants can disrupt the rhizosphere's microbial community. There is still a need to know about the beneficial bacterial community, their putative drivers, and the potential functions they may have. This study used different growth years of Sanqi ginseng (Panax notoginseng) with root rot to look at the beneficial microbial community structure, the function of microbial carbon source utilization, and the function of rhizosphere soil metabolism. The beneficial bacterial community changed and the relative abundance of beneficial agents was suppressed significantly with the successive Sanqi ginseng plantings. The carbon source utilization capacity and diversity increased significantly, whereas three autotoxin degradation-related pathways (biosynthesis of other secondary metabolites, metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism) were downregulated considerably with planting year extended. The changes in the beneficial agents were driven by the shifts in phenolic acid profiles, and the decline of beneficial microbes led to the loss of microbial autotoxin degradation functions. Overall, these results provide insight into beneficial microbes, microbial functions, phenolic acids, and their interactions, and these findings are essential for maintaining healthy and sustainable cultivation of Sanqi ginseng. IMPORTANCE Sanqi ginseng is a valuable perennial Chinese herb with various benefits for human health. However, continuous cultivation causes a high incidence of root rot disease, which leads to decreased yield and serious economic losses and ultimately impedes the sustainable development of Chinese medicine production. The significance of this study is to reveal the pattern of changes in beneficial bacteria and their related functions in root rot diseased rhizosphere with the successive planting years of Sanqi ginseng. This study found that the decline of beneficial bacterial agents mediated by phenolic acid profiles appears to be associated with the loss of microbial autotoxin degradation functions. This result may have new implications for deciphering the causes of Sanqi ginseng's continuous cropping obstacles.

Effects of Solidago canadensis L. on mineralization-immobilization turnover enhance its nitrogen competitiveness and invasiveness.

The effects of exotic plants on soil nitrogen (N) transformations may influence species invasion success. However, the complex interplay between invasive plant N uptake and N transformation in soils remains unclear. In the present study, a series of 15N-labeled pot experiments were carried out with Solidago canadensis L. (S. canadensis), an invasive plant, and the Ntrace tool was used to clarify the preferred inorganic N form and its effects on soil N transformation. According to the results, nitrate-N (NO3--N) uptake rates by S. canadensis were 2.38 and 2.28 mg N kg-1 d-1 in acidic and alkaline soil, respectively, which were significantly higher than the ammonium-N (NH4+-N) uptake rates (1.76 and 1.56 mg N kg-1 d-1, respectively), indicating that S. canadensis was a NO3--N-preferring plant, irrespective of pH condition. Gross N mineralization rate was 0.41 mg N kg-1 d-1 in alkaline soil in the presence of S. canadensis L., which was significantly lower than that in the control (no plant, CK, 2.44 mg N kg-1 d-1). Gross autotrophic nitrification rate also decreased from 5.95 mg N kg-1 d-1 in the CK to 0.04 mg N kg-1 d-1 in the presence of S. canadensis in alkaline soil. However, microbial N immobilization rate increased significantly from 1.09 to 2.16 mg N kg-1 d-1, and from 0.02 to 2.73 mg N kg-1 d-1 after S. canadensis planting, in acidic and alkaline soil, respectively. Heterotrophic nitrification rate was stimulated in the presence of S. canadensis to provide NO3--N to support the N requirements of plants and microbes. The results suggested that S. canadensis can influence the mineralization-immobilization turnover (MIT) to optimize its N requirements while limiting N supply for other plants in the system. The results of the present study enhance our understanding of the competitiveness and mechanisms of invasion of alien plants.

Garlic Substrate Induces Cucumber Growth Development and Decreases Fusarium Wilt through Regulation of Soil Microbial Community Structure and Diversity in Replanted Disturbed Soil.

Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, disease suppression and plant development, however, remains unclear, particularly in the degraded soil micro-ecological environment. In this study, garlic substrates as a soil amendment were incorporated with different ratios (1:100, 3:100 and 5:100 g/100 g of soil) in a replanted disturbed soil of long-term cucumber monoculture (annual double cropping system in a greenhouse). The results indicated that higher amount of C-amended garlic substrate significantly induced soil suppressiveness (35.9% greater than control (CK) against the foliar disease incidence rate. This inhibitory effect consequently improved the cucumber growth performance and fruit yield to 20% higher than the non-amended soil. Short-term garlic substrate addition modified the soil quality through an increase in soil organic matter (SOM), nutrient availability and enzymatic activities. Illumina MiSeq sequencing analysis revealed that soil bacterial and fungal communities in the garlic amendment were significantly different from the control. Species richness and diversity indices significantly increased under treated soil. The correlation-based heat map analysis suggested that soil OM, nutrient contents and biological activators were the primary drivers reshaping the microbial community structure. Furthermore, garlic substrate inhibited soil-borne pathogen taxa (Fusarium and Nematoda), and their reduced abundances, significantly affecting the crop yield. In addition, the host plant recruited certain plant-beneficial microbes due to substrate addition that could directly contribute to plant-pathogen inhibition and crop biomass production. For example, abundant Acidobacteria, Ascomycota and Glomeromycota taxa were significantly associated with cucumber yield promotion. Firmicutes, Actinobacteria, Bacteroidetes, Basidiomycota and Glomeromycota were the associated microbial taxa that possibly performed as antagonists of Fusarium wilt, with plant pathogen suppression potential in monocropped cucumber-planted soil.

Response of the nitrogen load and its driving forces in estuarine water to dam construction in Taihu Lake, China.

To regulate the water level and minimize the occurrence of water eutrophication in shallow lakes, dams and gates are often constructed in rivers. However, this practice may result in a deterioration of water quality in some estuaries. In the present study, using the correction of Nemerow pollution index (CNPI) and a redundancy analysis (RDA), water samples from different dammed rivers around Taihu Lake were compared to assess the pollution risk and identify the factors responsible for water eutrophication. The average total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC) concentrations, and chemical oxygen demand (CODMn) were 2.45 ± 2.28, 0.08 ± 0.06, 43.01 ± 18.75, and 10.78 ± 4.86 mg L-1, respectively. The CNPI values indicated that approximately 76.47% of the estuarine water was moderately polluted (1 < CNPI < 7.28). A positive correlation was observed between dam construction and nutrient concentrations (e.g., rTN = 0.38, p < 0.05; rTP = 0.89, p < 0.01). Under the effects of dam construction, land use change, estuary shape, and meteorological conditions, there was a clear spatial variation of the TN concentrations. Dams that were closed all year round accelerated the TN accumulation in the water around them. The pollution risk in a trumpet-shaped estuary was higher than that in other regions (t = 2.92, p = 0.02). Endogenous release of pollutants was an important factor that may have a priming effect on algal blooms and should be given more attention. In Wuli Lake, exogenous pollution was the dominant pollutant source. A total of 74.49% of the nitrogen losses with the runoff into the estuarine water in 2018 were derived from urban domestic sewage and constructed land, with the load being 4.40 times higher than in 2000. The RDA results revealed that dam construction was the main factor (43.70%) affecting water quality, while meteorological conditions, land use types, estuary shape, and other factors contributed 56.30%. Scientific regulation and control of dam operation is important to protect the water environment of Taihu Lake.

Nitrogen deposition affects both net and gross soil nitrogen transformations in forest ecosystems: A review.

Nitrogen (N) deposition has rapidly increased and is influencing forest ecosystem processes and functions on a global scale. Understanding process-specific N transformations, i.e., gross N transformations, in forest soils in response to N deposition is of great significance to gain mechanistic insights on the linkages between global N deposition and N availability or loss in forest soils. In this paper, we review factors controlling N mineralization, nitrification and N immobilization, particularly in relation to N deposition, discuss the limitations of net N transformation studies, and synthesize the literature on the effect of N deposition on gross N transformations in forest ecosystems. We found that more than 97% of published papers evaluating the effect of N deposition (including N addition experiments that simulate N deposition) on soil N cycle determined net rates of mineralization and nitrification, showing that N deposition significantly increased those rates by 24.9 and 153.9%, respectively. However, studies on net N transformation do not provide a mechanistic understanding of the effect of N deposition on N cycling. To date, a small number of studies (<20 published papers) have directly quantified the effect of N deposition on gross N transformation rates, limiting our understanding of the response of soil N cycling to N deposition. The responses to N deposition of specific N transformation processes such as autotrophic nitrification, heterotrophic nitrification, dissimilatory nitrate reduction to ammonium, N mineralization, and N immobilization are poorly studied. Future research needs to use more holistic approaches to study the impact of N deposition on gross N transformation rates, N loss and retention, and their microbial-driven mechanisms to provide a better understanding of the processes involved in N transformations, and to understand the differential responses between forest and other ecosystems.

Effects of long-term amendment of organic manure and nitrogen fertilizer on nitrous oxide emission in a sandy loam soil.

To understand the effects of long-term amendment of organic manure and N fertilizer on N2O emission in the North China Plain, a laboratory incubation at different temperatures and soil moistures were carried out using soils treated with organic manure (OM), half organic manure plus half fertilizer N (HOM), fertilizer NPK (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer PK (NK) and control (CK) since 1989. Cumulative N2O emission in OM soil during the 17 d incubation period was slightly higher than in NPK soil under optimum nitrification conditions (25 degrees C and 60% water-filled pore space, WFPS), but more than twice under the optimum denitrification conditions (35 degrees C and 90% WFPS). N2O produced by denitrification was 2.1-2.3 times greater than that by nitrification in OM and HOM soils, but only 1.5 times greater in NPK and NP soils. These results implied that the long-term amendment of organic manure could significantly increase the N2O emission via denitrification in OM soil as compared to NPK soil. This is quite different from field measurement between OM soil and NPK soil. Substantial inhibition of the formation of anaerobic environment for denitrification in field might result in no marked difference in N2O emission between OM and NPK soils. This is due in part to more rapid oxygen diffusion in coarse textured soils than consumption by aerobic microbes until WFPS was 75% and to low easily decomposed organic C of organic manure. This finding suggested that addition of organic manure in the tested sandy loam might be a good management option since it seldom caused a burst of N2O emission but sequestered atmospheric C and maintained efficiently applied N in soil.

[Responses of rice (Oryza sativa) growth and its C, N and P composition to FACE (free-air carbon dioxide enrichment) and N, P fertilization].

FACE (Free-air Carbon Dioxide Enrichment) was used to study the effects of elevated CO2 on rice (Oryza sativa) growth, tissue C/N, N and P concentration and uptake at different development stages under two N and two P levels. Results showed that elevated CO2 increased dry matter accumulation in rice stem, ear and root. Leaf dry matter was increased at tillering stage and no significant effect was found at jointing, heading and ripening stages. N concentration of stem and leaf was decreased. Ear N concentration at heading stage was increased but was decreased at ripening stage. No significant effect was found on root N concentration at tillering stage but root N concentration at jointing, heading and ripening was decreased. Leaf P concentration at jointing, heading and ripening was increased but no significant effect was found on P concentration in stem, ear and root. C content in various tissues changed unremarkably and the ratio of C over N (C/N) was increased. Elevated CO2 significantly increased P uptake in aboveground tissues; and increased N uptake, but the difference was not statistically significant. N and P fertilization had no significant effect on various tissue dry biomass. Tissue N content at higher N fertilization was higher than at lower N fertilization but no such effect of P fertilization on tissue P content was found. At higher N fertilization, elevated CO2 increased the ratio of below-ground biomass over above-ground biomass at ripening stage. Possible reasons are discussed for the differences of tissue N and P content and the ratio of below-ground biomass over above-ground biomass between elevated and ambient atmospheric CO2 concentrations.