Soil Microbial Community Shifts in Rhizosphere and Original Soils during Two and Three Years of Ginseng Cultivation

doi:10.21203/rs.3.rs-4955337/v1

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Soil Microbial Community Shifts in Rhizosphere and Original Soils during Two and Three Years of Ginseng Cultivation

https://doi.org/10.21203/rs.3.rs-4955337/v1

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Soil microbial communities play a key role in maintaining ecosystem functions; however, little is known about the specific changes in microbial communities in the Rhizosphere soil and Original soil of ginseng under different years of cultivation. We utilized Illumina MiSeq sequencing technology to investigate the differential effects of years of ginseng cultivation on the microbial communities in Rhizosphere Soil and Original soil. The physicochemical properties of the soil were analyzed using one-way analysis of variance (ANOVA). The results showed that the alpha-diversity of soil microorganisms showed a significant trend in both in Rhizosphere Soil and Original soil with the years of ginseng cultivation. Through NMDS analysis, we further found significant differences in soil microbial community composition between Rhizosphere Soil and Original soil. In order to visualize these differences, the top-ranked soil bacterial and fungal genera in Rhizosphere Soil and Original soil at different cropping years were depicted with the help of stacking diagrams. Soil bacteria and fungi in Rhizosphere Soil and Original soil were differentially analyzed using Kruskal-Wallis test. The complex relationship between soil physicochemical properties and different bacterial and fungal genera was deeply explored by correlation heatmap, RDA redundancy analysis and Mantel analysis. Therefore, this study not only sheds light on the specific effects of ginseng planting years on soil microbial communities in rhizosphere soils and primary soils, but also provides new scientific perspectives for further understanding the role of soil microbial communities in ecosystems.

Earth and environmental sciences/Biogeochemistry

Earth and environmental sciences/Ecology

Rhizosphere soil

Original soil

Soil bacteria

Soil fungi

High-throughput sequencing

Soil microorganisms are important components of soil ecosystems and play a crucial role in soil nutrient cycling, plant growth and health, and maintenance of soil environment¹. Among many plants, ginseng, as a valuable medicinal plant, is of particular interest because of the interrelationship between its growth and soil microorganisms². Ginseng Rhizosphere Soil refers to the soil area immediately adjacent to the ginseng root system, while Original soil refers to the original soil before ginseng planting^3,4. The study of soil microorganisms in ginseng Rhizosphere Soil and Original soil is of great theoretical and practical significance for the in-depth understanding of the microbial ecological characteristics of the ginseng growing environment^5,6, revealing the mechanism of interaction between microorganisms and ginseng as well as the maintenance of soil ecological balance⁷. Therefore, the aim of this paper is to investigate the changes of soil microorganisms in ginseng Rhizosphere Soil and Original soil under different years of cultivation, with a view to providing a scientific basis for the sustainable cultivation of ginseng and the rational utilization of soil microbial resources.

Soil is an important part of the ecosystem, and ginseng Rhizosphere Soil and Original soil, as two different types of soils, have special significance in ecological and soil studies^8,9. In Original soil, i.e., pristine soils that have not been disturbed by man, retain the natural properties and microbial community structure of the soil^10,11. In contrast, Rhizosphere Soils are areas of soil immediately adjacent to plant roots, and soils in this region are significantly influenced by root secretions and microbial activity^12,13, creating a unique ecological environment. In addition, soil microorganisms show significant differences between Rhizosphere Soil and Original soil: in Rhizosphere Soils, microorganisms are more abundant and active due to root activities and secretions, and the community structure is biased toward specific species that are symbiotic with plants, while the microorganisms in Original soil are more natural and diverse, with weaker interactions with plants^8,14,15. These differences not only affect the physical and chemical properties of the soil, but also play a key role in the growth and health of plants, thus deeply reflecting the complexity and functional diversity of soil ecosystems. The study of microbial communities, nutrient cycling, and their interrelationships with plant growth in ginseng Rhizosphere Soil and Original soil is of great significance for a deeper understanding of soil ecosystem functioning, optimizing agricultural management practices, conserving soil resources, and responding to the challenges posed by global change.

Previous studies have reported that soil microorganisms in ginseng Rhizosphere Soil and Original soil undergo dynamic changes during different years of cultivation^3,16. The microorganisms in the ginseng Rhizosphere Soil gradually showed higher diversity and activity as the years of cultivation increased¹⁷. Particularly, in the case of beneficial plant growth-promoting species, their numbers rose significantly with the increase in incubation time. By the 3rd year of planting, this increasing trend was more obvious, reflecting the important role of root secretions in shaping and selecting microbial communities¹⁸. At the same time, the microbial community in the Original soil was also changing quietly, but the changes appeared to be more subdued compared to the drastic changes in the Rhizosphere Soil¹⁴,¹⁹. These microorganisms seem to maintain their original natural state to a certain extent and are not strongly influenced by the plant root system as in the Rhizosphere Soil. Thus, it can be seen that ginseng cultivation of different ages has a profound effect on its Rhizosphere Soil microbial community, and the microbial compositions and activities of the Rhizosphere Soil and the Original soil are distinctly different. Given this background, we analyzed the differences in soil bacterial and fungal communities in ginseng Rhizosphere Soils and Original soils under different cropping years of two and three years. Soil bacterial and fungal communities were determined by high-throughput amplicon sequencing based on the Illumina MiSeq platform. We hypothesized that: (1) Changes in soil microbial communities in Rhizosphere soils and Original soils after 2 and 3 years of ginseng cultivation. (2) Soil physicochemical properties as drivers of changes in soil microbial communities in Rhizosphere soils and Original soils.

Study sites

This study located in the Tieli City, Heilongjiang Province (N:47°09'19.38", E:128°15' 50.30"). The climate is a typical temperate continental monsoon, with four distinct seasons. The average annual temperature is about 2.4℃, with maximum temperatures reaching 31.6℃ and minimum temperatures − 38.8℃. Five ginseng cultivation were selected: 2 years ginseng non-rhizosphere soil (PGOC2) and rhizosphere soil (PGRC2), 3 years ginseng non-rhizosphere soil (PGOC3) and rhizosphere soil (PGRC3), and no ginseng cultivation soil (PGC). The ginseng is planted in beds with loose, well-draining soil that has strong permeability and measures approximately 150-170cm wide. During the initial stage, 5 to 10 kilograms of farm fertilizer per square meter of planting land, along with about 50 grams of superphosphate or composite fertilizer per square meter, are applied into the ditch and covered with soil. The relative moisture content of the soil should be controlled within 80%. Three independent sampling sites measuring 10m × 10m were established in different years, and organic layer soil from 0 ~ 20cm depth was collected from each site for use as non-rhizosphere soil (OS) biological duplicates. The rhizosphere soil RS (approximately 1mm thick) tightly adhered to the root surface was manually brushed off using a sterile soft brush following the Riley and Barber shaking method. All OS and RS samples were collected into labeled sterile sampling bags and sealed for storage. Soil samples were placed in biological sampling boxes (with dry ice added beforehand) and transported to the laboratory at low temperatures. A soil sample sieve (2mm) was used to remove stones, visible roots, residue, and other debris. OS and RS were divided into two samples: one stored at4°C for determination of physicochemical properties of the soil, while the other was stored at -80°C for subsequent microbial analysis.

Soil chemical properties

Total phosphorus (TP), and accessible phosphorus (AP) were determined using an Inductively Coupled Plasma Emission Spectromete (Agilent 5100 ICP-OES)²⁰. Soil total nitrogen (TN) contents and total carbon (TC) were determined using the Vario Max CNS elemental analyzer (Elementar Analysensysteme GmbH, Hanau, Germany)²¹. Following the extraction of soil samples with NaHCO₃, the Mo-Sb colorimetry method (0.5 M) was utilized to assess the content of available phosphorus (AP). Additionally, soil organic matter (SOM) was determined through an external heating process involving potassium dichromate oxidation²². A suspension created by mixing soil with deionized water at a 1:2.5 weight-to-volume ratio was agitated for 30 minutes before its pH was measured using a pH meter (Thermo Scientific Orion 3-Star Benchtop, Cambridge, United Kingdom)²³. The soil moisture content (SWC) was ascertained through the drying process²⁴. The concentrations of nitrate nitrogen (NO₃^--N) and ammonium nitrogen (NH₄⁺-N) were ascertained with the help of an Autoanalyzer²⁵.

DNA extraction and high-throughput sequencing

The extraction of soil total DNA was carried out with the E.Z.N.A.® DNA Kit (OmegaBio-tek, Norcross, GA, USA). The quality and purity of DNA were assessed using a NanoDrop 2000 (NanoDrop Technologies, Wilmington, DE, USA), and further visualized through electrophoresis on 1% agarose gels. The primers used for bacteria detection were 515F (5′-GTGCCAGCMGCCGCGG-3′) paired with 806R (5′-GGACTACHVGGGTWTCTAAT-3′), while for fungi detection, the primers were ITS1F (5′-CTTGGTCATTTAGAGGAAGTAA-3′) and ITS2R (5′-GCTGCGTTCTTCATCGATGC-3′)^26,27. PCR products were recovered and refined by means of a 2% agarose gel along with Axy Prep DNA Gel Extraction Kits (Axygen Biosciences, Union City, CA, USA). Subsequently, sequencing was carried out on an Illumina MiSeq platform, facilitated by Shanghai Majorbio Bio-pharm Technology Co., Ltd. The Illumina MiSeq-PE300 platform (Illumina, San Diego, CA, USA) was successfully used to complete all sequencing. QIIME 2 was employed for microbiome bioinformatics analysis²⁸. The demux plugin was utilized to demultiplex the raw paired-end reads, followed by the removal of primers using the cut adapt plugin²⁹. Subsequently, the sequences underwent quality filtering and denoising through the Dada2 process as per previous studies. To ensure sequence quality and eliminate all sequencing errors, we applied the learnErrors, derepFastq, dada, and mergePairs methods with their default settings. Following this, the amplicon sequence variants (ASVs) representing single occurrences (singletons) were removed. Subsequently, the Silva v132 database (http://www.arb-silva.de)³⁰ was used to determine the taxonomic identity of bacteria, and the UNITE database (https://unite.ut.ee/)³¹ was used to determine the taxonomic identity of fungi.

Statistical analysis

Soil physical and chemical properties were analyzed by one-way ANOVA and t-test³². The Non-metric multidimensional scaling (NMDS) analysis, a powerful tool for visualizing and interpreting complex multivariate data, was conducted by employing the renowned “ggplot2” and “vegan” packages within the versatile R software environment³³. The stacked plots, which provide a visual representation of multiple variables across different categories, were carefully constructed using the “ggplot2” package in the R software³⁴. The metacoder taxonomy tree was drawn by using the “metacoder” package in the R software³⁵. We performed Kruskal-Wallis analysis with the help of the “stats” package in the R software³⁶. We plotted Correlation heatmap with the help of “corrmorant”, “pheatmap”, “corrplot” packages in the R software³⁷. Mantel test was performed with the assistance of the “vegan” and “ggcor” packages in the R software³⁸.

Soil physical and chemical properties

There were significant differences in some soil physicochemical properties under the five different treatments. For example, pH was lowest under the PGOC2 treatment; AP and TP were highest under the PGOC2 treatment; NH₄⁺-N was highest under the PGOC3 treatment; and NO₃⁻-N was highest under the PGRC3 treatment. However, SOM and TN were not significantly different under all the five treatments (Table S1).

Soil bacterial and fungal community diversity

Our study revealed that the alpha-diversity indices of both soil bacterial and fungal communities remained some change across the five treatments (Table S2; Table S3). The highest Chao1 index was observed for both soil bacterial and fungal communities under PGOC2 treatment (Figure. 1). As for Shannon index, soil bacterial communities Shannon index was highest under PGOC2 treatment and soil fungal communities Shannon index was highest under PGC treatment (Figure. 2).

Non-metric multidimensional scaling analysis (NMDS) showed large differences between the soil bacterial and fungal communities under PGC treatment and the other four treatments. In addition, Soil bacterial communities showed strong similarity under PGOC2, PGRC3 and PGRC2 treatments. Soil fungal communities had strong similarity under PGOC2 and PGRC2 treatments. And there was strong similarity under both PGOC3 and PGRC3 treatments in soil fungal communities (Figure. 3).

Soil bacterial and fungal community composition

The stacked plot demonstrated that HSB_OF53_FO7 had higher abundance under PGC and PGOC2 treatments than the other three treatments. Rhodanobacter had the highest abundance under PGOC3 treatment. While Gaiellales_norank had more similar abundance under the five treatments in soil baacterial communities (Figure. 4a). Among the soil fungal communities, Mortierella had relatively similar abundance under the five treatments, whereas Chaetomidium and Tausonia had the highest abundance under PGOC3 treatment (Figure. 4b).

The evolutionary classification tree of soil bacterial communities showed that Myxococcot, Steroidobacterales and Haliangiaceae were enriched under PGC (green) treatment; Elusimicrobiota, Bacilli and Gemmatimonadales were enriched under PGOC2 (green) treatment; Gemmatimonadetes and Paenibacillales were enriched under PGOC3 (green) treatment (Figure. 5a). Among the soil fungal communities evolutionary classification tree, Dothideomycetes and Pleosporales were enriched under PGRC2 (green) treatment. Hymenochaetales, Leucosporidiaceae and Agaricostilbales were enriched under PGRC3 (brown) treatment (Figure. 5b).

The Kruskal-Wallis test showed that Mycobacterium had similar abundance under PGOC2, PGOC3, PGRC2 and PGRC3 treatments. Paraburkholderia had the highest abundance under both PGRC2 and PGRC3 treatments. TK10 and Subgroup_7 had higher abundance under PGC and PGRC2 treatments compared to the other three treatments (Figure. 6a). Tausonia had higher abundance under both PGOC3 and PGRC3 treatments. While Aeremonium and Fusarium had the highest abundance under PGC treatment (Figure. 6b).

Factors affecting soil microbial communities

Among the top ranked genera of soil bacteria, Bradyrhizobium had significant negative correlation with soil TC, SOM, TN and SWC, while Acidobacteriales had significant positive correlation with SOM and TP. Rhizobiales and Chujaibaeter had significant negative correlation with pH (Figure. 7a). Among the top ranked genera of soil fungi, Trechispora had significant negative correlation with pH, while Fusarium and Mortierella had significant positive correlation with pH. Acremonium and Solicoccozyma had significant positive correlation with NH₄⁺-N (Figure. 7b).

Mantel analysis showed that soil bacterial communities Chao1 index had strong correlation with soil SWC and NH₄⁺-N, soil bacterial communities Shannon index had strong correlation with soil AP (Figure. 8a). In addition, soil fungal communities’ composition had strong correlation with NH₄⁺-N (Figure. 8b).

The RDA model explained 88.37% and 81.38% of the total variance in the soil bacterial and soil fungal communities, respectively. In the soil bacterial community, the RDA1 axis explained 62.39% of the total variance, suggesting that soil physico-chemical properties (NO₃⁻-N and TP) varying along the RDA1 axis were the dominant factors contributing to changes in the bacterial community. Mortierella was positively correlated with pH, and Chaetomidium was positively correlated with TC and NH₄⁺-N. Mortierella was found to be more susceptible under the PGC and PGOC3 treatments survived better (Fig. 9). Moreover, in soil fungal communities, the RDA1 axis explained 41.9% of the total variance, suggesting that soil physico-chemical properties (pH) varying along the RDA1 axis were the dominant factor contributing to the variation in fungal communities. Bradyrhizobium was positively correlated with pH. Moreover, Bradyrhizobium was also more suitable to survive under PGOC3 treatment (Figure. 9b).

Soil bacterial and fungal community diversity

The alpha-diversity and community structure of soil microorganisms, as key factors in biogeochemical cycles and ecological processes, are critical for soil health and ecosystem stability. Particularly in ginseng cultivation soils, differences in bacterial communities between Rhizosphere Soil and Original soil may affect plant growth and quality ¹⁶. However, there is still a lack of research on how planting year interacts with these factors to influence bacterial diversity. Therefore, we explored in depth the changes in alpha-diversity of soil bacterial and fungal communities at two and three planting years for both Rhizosphere Soil and Original soil of ginseng. Results showed that the Chao1 index and Shannon index of soil bacterial communities were higher in both Rhizosphere Soil and Original soil for two years than in Rhizosphere Soil and Original soil for three years (Fig. 1, 2). Such changes may be caused by a combination of factors: changes in the soil environment caused by the increase in the number of years of planting ginseng make it difficult for some bacterial species to adapt, and then the number of them decreases or disappears; at the same time, this may also lead to an imbalance of soil nutrients, structural damage and the accumulation of pests and diseases, which will have a negative impact on the environment in which microorganisms can survive^39,40. In addition, as the planting time goes on, changes in environmental factors such as nutrients, moisture and pH in the soil will also affect the survival and reproduction of bacteria^39,41. Coupled with the competition and succession among different species in the soil bacterial community, some less competitive bacteria may be eliminated, further reducing the diversity of soil bacteria.

From the NMDS analysis, it can be concluded that soil bacterial and fungal communities in both Rhizosphere Soil and Original soil exhibited a high degree of variability between two years of ginseng cultivation and three years of ginseng cultivation conditions (Fig. 3). This finding triggered an in-depth consideration of the effects of planting years and Rhizosphere soil and Original soil on soil bacterial and fungal communities. The interaction between the ginseng root system and soil microorganisms will evolve with the increase of planting years, and long-term planting will cause changes in the types and amounts of root secretions, which not only affect the community structure of soil microorganisms, but also accompany the dynamic depletion and replenishment of soil nutrients, which in turn directly affects the environment for microbial growth and reproduction⁵. As an active site of interaction between plant roots and soil microorganisms, soil bacteria and fungi in the Rhizosphere soil zone in particular undergo significant changes with the extension of planting years^42,43, which in turn leads to major adjustments in the structure of the microbial community, including turnover of microbial species, significant increases and decreases in their numbers, and profound changes in microbial interaction relationships.

Soil bacterial and fungal community composition

There is a complex and close correlation between soil physicochemical properties and soil bacteria and fungi, which is either positive or negative, profoundly revealing the close interaction between soil properties and microbial communities, which in turn may further have far-reaching effects on soil fertility and ecological functions. The stacking diagram showed that HSB_OF53_FO7 had the highest abundance in the Original soil that ginseng was planted for 2 years (Fig. 4). HSB_OF53_FO7 showed high abundance in the original soil planted with ginseng for two years, which was mainly attributed to its ecological niche adaptation to soil-specific pH, moisture, and nutrients, as well as its ability to efficiently utilize the organic matter and nutrients accumulated in ginseng soil⁴⁴. At the same time, this bacterium may have established symbiotic relationships with other microorganisms or dominated in competition, further consolidating its position in the microbial community⁴⁵. In addition, the good structure and aeration of the soil provide an ideal environment for its growth, while its strong resistance ensures stable survival in harsh or changing environments. The combined effect of these factors enabled HSB_OF53_FO7 to survive and multiply efficiently in the soil planted with two years of ginseng, thus maintaining a high abundance status.

While Tetracladium, a soil fungus, had the highest abundance in the Rhizosphere soil of ginseng planted for 3 years (Fig. 4). This phenomenon was closely related to the ecological niche construction of Tetracladium. Over a long period of time, Tetracladium gradually adapted to the unique pH and humidity of Rhizosphere Soil, as well as the gradually increasing nutrient content. Tetracladium excels in utilizing the specific organic matter and nutrients accumulated in the soil after a long period of ginseng cultivation, and these abundant resources provide what it needs for growth^46,47. In addition, Tetracladium successfully dominated the complex Rhizosphere Soil environment as the years of planting increased, which may be closely related to its ability to produce antimicrobial substances or occupy favorable ecological niches. Meanwhile, the soil structure changed with the increase of planting years, which provided a more suitable habitat for Tetracladium, while the Rhizosphere soil effect further promoted its proliferation.

The abundance of Paraburkholderia and Cladophialophora was much higher in the Rhizosphere soil than in the in situ soils, regardless of whether the ginseng was grown for two or three years (Fig. 6). This was mainly due to the fact that Paraburkholderia and Cladophialophora showed strong resistance and adaptability^48–50. Both microorganisms are not only able to survive tenaciously under complex and variable environmental stresses such as nutrient fluctuations and changes in soil pH, but also possess the ability to rapidly adjust their physiological and biochemical properties to cope with and adapt to the changing soil environment. This high degree of flexibility and adaptability enables them to survive stably in a variety of challenges, whether it is a sudden decrease in nutrients or a drastic change in soil pH, they are able to cope with it by adjusting their metabolic pathways, altering their cell membrane permeability, or activating specific anti-stress genes. This gives Paraburkholderia and Cladophialophora the ability to continue proliferating over long periods of cultivation, enabling them to stand out from other microorganisms.

Factors affecting soil microbial communities

There is a complex and close correlation between the physical and chemical properties of soils and the bacterial genera inhabiting them, a relationship that is either positive or negative, and which profoundly reveals the close interactions between soil properties and microbial communities. The correlation heat map demonstrated that Candidatus_Udaeobacter, Gemmatimonas were both significantly positively correlated with NH₄⁺-N (Fig. 7). In soil ecosystems, Candidatus_Udaeobacter and Gemmatimonas were significantly and positively correlated with the ammonium nitrogen (NH₄⁺-N) content of the soil^51,52, revealing their key roles in nitrogen cycling. Candidatus_Udaeobacter, by engaging in ammonification, which converts organic nitrogen in the soil to NH₄⁺-N, has Enhancing the ammonium nitrogen content in the soil has a positive impact on soil fertility, and it has been adapted to NH₄⁺-N rich environments and can grow and reproduce effectively under high ammonium nitrogen conditions ⁵¹. Gemmatimonas, on the other hand, has demonstrated the ability to efficiently utilize NH₄⁺-N as a nitrogen source, giving it a competitive advantage in nitrogen-rich soils⁵³, and it may have a symbiotic relationship with other NH₄⁺-N producing microorganisms, a symbiosis that further facilitates its thriving in high-ammonium nitrogen environments. The characteristics of these two bacteria make them important components of the soil ecosystem and play an important role in maintaining soil fertility and ecological balance. Among the fungal communities, Aeremonium, Solicoccozyma had a significant positive correlation with NH₄⁺-N. Aeremonium and Solicoccozyma had a close relationship with the ammonium nitrogen (NH₄⁺-N) content of the soil^54,55. Aeremonium fungi preferred to utilize NH₄⁺-N as the main source of nitrogen, because the NH₄⁺-N form is more easily absorbed and utilized by it to meet its growth and metabolic needs. In soils with high NH₄⁺-N content, Aeremonium can efficiently acquire nitrogen to support its vigorous growth. At the same time, it is extremely sensitive to changes in soil NH₄⁺-N content, has a sensing mechanism to rapidly detect changes in environmental NH₄⁺-N concentration, and can quickly adjust its growth strategy to adapt to and utilize abundant nitrogen sources, thus taking advantage of the variable soil environment. On the other hand, Solicoccozyma plays a key role in soil nitrogen transformation and may participate in the nitrogen cycle by decomposing organic matter and releasing NH₄⁺-N through its specific enzyme system to increase soil ammonium nitrogen content. Meanwhile, NH₄⁺-N, as an easily utilizable nitrogen source, provides Solicoccozyma with necessary nutrients to promote its growth and reproduction. In NH₄⁺-N rich soil, Solicoccozyma can acquire nitrogen more efficiently and realize rapid growth and biomass accumulation.

Mantal analysis showed that the Chao1 index of soil bacteria was highly correlated with SWC and NH₄⁺-N, while the composition of soil fungi was highly correlated with NH₄⁺-N (Fig. 8). The Chao1 index is an important tool for reflecting the diversity of soil bacterial communities^56,57, which integrates species richness and community complexity, and can be used as an indicator of environmental change and an assessment of ecological restoration and conservation. We hypothesized that the correlation of soil bacterial Chao1 index with soil water content (SWC) and ammonium nitrogen (NH₄⁺-N) mainly originated from the promotion of bacterial growth and reproduction by appropriate amount of water⁵⁸, which enabled the bacteria to carry out their metabolic activities more efficiently, and thus enhanced the diversity of bacterial communities. Meanwhile, the availability of NH₄⁺-N as an important nitrogen source in soil also directly affects the metabolism, growth rate and diversity of bacteria. Similarly, the community structure of soil fungi is also affected by the NH₄⁺-N concentration, because different fungi have different needs and utilization of nitrogen sources, so the concentration of ammonium nitrogen will change the composition of the fungal community, so that some fungal species more adapted to the specific nitrogen concentration will dominate.

RDA analysis showed that Ghaetomidium was positively correlated with NH₄⁺-N and TC and was suitable for survival in Rhizosphere soil planted with ginseng for 3 years (Fig. 9). Ghaetomidium, due to its efficient ammonium nitrogen (NH₄⁺-N) and total carbon (TC) utilization mechanisms^59,60, can grow rapidly in environments rich in these nutrients, especially in the Rhizosphere soil of ginseng planted for 3 years, where it fully utilized the abundant carbon and nitrogen sources provided by root secretions and residues. In addition, Ghaetomidium and ginseng may have established a symbiotic relationship that further optimizes nutrient utilization and may positively affect ginseng growth. Meanwhile, Ghaetomidium dominated the soil through competition and effectively suppressed other harmful microorganisms, further consolidating its survival advantage in specific soil environments.

Vibrionimonas showed a significant positive correlation with soil pH and was adapted to survive in the in situ soil environment for three years of planting (Fig. 9). This may be attributed to the fact that Vibrionimonas is better adapted to higher pH soil environments, as soil pH is a key factor in microbial growth, affecting nutrient availability and microbial metabolism. In alkaline or near-neutral soils, Vibrionimonas showed greater ability to survive, absorbing and utilizing nutrients from the soil more efficiently, thus promoting their growth and reproduction^61,62. Especially in the Original soil environment after three years of planting, the soil is more mature and richer in nutrients such as organic matter and minerals, which provides Vibrionimonas with a stable food source and a suitable environment for survival. At the same time, the root secretions, residues and other organic matter that gradually accumulate in the soil as the number of years of planting increases also provide nutrients and energy for microorganisms, such as Vibrionimonas, to flourish in the mature soil.

Conflicts of Interest:

The authors declare no conflicts of interest.

Availability of data and materials:

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

We ensure that we obtain permission to collect ginseng and samples of ginseng soil. The ginseng samples and soil samples were placed in the Laboratory of Chinese Medicine Chemistry at Heilongjiang University of Chinese Medicine. The plant samples were identified as Panax ginseng C. A. Mey. by Wang Zhenyue, an associate professor of Chinese medicine resources.

Author Contribution

Conceptualization, D.Q.Y. and Z.B.W.; methodology, D.Q.Y. and Z.B.W.; formal analysis, W.H.Y. and Z.P.X.; resources, Y.W.L, and X.Q.L; writing—original draft preparation, D.Q.Y.; writing—review and editing, Z.B.W.; project administration, Z.B.W.; funding acquisition, Z.B.W. and Y.Y.W. All authors have read and agreed to the published version of the manuscript.

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Soil Microbial Community Shifts in Rhizosphere and Original Soils during Two and Three Years of Ginseng Cultivation

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Abstract

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Introduction

Materials and Methods

Study sites

Soil chemical properties

DNA extraction and high-throughput sequencing

Statistical analysis

Results

Soil physical and chemical properties

Soil bacterial and fungal community diversity

Soil bacterial and fungal community composition

Factors affecting soil microbial communities

Discussion

Soil bacterial and fungal community diversity

Soil bacterial and fungal community composition

Factors affecting soil microbial communities

Declarations

Author Contribution

References

Additional Declarations

Supplementary Files

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